From 06a018923cc9ee5c5bd1dad78503f2ce37e0f28c Mon Sep 17 00:00:00 2001 From: chao1224 Date: Sun, 10 Mar 2024 10:53:49 -0400 Subject: [PATCH] Initial Commit, #1 --- LICENSE | 21 + ProteinDT/TAPE_benchmark/__init__.py | 4 + ProteinDT/TAPE_benchmark/datasets.py | 690 ++ ProteinDT/TAPE_benchmark/metrics.py | 92 + ProteinDT/TAPE_benchmark/models.py | 253 + ProteinDT/TAPE_benchmark/trainer.py | 269 + ProteinDT/datasets/__init__.py | 11 + ProteinDT/datasets/dataset_MISATO/__init__.py | 2 + .../dataset_MISATO/dataloader_MISATO.py | 79 + .../datasets/dataset_MISATO/dataset_MISATO.py | 286 + ProteinDT/datasets/dataset_Pin1.py | 46 + ProteinDT/datasets/dataset_Protein.py | 45 + .../datasets/dataset_RepresentationPair.py | 103 + .../datasets/dataset_SecondaryStructure.py | 110 + ProteinDT/datasets/dataset_Stability.py | 71 + ProteinDT/datasets/dataset_SwissProtCLAP.py | 105 + ProteinDT/datasets/dataset_Villin.py | 46 + ProteinDT/model_ColdDiffusionDecoder.py | 131 + ProteinDT/model_GaussianSDEDecoder.py | 238 + ProteinDT/model_LSTMDecoder.py | 103 + ProteinDT/model_LatentDiffusionDecoder.py | 152 + ProteinDT/model_SDE.py | 228 + ProteinDT/model_Sampler.py | 89 + ProteinDT/models/__init__.py | 9 + ProteinDT/models/model_BindingModel.py | 47 + ProteinDT/models/model_CDConv.py | 381 + .../model_FoldingBindingInferenceModel.py | 85 + ProteinDT/models/model_GaussianFacilitator.py | 25 + .../model_MultinomialDiffusionDecoder.py | 226 + ProteinDT/models/model_ProteinText.py | 21 + ProteinDT/models/model_RNNPrediction.py | 27 + ProteinDT/models/model_TransformerDecoder.py | 62 + .../models/score_networks/BertScoreNetwork.py | 118 + .../models/score_networks/RNNScoreNetwork.py | 41 + .../models/score_networks/ToyScoreNetwork.py | 34 + ProteinDT/models/score_networks/__init__.py | 3 + ProteinDT/utils/__init__.py | 0 ProteinDT/utils/tokenize.py | 48 + README.md | 317 +- README_checkpoints.md | 1 + README_data.md | 1 + examples/README.md | 27 + examples/downstream_Editing/README.md | 90 + ..._peptide_editing_raw_and_processed_data.py | 75 + .../prepare_01_stability_raw_data_Pin1.py | 53 + .../prepare_01_stability_raw_data_Villin.py | 53 + .../prepare_02_processed_data.py | 111 + ...pare_03_train_peptide_editing_evaluator.py | 134 + .../step_01_editing_Galactica.py | 184 + .../step_01_editing_latent_interpolation.py | 386 + .../step_01_editing_latent_optimization.py | 431 + .../step_01_evaluate_stability.py | 229 + .../step_01_evaluate_structure.py | 257 + .../step_02_binding_editing_Galactica.py | 188 + ...02_binding_editing_latent_interpolation.py | 401 + ..._02_binding_editing_latent_optimization.py | 446 + examples/downstream_Editing/test.py | 28 + examples/downstream_Editing/utils.py | 268 + examples/downstream_Editing/utils_analysis.py | 59 + .../utils_peptide_editing.py | 214 + examples/downstream_TAPE.py | 199 + examples/downstream_TAPE_analysis.py | 116 + .../step_01_text_retrieval.py | 52 + .../step_01_text_retrieval.txt | 10000 ++++++++++++++++ .../step_02_inference_ChatGPT.py | 243 + .../step_02_inference_Galactica.py | 227 + .../step_02_inference_ProteinDT.py | 304 + .../step_03_analyze.py | 132 + .../downstream_Text2Protein/step_04_gather.py | 100 + examples/downstream_Text2Protein/utils.py | 128 + examples/pretrain_step_01_CLAP.py | 288 + examples/pretrain_step_02_empty_sequence.py | 177 + ...retrain_step_02_pairwise_representation.py | 180 + examples/pretrain_step_03_facilitator.py | 177 + examples/pretrain_step_04_decoder.py | 226 + examples/pretrain_step_05_AE.py | 174 + examples/pretrain_step_05_inference.py | 194 + figures/final.gif | Bin 0 -> 18210548 bytes figures/pipeline.png | Bin 0 -> 646650 bytes figures/pretraining_roadmap.png | Bin 0 -> 198460 bytes preprocess/SwissProtCLAP/README.md | 17 + preprocess/SwissProtCLAP/step_01_parse_XML.py | 77 + .../step_02_generate_protein_text_pair.py | 56 + .../submit_step_01_Galactica.sh | 85 + ...tep_01_latent_interpolation_Multinomial.sh | 165 + .../submit_step_01_latent_interpolation_T5.sh | 160 + .../submit_step_01_latent_optimization.sh | 144 + .../submit_step_02_Galactica.sh | 45 + ...tep_02_latent_interpolation_Multinomial.sh | 113 + .../submit_step_02_latent_interpolation_T5.sh | 105 + .../submit_step_02_latent_optimization.sh | 86 + .../submit_Multinomial_BertBase.sh | 84 + .../submit_Multinomial_RNN.sh | 86 + .../submit_T5_T5Base.sh | 91 + setup.py | 8 + 95 files changed, 22492 insertions(+), 1 deletion(-) create mode 100644 LICENSE create mode 100644 ProteinDT/TAPE_benchmark/__init__.py create mode 100644 ProteinDT/TAPE_benchmark/datasets.py create mode 100644 ProteinDT/TAPE_benchmark/metrics.py create mode 100644 ProteinDT/TAPE_benchmark/models.py create mode 100644 ProteinDT/TAPE_benchmark/trainer.py create mode 100644 ProteinDT/datasets/__init__.py create mode 100644 ProteinDT/datasets/dataset_MISATO/__init__.py create mode 100644 ProteinDT/datasets/dataset_MISATO/dataloader_MISATO.py create mode 100644 ProteinDT/datasets/dataset_MISATO/dataset_MISATO.py create mode 100644 ProteinDT/datasets/dataset_Pin1.py create mode 100644 ProteinDT/datasets/dataset_Protein.py create mode 100644 ProteinDT/datasets/dataset_RepresentationPair.py create mode 100644 ProteinDT/datasets/dataset_SecondaryStructure.py create mode 100644 ProteinDT/datasets/dataset_Stability.py create mode 100644 ProteinDT/datasets/dataset_SwissProtCLAP.py create mode 100644 ProteinDT/datasets/dataset_Villin.py create mode 100644 ProteinDT/model_ColdDiffusionDecoder.py create mode 100644 ProteinDT/model_GaussianSDEDecoder.py create mode 100644 ProteinDT/model_LSTMDecoder.py create mode 100644 ProteinDT/model_LatentDiffusionDecoder.py create mode 100644 ProteinDT/model_SDE.py create mode 100644 ProteinDT/model_Sampler.py create mode 100644 ProteinDT/models/__init__.py create mode 100644 ProteinDT/models/model_BindingModel.py create mode 100644 ProteinDT/models/model_CDConv.py create mode 100644 ProteinDT/models/model_FoldingBindingInferenceModel.py create mode 100644 ProteinDT/models/model_GaussianFacilitator.py create mode 100644 ProteinDT/models/model_MultinomialDiffusionDecoder.py create mode 100644 ProteinDT/models/model_ProteinText.py create mode 100644 ProteinDT/models/model_RNNPrediction.py create mode 100644 ProteinDT/models/model_TransformerDecoder.py create mode 100644 ProteinDT/models/score_networks/BertScoreNetwork.py create mode 100644 ProteinDT/models/score_networks/RNNScoreNetwork.py create mode 100644 ProteinDT/models/score_networks/ToyScoreNetwork.py create mode 100644 ProteinDT/models/score_networks/__init__.py create mode 100644 ProteinDT/utils/__init__.py create mode 100644 ProteinDT/utils/tokenize.py create mode 100644 README_checkpoints.md create mode 100644 README_data.md create mode 100644 examples/README.md create mode 100644 examples/downstream_Editing/README.md create mode 100644 examples/downstream_Editing/prepare_01_peptide_editing_raw_and_processed_data.py create mode 100644 examples/downstream_Editing/prepare_01_stability_raw_data_Pin1.py create mode 100644 examples/downstream_Editing/prepare_01_stability_raw_data_Villin.py create mode 100644 examples/downstream_Editing/prepare_02_processed_data.py create mode 100644 examples/downstream_Editing/prepare_03_train_peptide_editing_evaluator.py create mode 100644 examples/downstream_Editing/step_01_editing_Galactica.py create mode 100644 examples/downstream_Editing/step_01_editing_latent_interpolation.py create mode 100644 examples/downstream_Editing/step_01_editing_latent_optimization.py create mode 100644 examples/downstream_Editing/step_01_evaluate_stability.py create mode 100644 examples/downstream_Editing/step_01_evaluate_structure.py create mode 100644 examples/downstream_Editing/step_02_binding_editing_Galactica.py create mode 100644 examples/downstream_Editing/step_02_binding_editing_latent_interpolation.py create mode 100644 examples/downstream_Editing/step_02_binding_editing_latent_optimization.py create mode 100644 examples/downstream_Editing/test.py create mode 100644 examples/downstream_Editing/utils.py create mode 100644 examples/downstream_Editing/utils_analysis.py create mode 100644 examples/downstream_Editing/utils_peptide_editing.py create mode 100644 examples/downstream_TAPE.py create mode 100644 examples/downstream_TAPE_analysis.py create mode 100644 examples/downstream_Text2Protein/step_01_text_retrieval.py create mode 100644 examples/downstream_Text2Protein/step_01_text_retrieval.txt create mode 100644 examples/downstream_Text2Protein/step_02_inference_ChatGPT.py create mode 100644 examples/downstream_Text2Protein/step_02_inference_Galactica.py create mode 100644 examples/downstream_Text2Protein/step_02_inference_ProteinDT.py create mode 100644 examples/downstream_Text2Protein/step_03_analyze.py create mode 100644 examples/downstream_Text2Protein/step_04_gather.py create mode 100644 examples/downstream_Text2Protein/utils.py create mode 100644 examples/pretrain_step_01_CLAP.py create mode 100644 examples/pretrain_step_02_empty_sequence.py create mode 100644 examples/pretrain_step_02_pairwise_representation.py create mode 100644 examples/pretrain_step_03_facilitator.py create mode 100644 examples/pretrain_step_04_decoder.py create mode 100644 examples/pretrain_step_05_AE.py create mode 100644 examples/pretrain_step_05_inference.py create mode 100644 figures/final.gif create mode 100644 figures/pipeline.png create mode 100644 figures/pretraining_roadmap.png create mode 100644 preprocess/SwissProtCLAP/README.md create mode 100644 preprocess/SwissProtCLAP/step_01_parse_XML.py create mode 100644 preprocess/SwissProtCLAP/step_02_generate_protein_text_pair.py create mode 100644 scripts/downstream_Editing/submit_step_01_Galactica.sh create mode 100644 scripts/downstream_Editing/submit_step_01_latent_interpolation_Multinomial.sh create mode 100644 scripts/downstream_Editing/submit_step_01_latent_interpolation_T5.sh create mode 100644 scripts/downstream_Editing/submit_step_01_latent_optimization.sh create mode 100644 scripts/downstream_Editing/submit_step_02_Galactica.sh create mode 100644 scripts/downstream_Editing/submit_step_02_latent_interpolation_Multinomial.sh create mode 100644 scripts/downstream_Editing/submit_step_02_latent_interpolation_T5.sh create mode 100644 scripts/downstream_Editing/submit_step_02_latent_optimization.sh create mode 100644 scripts/downstream_Text2Protein/submit_Multinomial_BertBase.sh create mode 100644 scripts/downstream_Text2Protein/submit_Multinomial_RNN.sh create mode 100644 scripts/downstream_Text2Protein/submit_T5_T5Base.sh create mode 100644 setup.py diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..e8b3d23 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2023 Shengchao Liu + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/ProteinDT/TAPE_benchmark/__init__.py b/ProteinDT/TAPE_benchmark/__init__.py new file mode 100644 index 0000000..176d22e --- /dev/null +++ b/ProteinDT/TAPE_benchmark/__init__.py @@ -0,0 +1,4 @@ +from ProteinDT.TAPE_benchmark.datasets import dataset_processor_mapping, output_mode_mapping +from ProteinDT.TAPE_benchmark.models import model_mapping, load_adam_optimizer_and_scheduler +from ProteinDT.TAPE_benchmark.trainer import OntoProteinTrainer +from ProteinDT.TAPE_benchmark.metrics import build_compute_metrics_fn \ No newline at end of file diff --git a/ProteinDT/TAPE_benchmark/datasets.py b/ProteinDT/TAPE_benchmark/datasets.py new file mode 100644 index 0000000..286ee80 --- /dev/null +++ b/ProteinDT/TAPE_benchmark/datasets.py @@ -0,0 +1,690 @@ +from typing import Union, List, Tuple, Sequence, Dict, Any, Optional, Collection +from pathlib import Path +from typing import Union + +import pickle as pkl +import lmdb +import numpy as np +import pandas as pd +import re +import torch +from scipy.spatial.distance import squareform, pdist +# from tape.datasets import pad_sequences, dataset_factory +from torch.utils.data import Dataset +import os + + +class JSONDataset(Dataset): + """Creates a dataset from a json file. Assumes that data is + a JSON serialized list of record, where each record is + a dictionary. + Args: + data_file (Union[str, Path]): Path to json file. + in_memory (bool): Dummy variable to match API of other datasets + """ + + def __init__(self, data_file: Union[str, Path], in_memory: bool = True): + import json + data_file = Path(data_file) + if not data_file.exists(): + raise FileNotFoundError(data_file) + records = json.loads(data_file.read_text()) + + if not isinstance(records, list): + raise TypeError(f"TAPE JSONDataset requires a json serialized list, " + f"received {type(records)}") + self._records = records + self._num_examples = len(records) + + def __len__(self) -> int: + return self._num_examples + + def __getitem__(self, index: int): + if not 0 <= index < self._num_examples: + raise IndexError(index) + + item = self._records[index] + if not isinstance(item, dict): + raise TypeError(f"Expected dataset to contain a list of dictionary " + f"records, received record of type {type(item)}") + if 'id' not in item: + item['id'] = str(index) + return item + + +def dataset_factory(data_file: Union[str, Path], *args, **kwargs) -> Dataset: + data_file = Path(data_file) + if not data_file.exists(): + raise FileNotFoundError(data_file) + if data_file.suffix == '.lmdb': + return LMDBDataset(data_file, *args, **kwargs) + elif data_file.suffix in {'.fasta', '.fna', '.ffn', '.faa', '.frn'}: + return FastaDataset(data_file, *args, **kwargs) + elif data_file.suffix == '.json': + return JSONDataset(data_file, *args, **kwargs) + elif data_file.is_dir(): + return NPZDataset(data_file, *args, **kwargs) + else: + raise ValueError(f"Unrecognized datafile type {data_file.suffix}") + + +def pad_sequences(sequences: Sequence, constant_value=0, dtype=None) -> np.ndarray: + batch_size = len(sequences) + shape = [batch_size] + np.max([seq.shape for seq in sequences], 0).tolist() + + if dtype is None: + dtype = sequences[0].dtype + + if isinstance(sequences[0], np.ndarray): + array = np.full(shape, constant_value, dtype=dtype) + elif isinstance(sequences[0], torch.Tensor): + array = torch.full(shape, constant_value, dtype=dtype) + + for arr, seq in zip(array, sequences): + arrslice = tuple(slice(dim) for dim in seq.shape) + arr[arrslice] = seq + + return array + + +class FastaDataset(Dataset): + """Creates a dataset from a fasta file. + Args: + data_file (Union[str, Path]): Path to fasta file. + in_memory (bool, optional): Whether to load the full dataset into memory. + Default: False. + """ + + def __init__(self, + data_file: Union[str, Path], + in_memory: bool = False): + + from Bio import SeqIO + data_file = Path(data_file) + if not data_file.exists(): + raise FileNotFoundError(data_file) + + cache = list(SeqIO.parse(str(data_file), 'fasta')) + num_examples = len(cache) + self._cache = cache + + self._in_memory = in_memory + self._num_examples = num_examples + + def __len__(self) -> int: + return self._num_examples + + def __getitem__(self, index: int): + if not 0 <= index < self._num_examples: + raise IndexError(index) + + # if self._in_memory and self._cache[index] is not None: + record = self._cache[index] + # else: + # key = self._keys[index] + # record = self._records[key] + # if self._in_memory: + # self._cache[index] = record + + item = {'id': record.id, + 'primary': str(record.seq), + 'protein_length': len(record.seq)} + return item + + +class LMDBDataset(Dataset): + def __init__(self, data_file, in_memory): + env = lmdb.open(data_file, max_readers=1, readonly=True, + lock=False, readahead=False, meminit=False) + + with env.begin(write=False) as txn: + num_examples = pkl.loads(txn.get(b'num_examples')) + + if in_memory: + cache = [None] * num_examples + self._cache = cache + + self._env = env + self._in_memory = in_memory + self._num_examples = num_examples + + def __len__(self): + return self._num_examples + + def __getitem__(self, index): + if self._in_memory and self._cache[index] is not None: + item = self._cache[index] + else: + with self._env.begin(write=False) as txn: + item = pkl.loads(txn.get(str(index).encode())) + if 'id' not in item: + item['id'] = str(index) + if self._in_memory: + self._cache[index] = item + return item + + +class DataProcessor: + """Base class for data converters for biological tasks data sets.""" + def get_train_examples(self, data_dir): + """Gets a collection of :class:`InputExample` for the train set.""" + raise NotImplementedError() + + def get_dev_examples(self, data_dir): + """Gets a collection of :class:`InputExample` for the dev set.""" + raise NotImplementedError() + + def get_test_examples(self, data_dir): + """Gets a collection of :class:`InputExample` for the test set.""" + raise NotImplementedError() + + def get_labels(self): + """Gets the list of labels for this data set.""" + raise NotImplementedError() + + +class FluorescenceProgress(DataProcessor): + def __init__(self, tokenizer): + super().__init__() + self.tokenizer = tokenizer + + def get_train_examples(self, data_dir, in_memory=True): + dataset = FluorescenceDataset(data_dir, split='train', tokenizer=self.tokenizer) + return dataset + + def get_dev_examples(self, data_dir, in_memory=True): + dataset = FluorescenceDataset(data_dir, split='valid', tokenizer=self.tokenizer) + return dataset + + def get_test_examples(self, data_dir, data_cat, in_memory=True): + if data_cat is not None: + dataset = FluorescenceDataset(data_dir, split=data_cat, tokenizer=self.tokenizer) + else: + dataset = FluorescenceDataset(data_dir, split='test', tokenizer=self.tokenizer) + return dataset + + def get_labels(self): + return list(range(1)) + + +class SecondaryStructureProcessor3(DataProcessor): + def __init__(self, tokenizer): + super().__init__() + self.tokenizer = tokenizer + + def get_train_examples(self, data_dir, in_memory=True): + dataset = SecondaryStructureDataset3(data_dir, split='train', tokenizer=self.tokenizer, target='ss3', in_memory=in_memory) + return dataset + + def get_dev_examples(self, data_dir, in_memory=True): + dataset = SecondaryStructureDataset3(data_dir, split='valid', tokenizer=self.tokenizer, target='ss3', in_memory=in_memory) + return dataset + + def get_test_examples(self, data_dir, data_cat, in_memory=True): + dataset = SecondaryStructureDataset3(data_dir, split=data_cat, tokenizer=self.tokenizer, target='ss3', in_memory=in_memory) + return dataset + + def get_labels(self): + return list(range(3)) + + +class SecondaryStructureProcessor8(DataProcessor): + def __init__(self, tokenizer): + super().__init__() + self.tokenizer = tokenizer + + def get_train_examples(self, data_dir, in_memory=True): + dataset = SecondaryStructureDataset8(data_dir, split='train', tokenizer=self.tokenizer, target='ss8', in_memory=in_memory) + return dataset + + def get_dev_examples(self, data_dir, in_memory=True): + dataset = SecondaryStructureDataset8(data_dir, split='valid', tokenizer=self.tokenizer, target='ss8', in_memory=in_memory) + return dataset + + def get_test_examples(self, data_dir, data_cat, in_memory=True): + dataset = SecondaryStructureDataset8(data_dir, split=data_cat, tokenizer=self.tokenizer, target='ss8', in_memory=in_memory) + return dataset + + def get_labels(self): + return list(range(8)) + + +class ContactProgress(DataProcessor): + def __init__(self, tokenizer): + super().__init__() + self.tokenizer = tokenizer + + def get_train_examples(self, data_dir, in_memory=True): + dataset = ProteinnetDataset(data_dir, split='train', tokenizer=self.tokenizer) + return dataset + + def get_dev_examples(self, data_dir, in_memory=True): + dataset = ProteinnetDataset(data_dir, split='valid', tokenizer=self.tokenizer) + return dataset + + def get_test_examples(self, data_dir, data_cat, in_memory=True): + if data_cat is not None: + dataset = ProteinnetDataset(data_dir, split=data_cat, tokenizer=self.tokenizer) + else: + dataset = ProteinnetDataset(data_dir, split='test', tokenizer=self.tokenizer) + return dataset + + def get_labels(self): + return list(range(2)) + + +class StabilityProgress(DataProcessor): + def __init__(self, tokenizer): + super().__init__() + self.tokenizer = tokenizer + + def get_train_examples(self, data_dir, in_memory=True): + dataset = StabilityDataset(data_dir, split='train', tokenizer=self.tokenizer) + return dataset + + def get_dev_examples(self, data_dir, in_memory=True): + dataset = StabilityDataset(data_dir, split='valid', tokenizer=self.tokenizer) + return dataset + + def get_test_examples(self, data_dir, data_cat, in_memory=True): + if data_cat is not None: + dataset = StabilityDataset(data_dir, split=data_cat, tokenizer=self.tokenizer) + else: + dataset = StabilityDataset(data_dir, split='test', tokenizer=self.tokenizer) + return dataset + + def get_labels(self): + return list(range(1)) + + +class RemoteHomologyProgress(DataProcessor): + def __init__(self, tokenizer): + super().__init__() + self.tokenizer = tokenizer + + def get_train_examples(self, data_dir, in_memory=True): + dataset = RemoteHomologyDataset(data_dir, split='train', tokenizer=self.tokenizer) + return dataset + + def get_dev_examples(self, data_dir, in_memory=True): + dataset = RemoteHomologyDataset(data_dir, split='valid', tokenizer=self.tokenizer) + return dataset + + def get_test_examples(self, data_dir, data_cat, in_memory=True): + if data_cat is not None: + dataset = RemoteHomologyDataset(data_dir, split=data_cat, tokenizer=self.tokenizer) + else: + dataset = RemoteHomologyDataset(data_dir, split='test', tokenizer=self.tokenizer) + return dataset + + def get_labels(self): + return list(range(1195)) + + +class ProteinnetDataset(Dataset): + + def __init__(self, + data_path: Union[str, Path], + split: str, + tokenizer): + + if split not in ('train', 'train_unfiltered', 'valid', 'test'): + raise ValueError(f"Unrecognized split: {split}. Must be one of " + f"['train', 'train_unfiltered', 'valid', 'test']") + + self.tokenizer = tokenizer + + data_path = Path(data_path) + data_file = f'proteinnet/proteinnet_{split}.json' + self.data = dataset_factory(data_path / data_file) + + def __len__(self) -> int: + return len(self.data) + + def __getitem__(self, index: int): + item = self.data[index] + + seq = list(re.sub(r"[UZOB]", "X", item['primary'])) + token_ids = self.tokenizer(seq, is_split_into_words=True) + token_ids = np.asarray(token_ids['input_ids'], dtype=int) + protein_length = len(seq) + #if protein_length > 1000: + # print(seq) + input_mask = np.ones_like(token_ids) + + valid_mask = item['valid_mask'] + valid_mask = np.array(valid_mask) + #print("type:", type(valid_mask)) + #print("valid_mask", valid_mask) + contact_map = np.less(squareform(pdist(torch.tensor(item['tertiary']))), 8.0).astype(np.int64) + + yind, xind = np.indices(contact_map.shape) + # DEL + invalid_mask = ~(valid_mask[:, None] & valid_mask[None, :]) + invalid_mask |= np.abs(yind - xind) < 6 + contact_map[invalid_mask] = -1 + + return token_ids, protein_length, input_mask, contact_map + + def collate_fn(self, batch): + input_ids, protein_length, input_mask, contact_labels = tuple(zip(*batch)) + + input_ids = torch.from_numpy(pad_sequences(input_ids, 0)) + input_mask = torch.from_numpy(pad_sequences(input_mask, 0)) + contact_labels = torch.from_numpy(pad_sequences(contact_labels, -1)) + protein_length = torch.LongTensor(protein_length) # type: ignore + + return {'input_ids': input_ids, + 'attention_mask': input_mask, + 'labels': contact_labels, + 'protein_length': protein_length} + + +class FluorescenceDataset(Dataset): + def __init__(self, file_path, split, tokenizer): + self.tokenizer = tokenizer + self.file_path = file_path + + if split not in ('train', 'valid', 'test'): + raise ValueError(f"Unrecognized split: {split}. Must be one of " + f"['train', 'valid', 'test'") + + data_file = f'{self.file_path}/fluorescence/fluorescence_{split}.json' + self.seqs, self.labels = self.get_data(data_file) + + def get_data(self, file): + # print(file) + fp = pd.read_json(file) + seqs = fp.primary + labels = fp.log_fluorescence + + return seqs, labels + + def __len__(self): + return len(self.labels) + + def __getitem__(self, index): + seq = list(re.sub(r"[UZOB]", "X", self.seqs[index])) + + input_ids = self.tokenizer(seq, is_split_into_words=True, truncation=True, padding="max_length", max_length=239) + input_ids = np.array(input_ids['input_ids']) + input_mask = np.ones_like(input_ids) + + label = self.labels[index] + + return input_ids, input_mask, label + + def collate_fn(self, batch): + input_ids, input_mask, fluorescence_true_value = tuple(zip(*batch)) + input_ids = torch.from_numpy(pad_sequences(input_ids, 0)) + input_mask = torch.from_numpy(pad_sequences(input_mask, 0)) + fluorescence_true_value = torch.FloatTensor(fluorescence_true_value) # type: ignore + + #print(fluorescence_true_value.shape) + return {'input_ids': input_ids, + 'attention_mask': input_mask, + 'labels': fluorescence_true_value} + +class StabilityDataset(Dataset): + def __init__(self, file_path, split, tokenizer): + self.file_path = file_path + self.tokenizer = tokenizer + + if split not in ('train', 'valid', 'test'): + raise ValueError(f"Unrecognized split: {split}. Must be one of " + f"['train', 'valid', 'test'") + + data_file = f'{self.file_path}/stability/stability_{split}.json' + self.seqs, self.labels = self.get_data(data_file) + + def get_data(self, path): + read_file = pd.read_json(path) + + seqs = read_file.primary + labels = read_file.stability_score + + return seqs, labels + + def __getitem__(self, index): + seq = list(re.sub(r"[UZOB]", "X", self.seqs[index])) + + input_ids = self.tokenizer(seq, is_split_into_words=True, padding="max_length", max_length=50, truncation=True) + input_ids = np.array(input_ids['input_ids']) + input_mask = np.ones_like(input_ids) + + label = self.labels[index] + + return input_ids, input_mask, label + + def __len__(self): + return len(self.labels) + + def collate_fn(self, batch): + input_ids, input_mask, stability_true_value = tuple(zip(*batch)) + input_ids = torch.from_numpy(pad_sequences(input_ids, 0)) + input_mask = torch.from_numpy(pad_sequences(input_mask, 0)) + stability_true_value = torch.FloatTensor(stability_true_value) # type: ignore + + return {'input_ids': input_ids, + 'attention_mask': input_mask, + 'labels': stability_true_value} + + +class RemoteHomologyDataset(Dataset): + def __init__(self, file_path, split, tokenizer): + self.tokenizer = tokenizer + self.file_path = file_path + + if split not in ('train', 'valid', 'test_fold_holdout', + 'test_family_holdout', 'test_superfamily_holdout'): + raise ValueError(f"Unrecognized split: {split}. Must be one of " + f"['train', 'valid', 'test_fold_holdout', " + f"'test_family_holdout', 'test_superfamily_holdout']") + + data_file = f'{self.file_path}/remote_homology/remote_homology_{split}.json' + + self.seqs, self.labels = self.get_data(data_file) + + def get_data(self, file): + fp = pd.read_json(file) + + seqs = fp.primary + labels = fp.fold_label + + return seqs, labels + + def __len__(self): + return len(self.labels) + + def __getitem__(self, index): + seq = list(re.sub(r"[UZOB]", "X", self.seqs[index])) + + input_ids = self.tokenizer(seq, is_split_into_words=True, truncation=True, padding="max_length", max_length=512) + input_ids = np.array(input_ids['input_ids']) + input_mask = np.ones_like(input_ids) + + label = self.labels[index] + + return input_ids, input_mask, label + + def collate_fn(self, batch): + input_ids, input_mask, fold_label = tuple(zip(*batch)) + input_ids = torch.from_numpy(pad_sequences(input_ids, 0)) + input_mask = torch.from_numpy(pad_sequences(input_mask, 0)) + fold_label = torch.LongTensor(fold_label) # type: ignore + + return {'input_ids': input_ids, + 'attention_mask': input_mask, + 'labels': fold_label} + + +class SecondaryStructureDataset3(Dataset): + def __init__( + self, + data_path, + split, + tokenizer, + in_memory, + target='ss3' + ): + self.tokenizer = tokenizer + data_file = f'secondary_structure/secondary_structure_{split}.lmdb' + print(data_file) + self.data = LMDBDataset(data_file=os.path.join(data_path, data_file), in_memory=in_memory) + self.target = target + + self.ignore_index: int = -100 + + def __len__(self): + return len(self.data) + + def __getitem__(self, index: int): + item = self.data[index] + if len(item['primary']) > 1024: + item['primary'] = item['primary'][:1024] + item['ss3'] = item['ss3'][:1024] + token_ids = self.tokenizer(list(item['primary']), is_split_into_words=True, return_offsets_mapping=True, truncation=False, padding=True) + token_ids = np.array(token_ids['input_ids']) + input_mask = np.ones_like(token_ids) + + # pad with -1s because of cls/sep tokens + labels = np.asarray(item['ss3'], np.int64) + labels = np.pad(labels, (1, 1), 'constant', constant_values=self.ignore_index) + + return token_ids, input_mask, labels + + def collate_fn(self, batch): + input_ids, input_mask, ss_label = tuple(zip(*batch)) + input_ids = torch.from_numpy(pad_sequences(input_ids, constant_value=self.tokenizer.pad_token_id)) + attention_mask = torch.from_numpy(pad_sequences(input_mask, constant_value=0)) + labels = torch.from_numpy(pad_sequences(ss_label, constant_value=self.ignore_index)) + + output = {'input_ids': input_ids, + 'attention_mask': attention_mask, + 'labels': labels} + + return output + + +class SecondaryStructureDataset8(Dataset): + def __init__( + self, + data_path, + split, + tokenizer, + in_memory, + target='ss8' + ): + self.tokenizer = tokenizer + data_file = f'secondary_structure/secondary_structure_{split}.lmdb' + self.data = LMDBDataset(data_file=os.path.join(data_path, data_file), in_memory=in_memory) + self.target = target + + self.ignore_index: int = -100 + + def __len__(self): + return len(self.data) + + def __getitem__(self, index: int): + item = self.data[index] + if len(item['primary']) > 1024: + item['primary'] = item['primary'][:1024] + item['ss8'] = item['ss8'][:1024] + token_ids = self.tokenizer(list(item['primary']), is_split_into_words=True, return_offsets_mapping=True, truncation=False, padding=True) + token_ids = np.array(token_ids['input_ids']) + input_mask = np.ones_like(token_ids) + + # pad with -1s because of cls/sep tokens + labels = np.asarray(item['ss8'], np.int64) + labels = np.pad(labels, (1, 1), 'constant', constant_values=self.ignore_index) + + return token_ids, input_mask, labels + + def collate_fn(self, batch): + input_ids, input_mask, ss_label = tuple(zip(*batch)) + + input_ids = torch.from_numpy(pad_sequences(input_ids, constant_value=self.tokenizer.pad_token_id)) + attention_mask = torch.from_numpy(pad_sequences(input_mask, constant_value=0)) + labels = torch.from_numpy(pad_sequences(ss_label, constant_value=self.ignore_index)) + + output = {'input_ids': input_ids, + 'attention_mask': attention_mask, + 'labels': labels} + + return output + + +output_mode_mapping = { + 'ss3': 'token-level-classification', + 'ss8': 'token-level-classification', + 'contact': 'token-level-classification', + 'remote_homology': 'sequence-level-classification', + 'fluorescence': 'sequence-level-regression', + 'stability': 'sequence-level-regression', +} + +dataset_processor_mapping = { + 'remote_homology': RemoteHomologyProgress, + 'fluorescence': FluorescenceProgress, + 'stability': StabilityProgress, + 'contact': ContactProgress, + 'ss3': SecondaryStructureProcessor3, + 'ss8': SecondaryStructureProcessor8 +} + + +if __name__ == "__main__": + from transformers import BertTokenizer + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../../data/temp_pretrained_ProtBert") + data_dir = "../../data/downstream_datasets" + + dataset_name_list = ['ss3', 'ss8', 'contact', 'remote_homology', 'fluorescence', 'stability'] + + for dataset_name in dataset_name_list: + print(dataset_name) + output_mode = output_mode_mapping[dataset_name] + processor = dataset_processor_mapping[dataset_name](protein_tokenizer) + num_labels = len(processor.get_labels()) + print("num labels: {}".format(num_labels)) + + train_dataset = (processor.get_train_examples(data_dir=data_dir)) + eval_dataset = (processor.get_dev_examples(data_dir=data_dir)) + print("train_dataset", len(train_dataset)) + print("eval_dataset", len(eval_dataset)) + + if dataset_name == 'remote_homology': + test_fold_dataset = ( + processor.get_test_examples(data_dir=data_dir, data_cat='test_fold_holdout') + ) + test_family_dataset = ( + processor.get_test_examples(data_dir=data_dir, data_cat='test_family_holdout') + ) + test_superfamily_dataset = ( + processor.get_test_examples(data_dir=data_dir, data_cat='test_superfamily_holdout') + ) + print("test_fold_dataset", len(test_fold_dataset)) + print("test_family_dataset", len(test_family_dataset)) + print("test_superfamily_dataset", len(test_superfamily_dataset)) + print("test in total", len(test_fold_dataset) + len(test_family_dataset) + len(test_superfamily_dataset)) + + elif dataset_name == 'ss3' or dataset_name == 'ss8': + cb513_dataset = ( + processor.get_test_examples(data_dir=data_dir, data_cat='cb513') + ) + ts115_dataset = ( + processor.get_test_examples(data_dir=data_dir, data_cat='ts115') + ) + casp12_dataset = ( + processor.get_test_examples(data_dir=data_dir, data_cat='casp12') + ) + print("cb513_dataset", len(cb513_dataset)) + print("ts115_dataset", len(ts115_dataset)) + print("casp12_dataset", len(casp12_dataset)) + print("test in total", len(cb513_dataset) + len(ts115_dataset) + len(casp12_dataset)) + + else: + test_dataset = ( + processor.get_test_examples(data_dir=data_dir, data_cat='test') + ) + print("test_dataset", len(test_dataset)) + print() diff --git a/ProteinDT/TAPE_benchmark/metrics.py b/ProteinDT/TAPE_benchmark/metrics.py new file mode 100644 index 0000000..9d4df1a --- /dev/null +++ b/ProteinDT/TAPE_benchmark/metrics.py @@ -0,0 +1,92 @@ +from typing import Sequence, Callable, Dict + +import numpy as np +import scipy +import torch +from seqeval.metrics import accuracy_score +from transformers import EvalPrediction + + +def accuracy_score_remote(y_true, y_pred): + pred_idx = np.argmax(y_pred, axis=1) + # for y_t, y_p in zip(y_true, pred_idx): + # print(y_t, y_p) + nb_correct = sum(y_t == y_p for y_t, y_p in zip(y_true, pred_idx)) + + nb_true = len(y_true) + score_top1 = nb_correct / nb_true + + return score_top1 + + +def spearmanr(target: Sequence[float], + prediction: Sequence[float]) -> float: + target_array = np.asarray(target) + prediction_array = np.asarray(prediction) + return scipy.stats.spearmanr(target_array, prediction_array).correlation + + +def compute_accuracy_metrics(task_name, preds, labels): + if task_name == 'remote_homology': + return { + "accuracy": accuracy_score_remote(labels, preds) + } + else: + raise KeyError(task_name) + + +def compute_spearmanr_metrics(task_name, preds, labels): + # print(p.label_ids.shape, p.predictions.shape) + if task_name == 'fluorescence' or task_name == 'stability': + return{ + "spearmanr": spearmanr(labels, preds) + } + else: + raise KeyError(task_name) + + +def simple_accuracy(preds, labels): + return (preds == labels).float().mean() + + +def bt_compute_metrics(task_name, preds, labels): + assert len(preds) == len(labels), f"Predictions and labels have mismatched lengths {len(preds)} and {len(labels)}" + + # TODO: complement remain tasks' metrics + if task_name == 'ss3' or task_name == 'ss8': + return {'acc': simple_accuracy(preds, labels)} + else: + raise KeyError(task_name) + + +def build_compute_metrics_fn(task_name: str, output_type: str) -> Callable[[EvalPrediction], Dict]: + def compute_metrics_fn(p: EvalPrediction): + if output_type == 'token-level-classification': + logits = p.predictions + preds = np.argmax(logits, axis=-1) + label_ids = torch.from_numpy(p.label_ids) + preds = torch.from_numpy(preds) + + active_index = (label_ids.view(-1) != -100) + active_preds = preds.view(-1)[active_index] + active_labels = label_ids.view(-1)[active_index] + return compute_metrics_mapping[task_name](task_name, active_preds, active_labels) + elif output_type == 'sequence-level-classification' or output_type == 'sequence-level-regression': + logits = p.predictions + # preds = np.argmax(logits, axis=1) + label_ids = p.label_ids + return compute_metrics_mapping[task_name](task_name, logits, label_ids) + else: + raise Exception("output type not supported.") + + return compute_metrics_fn + + +compute_metrics_mapping = { + 'ss3': bt_compute_metrics, + 'ss8': bt_compute_metrics, + 'remote_homology': compute_accuracy_metrics, + 'fluorescence': compute_spearmanr_metrics, + 'stability': compute_spearmanr_metrics, + 'contact': None +} diff --git a/ProteinDT/TAPE_benchmark/models.py b/ProteinDT/TAPE_benchmark/models.py new file mode 100644 index 0000000..33f2126 --- /dev/null +++ b/ProteinDT/TAPE_benchmark/models.py @@ -0,0 +1,253 @@ +from torch import nn +from torch.nn import MSELoss, CrossEntropyLoss, BCEWithLogitsLoss +from transformers import BertPreTrainedModel, BertModel, get_linear_schedule_with_warmup + +import torch +from transformers.modeling_outputs import SequenceClassifierOutput, TokenClassifierOutput + + +class PairwiseContactPredictionHead(nn.Module): + def __init__(self, hidden_size: int, ignore_index=-100): + super().__init__() + self.predict = nn.Sequential( + nn.Dropout(), nn.Linear(2 * hidden_size, 2)) + self._ignore_index = ignore_index + + def forward(self, inputs, sequence_lengths, targets=None): + prod = inputs[:, :, None, :] * inputs[:, None, :, :] + diff = inputs[:, :, None, :] - inputs[:, None, :, :] + pairwise_features = torch.cat((prod, diff), -1) + prediction = self.predict(pairwise_features) + prediction = (prediction + prediction.transpose(1, 2)) / 2 + prediction = prediction[:, 1:-1, 1:-1].contiguous() # remove start/stop tokens + outputs = (prediction,) + + if targets is not None: + loss_fct = nn.CrossEntropyLoss(ignore_index=self._ignore_index) + contact_loss = loss_fct( + prediction.view(-1, 2), targets.view(-1)) + metrics = {'precision_at_l5': + self.compute_precision_at_l5(sequence_lengths, prediction, targets)} + loss_and_metrics = (contact_loss, metrics) + outputs = (loss_and_metrics,) + outputs + + return outputs + + def compute_precision_at_l5(self, sequence_lengths, prediction, labels): + with torch.no_grad(): + valid_mask = labels != self._ignore_index + seqpos = torch.arange(valid_mask.size(1), device=sequence_lengths.device) + x_ind, y_ind = torch.meshgrid(seqpos, seqpos) + valid_mask &= ((y_ind - x_ind) >= 6).unsqueeze(0) + probs = F.softmax(prediction, 3)[:, :, :, 1] + valid_mask = valid_mask.type_as(probs) + correct = 0 + total = 0 + for length, prob, label, mask in zip(sequence_lengths, probs, labels, valid_mask): + masked_prob = (prob * mask).view(-1) + most_likely = masked_prob.topk(length // 5, sorted=False) + selected = label.view(-1).gather(0, most_likely.indices) + correct += selected.sum().float() + total += selected.numel() + return correct / total + + +class BertForOntoProteinContactPrediction(BertPreTrainedModel): + def __init__(self, config, mean_output): + super().__init__(config) + self.num_labels = config.num_labels + + self.bert = BertModel(config, add_pooling_layer=False) + + self.predict = PairwiseContactPredictionHead(config.hidden_size, ignore_index=-1) + self.classifier = nn.Linear(config.hidden_size, config.num_labels) + self.mean_output = mean_output + self.init_weights() + + def forward(self, input_ids, protein_length, attention_mask=None, labels=None): + targets = labels + outputs = self.bert(input_ids) + # targets + + sequence_output = outputs[0] + # print(sequence_output.shape) + output_precition = self.predict(sequence_output, protein_length, targets) + outputs[2:] + # (loss), prediction_scores, (hidden_states), (attentions) + outputs['loss'] = output_precition[0][0] + outputs['logits'] = output_precition[1] + outputs['prediction_score'] = output_precition[0][1] + return outputs + + +class BertForSequenceClassification2(BertPreTrainedModel): + def __init__(self, config, mean_output): + super().__init__(config) + self.num_labels = config.num_labels + self.config = config + + self.bert = BertModel(config) + self.dropout = nn.Dropout(config.hidden_dropout_prob) + self.classifier = nn.Linear(config.hidden_size, config.num_labels) + + self.mean_output = mean_output + + def forward( + self, + input_ids=None, + attention_mask=None, + token_type_ids=None, + position_ids=None, + head_mask=None, + inputs_embeds=None, + labels=None, + output_attentions=None, + output_hidden_states=None, + return_dict=True, + ): + return_dict = return_dict if return_dict is not None else self.config.use_return_dict + + outputs = self.bert( + input_ids, + attention_mask=attention_mask, + token_type_ids=token_type_ids, + position_ids=position_ids, + head_mask=head_mask, + inputs_embeds=inputs_embeds, + output_attentions=output_attentions, + output_hidden_states=output_hidden_states, + return_dict=return_dict, + ) + + if self.mean_output is not True: + outputs_ = outputs[1] + else: + outputs_ = outputs + attention_mask = attention_mask.bool() + num_batch_size = attention_mask.size(0) + outputs_ = torch.stack([outputs_.last_hidden_state[i, attention_mask[i, :], :].mean(dim=0) for i in + range(num_batch_size)], dim=0) + + outputs_ = self.dropout(outputs_) + logits = self.classifier(outputs_) + + loss = None + if labels is not None: + if self.config.problem_type is None: + if self.num_labels == 1: + self.config.problem_type = "regression" + elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int): + self.config.problem_type = "single_label_classification" + else: + self.config.problem_type = "multi_label_classification" + + if self.config.problem_type == "regression": + loss_fct = MSELoss() + if self.num_labels == 1: + loss = loss_fct(logits.squeeze(), labels.squeeze()) + else: + loss = loss_fct(logits, labels) + elif self.config.problem_type == "single_label_classification": + loss_fct = CrossEntropyLoss() + loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1)) + elif self.config.problem_type == "multi_label_classification": + loss_fct = BCEWithLogitsLoss() + loss = loss_fct(logits, labels) + + if not return_dict: + output = (logits,) + outputs[2:] + return ((loss,) + output) if loss is not None else output + + return SequenceClassifierOutput( + loss=loss, + logits=logits, + hidden_states=outputs.hidden_states, + attentions=outputs.attentions, + ) + + +def load_adam_optimizer_and_scheduler(model, args, train_dataset): + optimizer = torch.optim.Adam(model.parameters(), lr=args.learning_rate) + + total_steps = len(train_dataset) // args.train_batch_size // args.gradient_accumulation_steps * args.num_train_epochs + warmup_steps = int(0.1 * total_steps) + scheduler = get_linear_schedule_with_warmup(optimizer, warmup_steps, total_steps) + + return optimizer, scheduler + + +class BertForTokenClassification2(BertPreTrainedModel): + def __init__(self, config, mean_output): + super().__init__(config) + self.num_labels = config.num_labels + + self.bert = BertModel(config, add_pooling_layer=False) + self.dropout = nn.Dropout(config.hidden_dropout_prob) + self.classifier = nn.Linear(config.hidden_size, config.num_labels) + self.mean_output = mean_output + + def forward( + self, + input_ids=None, + attention_mask=None, + token_type_ids=None, + position_ids=None, + head_mask=None, + inputs_embeds=None, + labels=None, + output_attentions=None, + output_hidden_states=None, + return_dict=True, + ): + return_dict = return_dict if return_dict is not None else self.config.use_return_dict + + outputs = self.bert( + input_ids, + attention_mask=attention_mask, + token_type_ids=token_type_ids, + position_ids=position_ids, + head_mask=head_mask, + inputs_embeds=inputs_embeds, + output_attentions=output_attentions, + output_hidden_states=output_hidden_states, + return_dict=return_dict, + ) + + sequence_output = outputs[0] + + sequence_output = self.dropout(sequence_output) + logits = self.classifier(sequence_output) + + loss = None + if labels is not None: + loss_fct = CrossEntropyLoss() + # Only keep active parts of the loss + if attention_mask is not None: + active_loss = attention_mask.view(-1) == 1 + active_logits = logits.view(-1, self.num_labels) + active_labels = torch.where( + active_loss, labels.view(-1), torch.tensor(loss_fct.ignore_index).type_as(labels) + ) + loss = loss_fct(active_logits, active_labels) + else: + loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1)) + + if not return_dict: + output = (logits,) + outputs[2:] + return ((loss,) + output) if loss is not None else output + + return TokenClassifierOutput( + loss=loss, + logits=logits, + hidden_states=outputs.hidden_states, + attentions=outputs.attentions, + ) + + +model_mapping = { + 'remote_homology': BertForSequenceClassification2, + 'contact': BertForOntoProteinContactPrediction, + 'fluorescence': BertForSequenceClassification2, + 'stability': BertForSequenceClassification2, + 'ss3': BertForTokenClassification2, + 'ss8': BertForTokenClassification2 +} diff --git a/ProteinDT/TAPE_benchmark/trainer.py b/ProteinDT/TAPE_benchmark/trainer.py new file mode 100644 index 0000000..6fb345b --- /dev/null +++ b/ProteinDT/TAPE_benchmark/trainer.py @@ -0,0 +1,269 @@ +import collections +import warnings +from typing import Tuple, Optional, Union, Dict, Any, List + +import torch +import torch.nn as nn +from torch.cuda.amp import autocast +from torch.utils.data import IterableDataset, DataLoader +from transformers import Trainer, EvalPrediction, is_torch_tpu_available +from transformers.trainer_pt_utils import find_batch_size, nested_numpify +from transformers.trainer_utils import EvalLoopOutput, denumpify_detensorize, PredictionOutput +import numpy as np + + +class OntoProteinTrainer(Trainer): + + def prediction_step( + self, + model: nn.Module, + inputs: Dict[str, Union[torch.Tensor, Any]], + prediction_loss_only: False, + ignore_keys: Optional[List[str]] = None, + ) -> Tuple[Optional[torch.Tensor], Optional[torch.Tensor], Optional[torch.Tensor]]: + inputs = self._prepare_inputs(inputs) + with torch.no_grad(): + loss, outputs = self.compute_loss(model, inputs, return_outputs=True) + #loss tensor (batch_size, loss) + #dict: outputs['loss'] (batch_size, loss) + #outputs['logits'] (batch_size, protein_length, protein_length, num_labels) + #outputs['prediction_score'] dict{'precision_at_l5:' (batch_size, prediction_score)} + loss = loss.mean().detach() + if isinstance(outputs, dict): + logits = tuple(v for k, v in outputs.items()) + #logits: Tuple: + #logits[0] : model_output (batch_size, protein_length, hidden_size) + #logits[1] : prediction (batch_size, protein_length, protein_length, num_labels) + #logits[2] : dict{'precision_at_l5:' (batch_size, prediction_score)} + else: + logits = outputs[1:] + + if prediction_loss_only: + pass + #return (loss, None, None, None) + + logit = logits[2] + + prediction_score = {} + + prediction_score['precision_at_l5'] = logits[3]['precision_at_l5'] + prediction_score['precision_at_l2'] = logits[3]['precision_at_l2'] + prediction_score['precision_at_l'] = logits[3]['precision_at_l'] + labels = inputs['labels'] + if len(logits) == 1: + logit = logits[0] + + return (loss, logit, labels, prediction_score) + + def prediction_loop(self, dataloader: DataLoader, description: str, prediction_loss_only: Optional[bool] = None): + if hasattr(self, "_prediction_loop"): + warnings.warn( + "The `_prediction_loop` method is deprecated and won't be called in a future version, define `prediction_loop` in your subclass.", + FutureWarning, + ) + return self._prediction_loop(dataloader, description, prediction_loss_only=prediction_loss_only) + + if not isinstance(dataloader.dataset, collections.abc.Sized): + raise ValueError("dataset must implement __len__") + prediction_loss_only = ( + prediction_loss_only if prediction_loss_only is not None else self.args.prediction_loss_only + ) + + model = self.model + # multi-gpu eval + if self.args.n_gpu > 1: + model = torch.nn.DataParallel(model) + # Note: in torch.distributed mode, there's no point in wrapping the model + # inside a DistributedDataParallel as we'll be under `no_grad` anyways. + + batch_size = dataloader.batch_size + num_examples = self.num_examples(dataloader) + print("***** Running %s *****", description) + print(" Num examples = %d", num_examples) + print(" Batch size = %d", batch_size) + losses_host: torch.Tensor = None + #preds_host: Union[torch.Tensor, List[torch.Tensor]] = None + #labels_host: Union[torch.Tensor, List[torch.Tensor]] = None + + world_size = 1 + if is_torch_tpu_available(): + world_size = xm.xrt_world_size() + elif self.args.local_rank != -1: + world_size = torch.distributed.get_world_size() + world_size = max(1, world_size) + + eval_losses_gatherer = DistributedTensorGatherer(world_size, num_examples, make_multiple_of=batch_size) + #preds_gatherer = DistributedTensorGatherer(world_size, num_examples) + #labels_gatherer = DistributedTensorGatherer(world_size, num_examples) + + model.eval() + + if is_torch_tpu_available(): + dataloader = pl.ParallelLoader(dataloader, [self.args.device]).per_device_loader(self.args.device) + + if self.args.past_index >= 0: + self._past = None + + self.callback_handler.eval_dataloader = dataloader + + contact_meterics_l5 = [] + contact_meterics_l2 = [] + contact_meterics_l = [] + for step, inputs in enumerate(dataloader): + loss, logits, labels, prediction_score = self.prediction_step(model, inputs, prediction_loss_only) + contact_meterics_l5.append(torch.mean(prediction_score['precision_at_l5'])) + contact_meterics_l2.append(torch.mean(prediction_score['precision_at_l2'])) + contact_meterics_l.append(torch.mean(prediction_score['precision_at_l'])) + if loss is not None: + losses = loss.repeat(batch_size) + losses_host = losses if losses_host is None else torch.cat((losses_host, losses), dim=0) + + self.control = self.callback_handler.on_prediction_step(self.args, self.state, self.control) + + # Gather all tensors and put them back on the CPU if we have done enough accumulation steps. + if self.args.eval_accumulation_steps is not None and (step + 1) % self.args.eval_accumulation_steps == 0: + eval_losses_gatherer.add_arrays(self._gather_and_numpify(losses_host, "eval_losses")) + + # Set back to None to begin a new accumulation + losses_host = None + + if self.args.past_index and hasattr(self, "_past"): + # Clean the state at the end of the evaluation loop + delattr(self, "_past") + + # Gather all remaining tensors and put them back on the CPU + eval_losses_gatherer.add_arrays(self._gather_and_numpify(losses_host, "eval_losses")) + metrics = {} + eval_loss = eval_losses_gatherer.finalize() + metrics["accuracy_l5"] = sum(contact_meterics_l5) / len(contact_meterics_l5) + metrics["accuracy_l2"] = sum(contact_meterics_l2) / len(contact_meterics_l2) + metrics["accuracy_l"] = sum(contact_meterics_l) / len(contact_meterics_l) + metrics = denumpify_detensorize(metrics) + + return PredictionOutput(predictions=None, label_ids=None, metrics=metrics) + + def evaluation_loop( + self, + dataloader: DataLoader, + description: str, + prediction_loss_only: Optional[bool] = None, + ignore_keys: Optional[List[str]] = None, + metric_key_prefix: str = "eval", + ) -> EvalLoopOutput: + prediction_loss_only = ( + prediction_loss_only if prediction_loss_only is not None else self.args.prediction_loss_only + ) + + # if eval is called w/o train init deepspeed here + if self.args.deepspeed and not self.deepspeed: + + # XXX: eval doesn't have `resume_from_checkpoint` arg but we should be able to do eval + # from the checkpoint eventually + deepspeed_engine, _, _ = deepspeed_init(self, num_training_steps=0, resume_from_checkpoint=None) + self.model = deepspeed_engine.module + self.model_wrapped = deepspeed_engine + self.deepspeed = deepspeed_engine + # XXX: we don't need optim/sched for inference, but this needs to be sorted out, since + # for example the Z3-optimizer is a must for zero3 to work even for inference - what we + # don't need is the deepspeed basic optimizer which is self.optimizer.optimizer + deepspeed_engine.optimizer.optimizer = None + deepspeed_engine.lr_scheduler = None + + model = self._wrap_model(self.model, training=False) + + # if full fp16 is wanted on eval and this ``evaluation`` or ``predict`` isn't called while + # ``train`` is running, halve it first and then put on device + if not self.is_in_train and self.args.fp16_full_eval: + model = model.half().to(self.args.device) + + batch_size = dataloader.batch_size + + print(f"***** Running {description} *****") + if isinstance(dataloader.dataset, collections.abc.Sized): + print(f" Num examples = {self.num_examples(dataloader)}") + else: + print(" Num examples: Unknown") + print(f" Batch size = {batch_size}") + + model.eval() + + self.callback_handler.eval_dataloader = dataloader + # Do this before wrapping. + eval_dataset = dataloader.dataset + + if is_torch_tpu_available(): + dataloader = pl.ParallelLoader(dataloader, [self.args.device]).per_device_loader(self.args.device) + + if self.args.past_index >= 0: + self._past = None + + losses_host = None + + all_losses = None + + # Will be useful when we have an iterable dataset so don't know its length. + contact_meterics_l5 = [] + contact_meterics_l2 = [] + contact_meterics_l = [] + observed_num_examples = 0 + # Main evaluation loop + for step, inputs in enumerate(dataloader): + # Update the observed num examples + observed_batch_size = find_batch_size(inputs) + if observed_batch_size is not None: + observed_num_examples += observed_batch_size + + # Prediction step + loss, logits, labels, prediction_score = self.prediction_step(model, inputs, prediction_loss_only, ignore_keys=ignore_keys) + contact_meterics_l5.append(torch.mean(prediction_score['precision_at_l5'])) + contact_meterics_l2.append(torch.mean(prediction_score['precision_at_l2'])) + contact_meterics_l.append(torch.mean(prediction_score['precision_at_l'])) + # Update containers on host + if loss is not None: + losses = self._nested_gather(loss.repeat(batch_size)) + losses_host = losses if losses_host is None else torch.cat((losses_host, losses), dim=0) + + self.control = self.callback_handler.on_prediction_step(self.args, self.state, self.control) + + # Gather all tensors and put them back on the CPU if we have done enough accumulation steps. + if self.args.eval_accumulation_steps is not None and (step + 1) % self.args.eval_accumulation_steps == 0: + if losses_host is not None: + losses = nested_numpify(losses_host) + all_losses = losses if all_losses is None else np.concatenate((all_losses, losses), axis=0) + + # Set back to None to begin a new accumulation + losses_host, preds_host, labels_host = None, None, None + + if self.args.past_index and hasattr(self, "_past"): + # Clean the state at the end of the evaluation loop + delattr(self, "_past") + + # Gather all remaining tensors and put them back on the CPU + if losses_host is not None: + losses = nested_numpify(losses_host) + all_losses = losses if all_losses is None else np.concatenate((all_losses, losses), axis=0) + + # Number of samples + if not isinstance(eval_dataset, IterableDataset): + num_samples = len(eval_dataset) + # The instance check is weird and does not actually check for the type, but whether the dataset has the right + # methods. Therefore we need to make sure it also has the attribute. + elif isinstance(eval_dataset, IterableDatasetShard) and hasattr(eval_dataset, "num_examples"): + num_samples = eval_dataset.num_examples + else: + num_samples = observed_num_examples + + # Number of losses has been rounded to a multiple of batch_size and in a distributed training, the number of + # samplers has been rounded to a multiple of batch_size, so we truncate. + if all_losses is not None: + all_losses = all_losses[:num_samples] + + metrics = {} + #metrics = prediction_score # mean + metrics["accuracy_l5"] = sum(contact_meterics_l5) / len(contact_meterics_l5) + metrics["accuracy_l2"] = sum(contact_meterics_l2) / len(contact_meterics_l2) + metrics["accuracy_l"] = sum(contact_meterics_l) / len(contact_meterics_l) + # To be JSON-serializable, we need to remove numpy types or zero-d tensors + metrics = denumpify_detensorize(metrics) + + return EvalLoopOutput(predictions=None, label_ids=None, metrics=metrics, num_samples=num_samples) diff --git a/ProteinDT/datasets/__init__.py b/ProteinDT/datasets/__init__.py new file mode 100644 index 0000000..d6d9a9d --- /dev/null +++ b/ProteinDT/datasets/__init__.py @@ -0,0 +1,11 @@ +from ProteinDT.datasets.dataset_SwissProtCLAP import SwissProtCLAPDataset +from ProteinDT.datasets.dataset_RepresentationPair import RepresentationPairDataset, RepresentationPairWithRawDataDataset +from ProteinDT.datasets.dataset_Protein import ProteinSequenceDataset + +from ProteinDT.datasets.dataset_SecondaryStructure import SecondaryStructureDataset + +from ProteinDT.datasets.dataset_Stability import StabilityDataset +from ProteinDT.datasets.dataset_Villin import VillinDataset +from ProteinDT.datasets.dataset_Pin1 import Pin1Dataset + +from ProteinDT.datasets.dataset_MISATO import MISATODataset, MISATODataLoader diff --git a/ProteinDT/datasets/dataset_MISATO/__init__.py b/ProteinDT/datasets/dataset_MISATO/__init__.py new file mode 100644 index 0000000..135526d --- /dev/null +++ b/ProteinDT/datasets/dataset_MISATO/__init__.py @@ -0,0 +1,2 @@ +from .dataset_MISATO import MISATODataset +from .dataloader_MISATO import MISATODataLoader, BatchMISATO diff --git a/ProteinDT/datasets/dataset_MISATO/dataloader_MISATO.py b/ProteinDT/datasets/dataset_MISATO/dataloader_MISATO.py new file mode 100644 index 0000000..a5731b5 --- /dev/null +++ b/ProteinDT/datasets/dataset_MISATO/dataloader_MISATO.py @@ -0,0 +1,79 @@ +import random +import torch +from torch_geometric.data import Data +from torch.utils.data import DataLoader + + +class BatchMISATO(Data): + """A plain old python object modeling a batch of graphs as one big + (disconnected) graph. With :class:`torch_geometric.data.Data` being the + base class, all its methods can also be used here. + In addition, single graphs can be reconstructed via the assignment vector + :obj:`batch`, which maps each node to its respective graph identifier.""" + + def __init__(self, batch=None, **kwargs): + super(BatchMISATO, self).__init__(**kwargs) + self.batch = batch + + @staticmethod + def from_data_list(data_list): + """Constructs a batch object from a python list holding + :class:`torch_geometric.data.Data` objects. + The assignment vector :obj:`batch` is created on the fly.""" + keys = [set(data.keys) for data in data_list] + keys = list(set.union(*keys)) + assert 'batch' not in keys + + batch = BatchMISATO() + + for key in keys: + batch[key] = [] + batch.peptide_batch = [] + batch.protein_batch = [] + + cumsum_node_peptide = 0 + cumsum_node_protein = 0 + + for i, data in enumerate(data_list): + num_nodes_peptide = data.peptide_residue.size()[0] + num_nodes_protein = data.protein_residue.size()[0] + + batch.peptide_batch.append(torch.full((num_nodes_peptide,), i, dtype=torch.long)) + batch.protein_batch.append(torch.full((num_nodes_protein,), i, dtype=torch.long)) + + for key in data.keys: + item = data[key] + batch[key].append(item) + + cumsum_node_peptide += num_nodes_peptide + cumsum_node_protein += num_nodes_protein + + for key in keys: + batch[key] = torch.cat(batch[key], dim=data_list[0].__cat_dim__(key, batch[key][0])) + batch.peptide_batch = torch.cat(batch.peptide_batch, dim=-1) + batch.protein_batch = torch.cat(batch.protein_batch, dim=-1) + return batch.contiguous() + + @property + def num_graphs(self): + """Returns the number of graphs in the batch.""" + return self.batch[-1].item() + 1 + + +class MISATODataLoader(DataLoader): + """Data loader which merges data objects from a + :class:`torch_geometric.data.dataset` to a mini-batch. + Args: + dataset (Dataset): The dataset from which to load the data. + batch_size (int, optional): How may samples per batch to load. + (default: :obj:`1`) + shuffle (bool, optional): If set to :obj:`True`, the data will be + reshuffled at every epoch (default: :obj:`True`) """ + + def __init__(self, dataset, batch_size=1, shuffle=True, **kwargs): + super(MISATODataLoader, self).__init__( + dataset, + batch_size, + shuffle, + collate_fn=lambda data_list: BatchMISATO.from_data_list(data_list), + **kwargs) \ No newline at end of file diff --git a/ProteinDT/datasets/dataset_MISATO/dataset_MISATO.py b/ProteinDT/datasets/dataset_MISATO/dataset_MISATO.py new file mode 100644 index 0000000..1f57fd7 --- /dev/null +++ b/ProteinDT/datasets/dataset_MISATO/dataset_MISATO.py @@ -0,0 +1,286 @@ +import os +import numpy as np +import h5py +from tqdm import tqdm +import pickle +from Bio.PDB.Polypeptide import three_to_one, is_aa + +import torch +from torch.utils.data import Dataset +from torch_geometric.data import Data, InMemoryDataset + +utils_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), "utils") + + +def update_residue_indices(i, type_string, protein_atom_index, residue_index, residue_name, current_residue_index, current_atom_in_residue_index, residue_Map, protein_atom_index2standard_name_dict, molecules_begin_atom_index): + if i < len(protein_atom_index)-1: + if type_string == 'O' and protein_atom_index2standard_name_dict[protein_atom_index[i+1]] == 'N' or residue_Map[residue_index[i+1]]=='MOL': + # GLN has a O N sequence within the AA + if not ((residue_name == 'GLN' and current_atom_in_residue_index==12) or (residue_name == 'ASN' and current_atom_in_residue_index==9)): + current_residue_index +=1 + current_atom_in_residue_index = 0 + + if i+1 in molecules_begin_atom_index: + current_residue_index +=1 + current_atom_in_residue_index = 0 + + return current_residue_index, current_atom_in_residue_index + + +def get_aa_index(residue): + letter_to_num = {'C': 4, 'D': 3, 'S': 15, 'Q': 5, 'K': 11, 'I': 9, + 'P': 14, 'T': 16, 'F': 13, 'A': 0, 'G': 7, 'H': 8, + 'E': 6, 'L': 10, 'R': 1, 'W': 17, 'V': 19, + 'N': 2, 'Y': 18, 'M': 12, "X":20} + + if not is_aa(residue, standard=True): + return 'X' + # return 20 + + one_letter = three_to_one(residue) + + return one_letter + # return letter_to_num[one_letter] + + +def get_atom_and_residue_type(protein_atom_index, residue_index, atom_index, protein_atom_index2standard_name_dict, residue_index2name_dict, atom_reisdue2standard_atom_name_dict, atom_index2name_dict, molecules_begin_atom_index): + current_residue_index = 1 + current_atom_in_residue_index = 0 + standard_atom_name_list = [] + current_atom_in_residue_list = [] + residue_type_list = [] + + L = len(protein_atom_index) + for i in range(L): + current_atom_in_residue_index += 1 + atom_type_string = protein_atom_index2standard_name_dict[protein_atom_index[i]] + residue_name_string = residue_index2name_dict[residue_index[i]] + try: + standard_atom_name_string = atom_reisdue2standard_atom_name_dict[(residue_name_string, current_atom_in_residue_index-1, atom_type_string)] + except KeyError: + # standard atom name: atomic_number + current_atom_in_residue_index + standard_atom_name_string = atom_index2name_dict[atom_index[i]] + str(current_atom_in_residue_index) + + neo_current_residue_index, current_atom_in_residue_index = update_residue_indices(i, atom_type_string, protein_atom_index, residue_index, residue_name_string, current_residue_index, current_atom_in_residue_index, residue_index2name_dict, protein_atom_index2standard_name_dict, molecules_begin_atom_index) + + if neo_current_residue_index != current_residue_index: + current_residue_index = neo_current_residue_index + + current_atom_in_residue_list = np.array(current_atom_in_residue_list) + residue_type_list.append(get_aa_index(residue_name_string)) + if np.count_nonzero(current_atom_in_residue_list == "CA") == np.count_nonzero(current_atom_in_residue_list == "C") and np.count_nonzero(current_atom_in_residue_list == "N") == np.count_nonzero(current_atom_in_residue_list == "C"): + standard_atom_name_list.append(current_atom_in_residue_list) + else: + standard_atom_name_list.append(np.full(len(current_atom_in_residue_list), 'X', dtype=str)) + current_atom_in_residue_list = [] + + current_atom_in_residue_list.append(standard_atom_name_string) + + # handle the last residue + current_atom_in_residue_list = np.array(current_atom_in_residue_list) + residue_type_list.append(get_aa_index(residue_name_string)) + if np.count_nonzero(current_atom_in_residue_list == "CA") == np.count_nonzero(current_atom_in_residue_list == "C") and np.count_nonzero(current_atom_in_residue_list == "N") == np.count_nonzero(current_atom_in_residue_list == "C"): + standard_atom_name_list.append(current_atom_in_residue_list) + else: + standard_atom_name_list.append(np.full(len(current_atom_in_residue_list), 'X', dtype=str)) + + flattened_standard_atom_name_list = [atom for residue in standard_atom_name_list for atom in residue] + return np.array(flattened_standard_atom_name_list), residue_type_list + + +def extract_sequence_and_structure(protein_atom_index, residue_index, atom_index, protein_atom_index2standard_name_dict, residue_index2name_dict, atom_reisdue2standard_atom_name_dict, atom_index2name_dict, molecules_begin_atom_index): + """ + protein_atom_index2standard_name_dict: {1: '2C', 2: '3C', 3: 'C', 4: 'C*', 5: 'C8', 6: 'CA', 7: 'CB', 8: 'CC', 9: 'CN', 10: 'CO', 11: 'CR', 12: 'CT', 13: 'CW', 14: 'CX', 15: 'H', 16: 'H1', 17: 'H4', 18: 'H5', 19: 'HA', 20: 'HC', 21: 'HO', 22: 'HP', 23: 'HS', 24: 'N', 25: 'N2', 26: 'N3', 27: 'NA', 28: 'NB', 29: 'O', 30: 'O2', 31: 'OH', 32: 'S', 33: 'SH', 34: 'br', 35: 'c', 36: 'c1', 37: 'c2', 38: 'c3', 39: 'ca', 40: 'cc', 41: 'cd', 42: 'ce', 43: 'cf', 44: 'cg', 45: 'ch', 46: 'cl', 47: 'cp', 48: 'cq', 49: 'cs', 50: 'cu', 51: 'cx', 52: 'cy', 53: 'cz', 54: 'f', 55: 'h1', 56: 'h2', 57: 'h3', 58: 'h4', 59: 'h5', 60: 'ha', 61: 'hc', 62: 'hn', 63: 'ho', 64: 'hp', 65: 'hs', 66: 'hx', 67: 'i', 68: 'n', 69: 'n1', 70: 'n2', 71: 'n3', 72: 'n4', 73: 'n7', 74: 'n8', 75: 'na', 76: 'nb', 77: 'nc', 78: 'nd', 79: 'ne', 80: 'nf', 81: 'nh', 82: 'ni', 83: 'nj', 84: 'nk', 85: 'nl', 86: 'nm', 87: 'nn', 88: 'no', 89: 'nq', 90: 'ns', 91: 'nt', 92: 'nu', 93: 'nv', 94: 'nx', 95: 'ny', 96: 'nz', 97: 'o', 98: 'oh', 99: 'op', 100: 'oq', 101: 'os', 102: 'p5', 103: 'py', 104: 's', 105: 's4', 106: 's6', 107: 'sh', 108: 'ss', 109: 'sx', 110: 'sy'} + + residue_index2name_dict {0: 'MOL', 1: 'ACE', 2: 'ALA', 3: 'ARG', 4: 'ASN', 5: 'ASP', 6: 'CYS', 7: 'CYX', 8: 'GLN', 9: 'GLU', 10: 'GLY', 11: 'HIE', 12: 'ILE', 13: 'LEU', 14: 'LYS', 15: 'MET', 16: 'PHE', 17: 'PRO', 18: 'SER', 19: 'THR', 20: 'TRP', 21: 'TYR', 22: 'VAL'} + + atom_reisdue2standard_atom_name_dict {('PRO', 0, 'N3'): 'N', ('PRO', 1, 'H'): 'H2', ('PRO', 2, 'H'): 'H3', ('PRO', 3, 'CT'): 'CD', ('PRO', 4, 'HP'): 'HD2', ('PRO', 5, 'HP'): 'HD3', ('PRO', 6, 'CT'): 'CG', ('PRO', 7, 'HC'): 'HG2', ('PRO', 8, 'HC'): 'HB2', ('PRO', 9, 'CT'): 'CB', ('PRO', 10, 'HC'): 'HB2', ('PRO', 11, 'HC'): 'HB3', ('PRO', 12, 'CX'): 'CA', ('PRO', 13, 'HP'): 'HA', ('PRO', 14, 'C'): 'C', ('PRO', 15, 'O'): 'O', ('TYR', 0, 'N'): 'N', ('TYR', 1, 'H'): 'H', ('TYR', 2, 'CX'): 'CA', ('TYR', 3, 'H1'): 'HA', ('TYR', 4, 'CT'): 'CB', ('TYR', 5, 'HC'): 'HB2', ('TYR', 6, 'HC'): 'HB3', ('TYR', 7, 'CA'): 'CG', ('TYR', 8, 'CA'): 'CD1', ('TYR', 9, 'HA'): 'HD1', ('TYR', 10, 'CA'): 'CE1', ('TYR', 11, 'HA'): 'HE1', ('TYR', 12, 'C'): 'CZ', ('TYR', 13, 'OH'): 'OH', ('TYR', 14, 'HO'): 'HH', ('TYR', 15, 'CA'): 'CE2', ('TYR', 16, 'HA'): 'HE2', ('TYR', 17, 'CA'): 'CD2', ('TYR', 18, 'HA'): 'HD2', ('TYR', 19, 'C'): 'C', ('TYR', 20, 'O'): 'O', ('THR', 0, 'N'): 'N', ('THR', 1, 'H'): 'H', ('THR', 2, 'CX'): 'CA', ('THR', 3, 'H1'): 'HA', ('THR', 4, '3C'): 'CB', ('THR', 5, 'H1'): 'HB', ('THR', 6, 'CT'): 'CG2', ('THR', 7, 'HC'): 'HG21', ('THR', 8, 'HC'): 'HG22', ('THR', 9, 'HC'): 'HG23', ('THR', 10, 'OH'): 'OG1', ('THR', 11, 'HO'): 'HG1', ('THR', 12, 'C'): 'C', ('THR', 13, 'O'): 'O', ('VAL', 0, 'N'): 'N', ('VAL', 1, 'H'): 'H', ('VAL', 2, 'CX'): 'CA', ('VAL', 3, 'H1'): 'HA', ('VAL', 4, '3C'): 'CB', ('VAL', 5, 'HC'): 'HB', ('VAL', 6, 'CT'): 'CG1', ('VAL', 7, 'HC'): 'HG11', ('VAL', 8, 'HC'): 'HG12', ('VAL', 9, 'HC'): 'HG13', ('VAL', 10, 'CT'): 'CG2', ('VAL', 11, 'HC'): 'HG21', ('VAL', 12, 'HC'): 'HG22', ('VAL', 13, 'HC'): 'HG23', ('VAL', 14, 'C'): 'C', ('VAL', 15, 'O'): 'O', ('PHE', 0, 'N'): 'N', ('PHE', 1, 'H'): 'H', ('PHE', 2, 'CX'): 'CA', ('PHE', 3, 'H1'): 'HA', ('PHE', 4, 'CT'): 'CB', ('PHE', 5, 'HC'): 'HB2', ('PHE', 6, 'HC'): 'HB3', ('PHE', 7, 'CA'): 'CG', ('PHE', 8, 'CA'): 'CD1', ('PHE', 9, 'HA'): 'HD1', ('PHE', 10, 'CA'): 'CE1', ('PHE', 11, 'HA'): 'HE1', ('PHE', 12, 'CA'): 'CZ', ('PHE', 13, 'HA'): 'HZ', ('PHE', 14, 'CA'): 'CE2', ('PHE', 15, 'HA'): 'HE2', ('PHE', 16, 'CA'): 'CD2', ('PHE', 17, 'HA'): 'HD2', ('PHE', 18, 'C'): 'C', ('PHE', 19, 'O'): 'O', ('PRO', 0, 'N'): 'N', ('PRO', 1, 'CT'): 'CD', ('PRO', 2, 'H1'): 'HD2', ('PRO', 3, 'H1'): 'HD3', ('PRO', 4, 'CT'): 'CG', ('PRO', 5, 'HC'): 'HG2', ('PRO', 6, 'HC'): 'HG3', ('PRO', 7, 'CT'): 'CB', ('PRO', 9, 'HC'): 'HB3', ('PRO', 10, 'CX'): 'CA', ('PRO', 11, 'H1'): 'HA', ('PRO', 12, 'C'): 'C', ('PRO', 13, 'O'): 'O', ('ARG', 0, 'N'): 'N', ('ARG', 1, 'H'): 'H', ('ARG', 2, 'CX'): 'CA', ('ARG', 3, 'H1'): 'HA', ('ARG', 4, 'C8'): 'CB', ('ARG', 5, 'HC'): 'HB2', ('ARG', 6, 'HC'): 'HB3', ('ARG', 7, 'C8'): 'CG', ('ARG', 8, 'HC'): 'HG2', ('ARG', 9, 'HC'): 'HG3', ('ARG', 10, 'C8'): 'CD', ('ARG', 11, 'H1'): 'HD2', ('ARG', 12, 'H1'): 'HD3', ('ARG', 13, 'N2'): 'NE', ('ARG', 14, 'H'): 'HE', ('ARG', 15, 'CA'): 'CZ', ('ARG', 16, 'N2'): 'NH1', ('ARG', 17, 'H'): 'HH11', ('ARG', 18, 'H'): 'HH12', ('ARG', 19, 'N2'): 'NH2', ('ARG', 20, 'H'): 'HH21', ('ARG', 21, 'H'): 'HH22', ('ARG', 22, 'C'): 'C', ('ARG', 23, 'O'): 'O', ('GLY', 0, 'N'): 'N', ('GLY', 1, 'H'): 'H', ('GLY', 2, 'CX'): 'CA', ('GLY', 3, 'H1'): 'HA2', ('GLY', 4, 'H1'): 'HA3', ('GLY', 5, 'C'): 'C', ('GLY', 6, 'O'): 'O', ('CYS', 0, 'N'): 'N', ('CYS', 1, 'H'): 'H', ('CYS', 2, 'CX'): 'CA', ('CYS', 3, 'H1'): 'HA', ('CYS', 4, '2C'): 'CB', ('CYS', 5, 'H1'): 'HB2', ('CYS', 6, 'H1'): 'HB3', ('CYS', 7, 'SH'): 'SG', ('CYS', 8, 'HS'): 'HG', ('CYS', 9, 'C'): 'C', ('CYS', 10, 'O'): 'O', ('ALA', 0, 'N'): 'N', ('ALA', 1, 'H'): 'H', ('ALA', 2, 'CX'): 'CA', ('ALA', 3, 'H1'): 'HA', ('ALA', 4, 'CT'): 'CB', ('ALA', 5, 'HC'): 'HB1', ('ALA', 6, 'HC'): 'HB2', ('ALA', 7, 'HC'): 'HB3', ('ALA', 8, 'C'): 'C', ('ALA', 9, 'O'): 'O', ('LEU', 0, 'N'): 'N', ('LEU', 1, 'H'): 'H', ('LEU', 2, 'CX'): 'CA', ('LEU', 3, 'H1'): 'HA', ('LEU', 4, '2C'): 'CB', ('LEU', 5, 'HC'): 'HB2', ('LEU', 6, 'HC'): 'HB3', ('LEU', 7, '3C'): 'CG', ('LEU', 8, 'HC'): 'HG', ('LEU', 9, 'CT'): 'CD1', ('LEU', 10, 'HC'): 'HD11', ('LEU', 11, 'HC'): 'HD12', ('LEU', 12, 'HC'): 'HD13', ('LEU', 13, 'CT'): 'CD2', ('LEU', 14, 'HC'): 'HD21', ('LEU', 15, 'HC'): 'HD22', ('LEU', 16, 'HC'): 'HD23', ('LEU', 17, 'C'): 'C', ('LEU', 18, 'O'): 'O', ('MET', 0, 'N'): 'N', ('MET', 1, 'H'): 'H', ('MET', 2, 'CX'): 'CA', ('MET', 3, 'H1'): 'HA', ('MET', 4, '2C'): 'CB', ('MET', 5, 'HC'): 'HB2', ('MET', 6, 'HC'): 'HB3', ('MET', 7, '2C'): 'CG', ('MET', 8, 'H1'): 'HG2', ('MET', 9, 'H1'): 'HG3', ('MET', 10, 'S'): 'SD', ('MET', 11, 'CT'): 'CE', ('MET', 12, 'H1'): 'HE1', ('MET', 13, 'H1'): 'HE2', ('MET', 14, 'H1'): 'HE3', ('MET', 15, 'C'): 'C', ('MET', 16, 'O'): 'O', ('ASP', 0, 'N'): 'N', ('ASP', 1, 'H'): 'H', ('ASP', 2, 'CX'): 'CA', ('ASP', 3, 'H1'): 'HA', ('ASP', 4, '2C'): 'CB', ('ASP', 5, 'HC'): 'HB2', ('ASP', 6, 'HC'): 'HB3', ('ASP', 7, 'CO'): 'CG', ('ASP', 8, 'O2'): 'OD1', ('ASP', 9, 'O2'): 'OD2', ('ASP', 10, 'C'): 'C', ('ASP', 11, 'O'): 'O', ('GLN', 0, 'N'): 'N', ('GLN', 1, 'H'): 'H', ('GLN', 2, 'CX'): 'CA', ('GLN', 3, 'H1'): 'HA', ('GLN', 4, '2C'): 'CB', ('GLN', 5, 'HC'): 'HB2', ('GLN', 6, 'HC'): 'HB3', ('GLN', 7, '2C'): 'CG', ('GLN', 8, 'HC'): 'HG2', ('GLN', 9, 'HC'): 'HG3', ('GLN', 10, 'C'): 'CD', ('GLN', 11, 'O'): 'OE1', ('GLN', 12, 'N'): 'NE2', ('GLN', 13, 'H'): 'HE21', ('GLN', 14, 'H'): 'HE22', ('GLN', 15, 'C'): 'C', ('GLN', 16, 'O'): 'O', ('SER', 0, 'N'): 'N', ('SER', 1, 'H'): 'H', ('SER', 2, 'CX'): 'CA', ('SER', 3, 'H1'): 'HA', ('SER', 4, '2C'): 'CB', ('SER', 5, 'H1'): 'HB2', ('SER', 6, 'H1'): 'HB3', ('SER', 7, 'OH'): 'OG', ('SER', 8, 'HO'): 'HG', ('SER', 9, 'C'): 'C', ('SER', 10, 'O'): 'O', ('TRP', 0, 'N'): 'N', ('TRP', 1, 'H'): 'H', ('TRP', 2, 'CX'): 'CA', ('TRP', 3, 'H1'): 'HA', ('TRP', 4, 'CT'): 'CB', ('TRP', 5, 'HC'): 'HB2', ('TRP', 6, 'HC'): 'HB3', ('TRP', 7, 'C*'): 'CG', ('TRP', 8, 'CW'): 'CD1', ('TRP', 9, 'H4'): 'HD1', ('TRP', 10, 'NA'): 'NE1', ('TRP', 11, 'H'): 'HE1', ('TRP', 12, 'CN'): 'CE2', ('TRP', 13, 'CA'): 'CZ2', ('TRP', 14, 'HA'): 'HZ2', ('TRP', 15, 'CA'): 'CH2', ('TRP', 16, 'HA'): 'HH2', ('TRP', 17, 'CA'): 'CZ3', ('TRP', 18, 'HA'): 'HZ3', ('TRP', 19, 'CA'): 'CE3', ('TRP', 20, 'HA'): 'HE3', ('TRP', 21, 'CB'): 'CD2', ('TRP', 22, 'C'): 'C', ('TRP', 23, 'O'): 'O', ('LYS', 0, 'N'): 'N', ('LYS', 1, 'H'): 'H', ('LYS', 2, 'CX'): 'CA', ('LYS', 3, 'H1'): 'HA', ('LYS', 4, 'C8'): 'CB', ('LYS', 5, 'HC'): 'HB2', ('LYS', 6, 'HC'): 'HB3', ('LYS', 7, 'C8'): 'CG', ('LYS', 8, 'HC'): 'HG2', ('LYS', 9, 'HC'): 'HG3', ('LYS', 10, 'C8'): 'CD', ('LYS', 11, 'HC'): 'HD2', ('LYS', 12, 'HC'): 'HD3', ('LYS', 13, 'C8'): 'CE', ('LYS', 14, 'HP'): 'HE2', ('LYS', 15, 'HP'): 'HE3', ('LYS', 16, 'N3'): 'NZ', ('LYS', 17, 'H'): 'HZ1', ('LYS', 18, 'H'): 'HZ2', ('LYS', 19, 'H'): 'HZ3', ('LYS', 20, 'C'): 'C', ('LYS', 21, 'O'): 'O', ('GLU', 0, 'N'): 'N', ('GLU', 1, 'H'): 'H', ('GLU', 2, 'CX'): 'CA', ('GLU', 3, 'H1'): 'HA', ('GLU', 4, '2C'): 'CB', ('GLU', 5, 'HC'): 'HB2', ('GLU', 6, 'HC'): 'HB3', ('GLU', 7, '2C'): 'CG', ('GLU', 8, 'HC'): 'HG2', ('GLU', 9, 'HC'): 'HG3', ('GLU', 10, 'CO'): 'CD', ('GLU', 11, 'O2'): 'OE1', ('GLU', 12, 'O2'): 'OE2', ('GLU', 13, 'C'): 'C', ('GLU', 14, 'O'): 'O', ('ASN', 0, 'N'): 'N', ('ASN', 1, 'H'): 'H', ('ASN', 2, 'CX'): 'CA', ('ASN', 3, 'H1'): 'HA', ('ASN', 4, '2C'): 'CB', ('ASN', 5, 'HC'): 'HB2', ('ASN', 6, 'HC'): 'HB3', ('ASN', 7, 'C'): 'CG', ('ASN', 8, 'O'): 'OD1', ('ASN', 9, 'N'): 'ND2', ('ASN', 10, 'H'): 'HD21', ('ASN', 11, 'H'): 'HD22', ('ASN', 12, 'C'): 'C', ('ASN', 13, 'O'): 'O', ('ILE', 0, 'N'): 'N', ('ILE', 1, 'H'): 'H', ('ILE', 2, 'CX'): 'CA', ('ILE', 3, 'H1'): 'HA', ('ILE', 4, '3C'): 'CB', ('ILE', 5, 'HC'): 'HB', ('ILE', 6, 'CT'): 'CG2', ('ILE', 7, 'HC'): 'HG21', ('ILE', 8, 'HC'): 'HG22', ('ILE', 9, 'HC'): 'HG23', ('ILE', 10, '2C'): 'CG1', ('ILE', 11, 'HC'): 'HG12', ('ILE', 12, 'HC'): 'HG13', ('ILE', 13, 'CT'): 'CD1', ('ILE', 14, 'HC'): 'HD11', ('ILE', 15, 'HC'): 'HD12', ('ILE', 16, 'HC'): 'HD13', ('ILE', 17, 'C'): 'C', ('ILE', 18, 'O'): 'O', ('HIE', 0, 'N'): 'N', ('HIE', 1, 'H'): 'H', ('HIE', 2, 'CX'): 'CA', ('HIE', 3, 'H1'): 'HA', ('HIE', 4, 'CT'): 'CB', ('HIE', 5, 'HC'): 'HB2', ('HIE', 6, 'HC'): 'HB3', ('HIE', 7, 'CC'): 'CG', ('HIE', 8, 'NB'): 'ND1', ('HIE', 9, 'CR'): 'CE1', ('HIE', 10, 'H5'): 'HE1', ('HIE', 11, 'NA'): 'NE2', ('HIE', 12, 'H'): 'HE2', ('HIE', 13, 'CW'): 'CD2', ('HIE', 14, 'H4'): 'HD2', ('HIE', 15, 'C'): 'C', ('HIE', 16, 'O'): 'O', ('GLN', 16, 'O2'): 'O', ('GLN', 17, 'O2'): 'OXT', ('MET', 0, 'N3'): 'N', ('MET', 2, 'H'): 'H2', ('MET', 3, 'H'): 'H3', ('MET', 4, 'CX'): 'CA', ('MET', 5, 'HP'): 'HA', ('MET', 6, '2C'): 'CB', ('MET', 7, 'HC'): 'HB2', ('MET', 8, 'HC'): 'HB3', ('MET', 9, '2C'): 'CG', ('MET', 10, 'H1'): 'HG2', ('MET', 11, 'H1'): 'HG3', ('MET', 12, 'S'): 'SD', ('MET', 13, 'CT'): 'CE', ('MET', 15, 'H1'): 'HE2', ('MET', 16, 'H1'): 'HE3', ('MET', 17, 'C'): 'C', ('MET', 18, 'O'): 'O', ('GLU', 0, 'N3'): 'N', ('GLU', 2, 'H'): 'H2', ('GLU', 3, 'H'): 'H3', ('GLU', 4, 'CX'): 'CA', ('GLU', 5, 'HP'): 'HA', ('GLU', 6, '2C'): 'CB', ('GLU', 7, 'HC'): 'HB2', ('GLU', 9, '2C'): 'CG', ('GLU', 10, 'HC'): 'HG2', ('GLU', 11, 'HC'): 'HG3', ('GLU', 12, 'CO'): 'CD', ('GLU', 13, 'O2'): 'OE1', ('GLU', 14, 'O2'): 'O', ('GLU', 15, 'C'): 'C', ('GLU', 16, 'O'): 'O', ('LYS', 21, 'O2'): 'O', ('LYS', 22, 'O2'): 'OXT', ('SER', 0, 'N3'): 'N', ('SER', 2, 'H'): 'H2', ('SER', 3, 'H'): 'H3', ('SER', 4, 'CX'): 'CA', ('SER', 5, 'HP'): 'HA', ('SER', 6, '2C'): 'CB', ('SER', 7, 'H1'): 'HB2', ('SER', 8, 'H1'): 'HB3', ('SER', 9, 'OH'): 'OG', ('SER', 10, 'HO'): 'HG', ('SER', 11, 'C'): 'C', ('SER', 12, 'O'): 'O', ('PRO', 13, 'O2'): 'O', ('PRO', 14, 'O2'): 'OXT', ('ILE', 0, 'N3'): 'N', ('ILE', 2, 'H'): 'H2', ('ILE', 3, 'H'): 'H3', ('ILE', 4, 'CX'): 'CA', ('ILE', 5, 'HP'): 'HA', ('ILE', 6, '3C'): 'CB', ('ILE', 8, 'CT'): 'CG2', ('ILE', 10, 'HC'): 'HG22', ('ILE', 12, '2C'): 'CG1', ('ILE', 13, 'HC'): 'HG12', ('ILE', 15, 'CT'): 'CD1', ('ILE', 17, 'HC'): 'HD12', ('ILE', 18, 'HC'): 'HD13', ('ILE', 19, 'C'): 'C', ('ILE', 20, 'O'): 'O', ('ASP', 0, 'N3'): 'N', ('ASP', 2, 'H'): 'H2', ('ASP', 3, 'H'): 'H3', ('ASP', 4, 'CX'): 'CA', ('ASP', 5, 'HP'): 'HA', ('ASP', 6, '2C'): 'CB', ('ASP', 7, 'HC'): 'HB2', ('ASP', 8, 'HC'): 'HB3', ('ASP', 9, 'CO'): 'CG', ('ASP', 10, 'O2'): 'OD1', ('ASP', 11, 'O2'): 'O', ('ASP', 12, 'C'): 'C', ('ASP', 13, 'O'): 'O', ('ALA', 0, 'N3'): 'N', ('ALA', 2, 'H'): 'H2', ('ALA', 3, 'H'): 'H3', ('ALA', 4, 'CX'): 'CA', ('ALA', 5, 'HP'): 'HA', ('ALA', 6, 'CT'): 'CB', ('ALA', 8, 'HC'): 'HB2', ('ALA', 9, 'HC'): 'HB3', ('ALA', 10, 'C'): 'C', ('ALA', 11, 'O'): 'O', ('CYX', 0, 'N'): 'N', ('CYX', 1, 'H'): 'H', ('CYX', 2, 'CX'): 'CA', ('CYX', 3, 'H1'): 'HA', ('CYX', 4, '2C'): 'CB', ('CYX', 5, 'H1'): 'HB2', ('CYX', 6, 'H1'): 'HB3', ('CYX', 7, 'S'): 'SG', ('CYX', 8, 'C'): 'C', ('CYX', 9, 'O'): 'O', ('GLU', 15, 'O2'): 'OXT', ('VAL', 0, 'N3'): 'N', ('VAL', 2, 'H'): 'H2', ('VAL', 3, 'H'): 'H3', ('VAL', 4, 'CX'): 'CA', ('VAL', 5, 'HP'): 'HA', ('VAL', 6, '3C'): 'CB', ('VAL', 8, 'CT'): 'CG1', ('VAL', 10, 'HC'): 'HG12', ('VAL', 12, 'CT'): 'CG2', ('VAL', 14, 'HC'): 'HG22', ('VAL', 15, 'HC'): 'HG23', ('VAL', 16, 'C'): 'C', ('VAL', 17, 'O'): 'O', ('TYR', 20, 'O2'): 'O', ('TYR', 21, 'O2'): 'OXT', ('GLN', 0, 'N3'): 'N', ('GLN', 2, 'H'): 'H2', ('GLN', 3, 'H'): 'H3', ('GLN', 4, 'CX'): 'CA', ('GLN', 5, 'HP'): 'HA', ('GLN', 6, '2C'): 'CB', ('GLN', 7, 'HC'): 'HB2', ('GLN', 9, '2C'): 'CG', ('GLN', 10, 'HC'): 'HG2', ('GLN', 11, 'HC'): 'HG3', ('GLN', 12, 'C'): 'CD', ('GLN', 13, 'O'): 'OE1', ('GLN', 14, 'N'): 'NE2', ('GLN', 15, 'H'): 'HE21', ('GLN', 16, 'H'): 'HE22', ('GLN', 17, 'C'): 'C', ('GLN', 18, 'O'): 'O', ('THR', 0, 'N3'): 'N', ('THR', 2, 'H'): 'H2', ('THR', 3, 'H'): 'H3', ('THR', 4, 'CX'): 'CA', ('THR', 5, 'HP'): 'HA', ('THR', 6, '3C'): 'CB', ('THR', 7, 'H1'): 'HB', ('THR', 8, 'CT'): 'CG2', ('THR', 10, 'HC'): 'HG22', ('THR', 11, 'HC'): 'HG23', ('THR', 12, 'OH'): 'OG1', ('THR', 13, 'HO'): 'HG1', ('THR', 14, 'C'): 'C', ('THR', 15, 'O'): 'O', ('ARG', 23, 'O2'): 'O', ('ARG', 24, 'O2'): 'OXT', ('THR', 13, 'O2'): 'O', ('THR', 14, 'O2'): 'OXT', ('GLY', 0, 'N3'): 'N', ('GLY', 2, 'H'): 'H2', ('GLY', 3, 'H'): 'H3', ('GLY', 4, 'CX'): 'CA', ('GLY', 5, 'HP'): 'HA2', ('GLY', 6, 'HP'): 'HA3', ('GLY', 7, 'C'): 'C', ('GLY', 8, 'O'): 'O', ('PHE', 19, 'O2'): 'O', ('PHE', 20, 'O2'): 'OXT', ('LEU', 18, 'O2'): 'O', ('LEU', 19, 'O2'): 'OXT', ('ILE', 18, 'O2'): 'O', ('ILE', 19, 'O2'): 'OXT', ('LYS', 0, 'N3'): 'N', ('LYS', 2, 'H'): 'H2', ('LYS', 3, 'H'): 'H3', ('LYS', 4, 'CX'): 'CA', ('LYS', 5, 'HP'): 'HA', ('LYS', 6, 'C8'): 'CB', ('LYS', 7, 'HC'): 'HB2', ('LYS', 9, 'C8'): 'CG', ('LYS', 10, 'HC'): 'HG2', ('LYS', 12, 'C8'): 'CD', ('LYS', 13, 'HC'): 'HD2', ('LYS', 14, 'HC'): 'HD3', ('LYS', 15, 'C8'): 'CE', ('LYS', 16, 'HP'): 'HE2', ('LYS', 17, 'HP'): 'HE3', ('LYS', 18, 'N3'): 'NZ', ('LYS', 20, 'H'): 'HZ2', ('LYS', 21, 'H'): 'HZ3', ('LYS', 22, 'C'): 'C', ('LYS', 23, 'O'): 'O', ('HIE', 0, 'N3'): 'N', ('HIE', 2, 'H'): 'H2', ('HIE', 3, 'H'): 'H3', ('HIE', 4, 'CX'): 'CA', ('HIE', 5, 'HP'): 'HA', ('HIE', 6, 'CT'): 'CB', ('HIE', 7, 'HC'): 'HB2', ('HIE', 8, 'HC'): 'HB3', ('HIE', 9, 'CC'): 'CG', ('HIE', 10, 'NB'): 'ND1', ('HIE', 11, 'CR'): 'CE1', ('HIE', 12, 'H5'): 'HE1', ('HIE', 13, 'NA'): 'NE2', ('HIE', 14, 'H'): 'HE2', ('HIE', 15, 'CW'): 'CD2', ('HIE', 16, 'H4'): 'HD2', ('HIE', 17, 'C'): 'C', ('HIE', 18, 'O'): 'O', ('GLY', 6, 'O2'): 'O', ('GLY', 7, 'O2'): 'OXT', ('ASN', 13, 'O2'): 'O', ('ASN', 14, 'O2'): 'OXT', ('LEU', 0, 'N3'): 'N', ('LEU', 2, 'H'): 'H2', ('LEU', 3, 'H'): 'H3', ('LEU', 4, 'CX'): 'CA', ('LEU', 5, 'HP'): 'HA', ('LEU', 6, '2C'): 'CB', ('LEU', 7, 'HC'): 'HB2', ('LEU', 9, '3C'): 'CG', ('LEU', 11, 'CT'): 'CD1', ('LEU', 13, 'HC'): 'HD12', ('LEU', 15, 'CT'): 'CD2', ('LEU', 17, 'HC'): 'HD22', ('LEU', 18, 'HC'): 'HD23', ('LEU', 19, 'C'): 'C', ('LEU', 20, 'O'): 'O', ('SER', 10, 'O2'): 'O', ('SER', 11, 'O2'): 'OXT', ('ASN', 0, 'N3'): 'N', ('ASN', 2, 'H'): 'H2', ('ASN', 3, 'H'): 'H3', ('ASN', 4, 'CX'): 'CA', ('ASN', 5, 'HP'): 'HA', ('ASN', 6, '2C'): 'CB', ('ASN', 7, 'HC'): 'HB2', ('ASN', 8, 'HC'): 'HB3', ('ASN', 9, 'C'): 'CG', ('ASN', 10, 'O'): 'OD1', ('ASN', 11, 'N'): 'ND2', ('ASN', 12, 'H'): 'HD21', ('ASN', 13, 'H'): 'HD22', ('ASN', 14, 'C'): 'C', ('ASN', 15, 'O'): 'O', ('ARG', 0, 'N3'): 'N', ('ARG', 2, 'H'): 'H2', ('ARG', 3, 'H'): 'H3', ('ARG', 4, 'CX'): 'CA', ('ARG', 5, 'HP'): 'HA', ('ARG', 6, 'C8'): 'CB', ('ARG', 7, 'HC'): 'HB2', ('ARG', 9, 'C8'): 'CG', ('ARG', 10, 'HC'): 'HG2', ('ARG', 11, 'HC'): 'HG3', ('ARG', 12, 'C8'): 'CD', ('ARG', 13, 'H1'): 'HD2', ('ARG', 14, 'H1'): 'HD3', ('ARG', 15, 'N2'): 'NE', ('ARG', 16, 'H'): 'HE', ('ARG', 17, 'CA'): 'CZ', ('ARG', 18, 'N2'): 'NH1', ('ARG', 19, 'H'): 'HH11', ('ARG', 21, 'N2'): 'NH2', ('ARG', 22, 'H'): 'HH21', ('ARG', 23, 'H'): 'HH22', ('ARG', 24, 'C'): 'C', ('ARG', 25, 'O'): 'O', ('MET', 16, 'O2'): 'O', ('MET', 17, 'O2'): 'OXT', ('PHE', 0, 'N3'): 'N', ('PHE', 2, 'H'): 'H2', ('PHE', 3, 'H'): 'H3', ('PHE', 4, 'CX'): 'CA', ('PHE', 5, 'HP'): 'HA', ('PHE', 6, 'CT'): 'CB', ('PHE', 7, 'HC'): 'HB2', ('PHE', 8, 'HC'): 'HB3', ('PHE', 9, 'CA'): 'CG', ('PHE', 18, 'CA'): 'CD2', ('PHE', 19, 'HA'): 'HD2', ('PHE', 20, 'C'): 'C', ('PHE', 21, 'O'): 'O', ('ASP', 12, 'O2'): 'OXT', ('CYS', 0, 'N3'): 'N', ('CYS', 2, 'H'): 'H2', ('CYS', 3, 'H'): 'H3', ('CYS', 4, 'CX'): 'CA', ('CYS', 5, 'HP'): 'HA', ('CYS', 6, '2C'): 'CB', ('CYS', 7, 'H1'): 'HB2', ('CYS', 8, 'H1'): 'HB3', ('CYS', 9, 'SH'): 'SG', ('CYS', 10, 'HS'): 'HG', ('CYS', 11, 'C'): 'C', ('CYS', 12, 'O'): 'O', ('ALA', 9, 'O2'): 'O', ('ALA', 10, 'O2'): 'OXT', ('TRP', 23, 'O2'): 'O', ('TRP', 24, 'O2'): 'OXT', ('HIE', 16, 'O2'): 'O', ('HIE', 17, 'O2'): 'OXT', ('CYX', 9, 'O2'): 'O', ('CYX', 10, 'O2'): 'OXT', ('TYR', 0, 'N3'): 'N', ('TYR', 2, 'H'): 'H2', ('TYR', 3, 'H'): 'H3', ('TYR', 4, 'CX'): 'CA', ('TYR', 5, 'HP'): 'HA', ('TYR', 6, 'CT'): 'CB', ('TYR', 7, 'HC'): 'HB2', ('TYR', 8, 'HC'): 'HB3', ('TYR', 9, 'CA'): 'CG', ('TYR', 12, 'CA'): 'CE1', ('TYR', 13, 'HA'): 'HE1', ('TYR', 14, 'C'): 'CZ', ('TYR', 15, 'OH'): 'OH', ('TYR', 16, 'HO'): 'HH', ('TYR', 19, 'CA'): 'CD2', ('TYR', 20, 'HA'): 'HD2', ('TYR', 21, 'C'): 'C', ('TYR', 22, 'O'): 'O', ('VAL', 15, 'O2'): 'O', ('VAL', 16, 'O2'): 'OXT', ('CYX', 0, 'N3'): 'N', ('CYX', 2, 'H'): 'H2', ('CYX', 3, 'H'): 'H3', ('CYX', 4, 'CX'): 'CA', ('CYX', 5, 'HP'): 'HA', ('CYX', 6, '2C'): 'CB', ('CYX', 7, 'H1'): 'HB2', ('CYX', 8, 'H1'): 'HB3', ('CYX', 9, 'S'): 'SG', ('CYX', 10, 'C'): 'C', ('CYX', 11, 'O'): 'O', ('CYS', 10, 'O2'): 'O', ('CYS', 11, 'O2'): 'OXT', ('TRP', 0, 'N3'): 'N', ('TRP', 2, 'H'): 'H2', ('TRP', 3, 'H'): 'H3', ('TRP', 4, 'CX'): 'CA', ('TRP', 5, 'HP'): 'HA', ('TRP', 6, 'CT'): 'CB', ('TRP', 7, 'HC'): 'HB2', ('TRP', 8, 'HC'): 'HB3', ('TRP', 9, 'C*'): 'CG', ('TRP', 10, 'CW'): 'CD1', ('TRP', 11, 'H4'): 'HD1', ('TRP', 12, 'NA'): 'NE1', ('TRP', 13, 'H'): 'HE1', ('TRP', 14, 'CN'): 'CE2', ('TRP', 21, 'CA'): 'CE3', ('TRP', 22, 'HA'): 'HE3', ('TRP', 23, 'CB'): 'CD2', ('TRP', 24, 'C'): 'C', ('TRP', 25, 'O'): 'O'} + + atom_index2name_dict {1: 'H', 5: 'B', 6: 'C', 7: 'N', 8: 'O', 9: 'F', 11: 'Na', 12: 'Mg', 13: 'Al', 14: 'Si', 15: 'P', 16: 'S', 17: 'Cl', 19: 'K', 20: 'Ca', 34: 'Se', 35: 'Br', 53: 'I'} + """ + # get standard atom name for proteins + # CA, C, N, H, H2, H3, HA, CB, O ... + protein_atom_index, sequences = get_atom_and_residue_type(protein_atom_index, residue_index, atom_index, protein_atom_index2standard_name_dict, residue_index2name_dict, atom_reisdue2standard_atom_name_dict, atom_index2name_dict, molecules_begin_atom_index) + mask_backbone = (protein_atom_index == "CA") | (protein_atom_index == "C") | (protein_atom_index == "N") + + protein_backbone_atom_type = protein_atom_index[mask_backbone] + protein_mask_ca = protein_backbone_atom_type == "CA" + protein_mask_c = protein_backbone_atom_type == "C" + protein_mask_n = protein_backbone_atom_type == "N" + assert np.sum(protein_mask_ca) == np.sum(protein_mask_c) == np.sum(protein_mask_n) + return mask_backbone, protein_mask_ca, protein_mask_c, protein_mask_n, sequences + + +def parse_MISATO_data(misato_data, atom_index2name_dict, atom_num2atom_mass, residue_index2name_dict, protein_atom_index2standard_name_dict, atom_reisdue2standard_atom_name_dict): + ligand_begin_index = misato_data["molecules_begin_atom_index"][:][-1] + + atom_index = misato_data["atoms_number"][:] + protein_atom_index = misato_data["atoms_type"][:] + residue_number = misato_data["atoms_residue"][:] + + frames_interaction_energy = np.expand_dims(misato_data["frames_interaction_energy"][0], 0) # 1 + + # for protein + protein_coordinates = misato_data["trajectory_coordinates"][0][:][:ligand_begin_index] + protein_mask_backbone, protein_mask_ca, protein_mask_c, protein_mask_n, protein_sequence = extract_sequence_and_structure(protein_atom_index[:ligand_begin_index], residue_number[:ligand_begin_index], atom_index[:ligand_begin_index], protein_atom_index2standard_name_dict, residue_index2name_dict, atom_reisdue2standard_atom_name_dict, atom_index2name_dict, misato_data["molecules_begin_atom_index"][:][:-1]) + protein_coordinates = protein_coordinates[protein_mask_backbone, :] + protein_coordinates = torch.tensor(protein_coordinates, dtype=torch.float32) + protein_residue = residue_number[:ligand_begin_index][protein_mask_backbone][protein_mask_ca] + protein_residue = torch.tensor(protein_residue, dtype=torch.int64) + assert protein_residue.min() >= 1 + protein_residue -= 1 + protein_mask_ca = torch.tensor(protein_mask_ca, dtype=torch.bool) + protein_mask_c = torch.tensor(protein_mask_c, dtype=torch.bool) + protein_mask_n = torch.tensor(protein_mask_n, dtype=torch.bool) + + # for peptide + peptide_coordinates = misato_data["trajectory_coordinates"][0][:][ligand_begin_index:] + peptide_mask_backbone, peptide_mask_ca, peptide_mask_c, peptide_mask_n, peptide_sequence = extract_sequence_and_structure(protein_atom_index[ligand_begin_index:], residue_number[ligand_begin_index:], atom_index[ligand_begin_index:], protein_atom_index2standard_name_dict, residue_index2name_dict, atom_reisdue2standard_atom_name_dict, atom_index2name_dict, [misato_data["molecules_begin_atom_index"][:][-1]]) + peptide_coordinates = peptide_coordinates[peptide_mask_backbone, :] + peptide_coordinates = torch.tensor(peptide_coordinates, dtype=torch.float32) + peptide_residue = residue_number[ligand_begin_index:][peptide_mask_backbone][peptide_mask_ca] + peptide_residue = torch.tensor(peptide_residue, dtype=torch.int64) + assert peptide_residue.min() >= 1 + peptide_residue -= 1 + peptide_mask_ca = torch.tensor(peptide_mask_ca, dtype=torch.bool) + peptide_mask_c = torch.tensor(peptide_mask_c, dtype=torch.bool) + peptide_mask_n = torch.tensor(peptide_mask_n, dtype=torch.bool) + + # 1 + frames_interaction_energy = torch.tensor(frames_interaction_energy, dtype=torch.float32) + + data = Data( + protein_pos=protein_coordinates, + protein_residue=protein_residue, + protein_mask_ca=protein_mask_ca, + protein_mask_c=protein_mask_c, + protein_mask_n=protein_mask_n, + # + peptide_pos=peptide_coordinates, + peptide_residue=peptide_residue, + peptide_mask_ca=peptide_mask_ca, + peptide_mask_c=peptide_mask_c, + peptide_mask_n=peptide_mask_n, + # + energy=frames_interaction_energy, + ) + return data, protein_sequence, peptide_sequence + + +class MISATODataset(InMemoryDataset): + def __init__(self, root): + self.root = root + self.c_alpha_atom_type = 6 + self.c_atom_type = 3 + self.n_atom_type = 24 + super(MISATODataset, self).__init__(root, None, None, None) + + self.data, self.slices = torch.load(self.processed_paths[0]) + + f_ = open(self.processed_paths[1], "r") + PDB_idx_list, peptide_sequence_list, protein_sequence_list = [], [], [] + for line in f_.readlines(): + line = line.strip() + line = line.split(",") + peptide_idx = line[0] + peptide_sequence = line[1] + protein_sequence = line[2] + PDB_idx_list.append(peptide_idx) + peptide_sequence_list.append(peptide_sequence) + protein_sequence_list.append(protein_sequence) + self.PDB_idx_list = PDB_idx_list + self.peptide_sequence_list = peptide_sequence_list + self.protein_sequence_list = protein_sequence_list + return + + @property + def raw_file_names(self): + file_name = "MD.hdf5" + return [file_name] + + @property + def raw_dir(self): + return os.path.join(self.root, "raw") + + @property + def processed_file_names(self): + return ["geometric_data_processed.pt", "PDB_id_and_sequence.txt"] + + @property + def processed_dir(self): + return os.path.join(self.root, "processed") + + def process(self): + MD_file_path = self.raw_paths[0] + MD_data = h5py.File(MD_file_path, "r") + + residue_index2name_dict = pickle.load(open(os.path.join(utils_dir, 'atoms_residue_map.pickle'),'rb')) + protein_atom_index2standard_name_dict = pickle.load(open(os.path.join(utils_dir, 'atoms_type_map.pickle'),'rb')) + atom_reisdue2standard_atom_name_dict = pickle.load(open(os.path.join(utils_dir, 'atoms_name_map_for_pdb.pickle'),'rb')) + + peptides_file = os.path.join(utils_dir, "peptides.txt") + peptides_idx_list = [] + with open(peptides_file) as f: + for line in f.readlines(): + peptides_idx_list.append(line.strip().upper()) + + atom_index2name_dict = {1:'H', 5:'B', 6:'C', 7:'N', 8:'O', 9:'F', 11:'Na', 12:'Mg', 13:'Al', 14:'Si', 15:'P', 16:'S', 17:'Cl', 19:'K', 20:'Ca', 34:'Se', 35:'Br', 53:'I'} + + import importlib.resources + import ProteinDT.datasets + import pandas as pd + with importlib.resources.path(ProteinDT.datasets, 'periodic_table.csv') as file_name: + periodic_table_file = file_name + periodic_table_data = pd.read_csv(periodic_table_file) + atom_num2atom_mass = {} + for i in range(1, 119): + atom_mass = periodic_table_data.loc[i-1]['AtomicMass'] + atom_num2atom_mass[i] = atom_mass + + data_list, PDB_idx_list, protein_sequence_list, peptide_sequence_list = [], [], [], [] + for idx in tqdm(peptides_idx_list): + try: + misato_data = MD_data[idx] + print(idx) + except: + continue + + if misato_data is None: + print("misato_data", misato_data, idx) + continue + data, protein_sequence, peptide_sequence = parse_MISATO_data( + misato_data, atom_index2name_dict=atom_index2name_dict, atom_num2atom_mass=atom_num2atom_mass, + residue_index2name_dict=residue_index2name_dict, protein_atom_index2standard_name_dict=protein_atom_index2standard_name_dict, atom_reisdue2standard_atom_name_dict=atom_reisdue2standard_atom_name_dict) + protein_sequence = ''.join(protein_sequence) + peptide_sequence = ''.join(peptide_sequence) + if not (5 <= len(peptide_sequence) <= 20): + continue + data_list.append(data) + PDB_idx_list.append(idx) + protein_sequence_list.append(protein_sequence) + peptide_sequence_list.append(peptide_sequence) + + data, slices = self.collate(data_list) + torch.save((data, slices), self.processed_paths[0]) + + f_ = open(self.processed_paths[1], "w") + for PDB_idx, peptide_sequence, protein_sequence in zip(PDB_idx_list, peptide_sequence_list, protein_sequence_list): + print("{},{},{}".format(PDB_idx, peptide_sequence, protein_sequence), file=f_) + f_.flush() + f_.close() + + return + + def get_peptide_idx2data(self): + record = {} + for i in range(len(self.PDB_idx_list)): + PDB_idx = self.PDB_idx_list[i] + data = self.get(i) + record[PDB_idx] = data + return record + + +if __name__ == "__main__": + data_root_list = ["../../../data/MISATO"] + for data_root in data_root_list: + dataset = MISATODataset(data_root) diff --git a/ProteinDT/datasets/dataset_Pin1.py b/ProteinDT/datasets/dataset_Pin1.py new file mode 100644 index 0000000..ada4c0d --- /dev/null +++ b/ProteinDT/datasets/dataset_Pin1.py @@ -0,0 +1,46 @@ +import os +import re +from torch.utils.data import Dataset +from sklearn.utils import shuffle + + +class Pin1Dataset(Dataset): + def __init__(self, data_file_path, protein_tokenizer, protein_max_sequence_len): + self.labels, self.seqs = [], [] + + self.protein_sequnece_list, self.label_list = [], [] + f = open(data_file_path, 'r') + for line in f.readlines(): + line = line.strip() + line = line.split(",") + + protein_sequence = line[0] + assert len(protein_sequence) == 39 + protein_sequence = re.sub(r"[UZOB]", "X", protein_sequence) + protein_sequence = " ".join(protein_sequence) + + label = float(line[1]) + self.protein_sequnece_list.append(protein_sequence) + self.label_list.append(label) + + self.protein_tokenizer = protein_tokenizer + self.protein_max_sequence_len = protein_max_sequence_len + return + + def __getitem__(self, index): + protein_sequence = self.protein_sequnece_list[index] + label = self.label_list[index] + protein_sequence_encode = self.protein_tokenizer(protein_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze() + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze() + + output = { + "protein_sequence": protein_sequence, + "protein_sequence_input_ids": protein_sequence_input_ids, + "protein_sequence_attention_mask": protein_sequence_attention_mask, + "label": label, + } + return output + + def __len__(self): + return len(self.label_list) diff --git a/ProteinDT/datasets/dataset_Protein.py b/ProteinDT/datasets/dataset_Protein.py new file mode 100644 index 0000000..c6d26eb --- /dev/null +++ b/ProteinDT/datasets/dataset_Protein.py @@ -0,0 +1,45 @@ +import os +import torch +from torch.utils.data import Dataset +import numpy as np + + +def load_file(file_path): + f = open(file_path, 'r') + seq_list = [] + for line_idx, line in enumerate(f.readlines()): + seq = line.strip() + seq_list.append(seq) + return seq_list + + +class ProteinSequenceDataset(Dataset): + def __init__(self, root, protein_tokenizer, protein_max_sequence_len): + self.root = root + + protein_sequence_file = os.path.join(self.root, "protein_sequence.txt") + self.protein_sequence_list = load_file(protein_sequence_file) + print("len of protein_sequence {}".format(len(self.protein_sequence_list))) + + self.protein_tokenizer = protein_tokenizer + self.protein_max_sequence_len = protein_max_sequence_len + + return + + def __getitem__(self, index): + protein_sequence = self.protein_sequence_list[index] + + protein_sequence_encode = self.protein_tokenizer(protein_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze() + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze() + + batch = { + "protein_sequence": protein_sequence, + "protein_sequence_input_ids": protein_sequence_input_ids, + "protein_sequence_attention_mask": protein_sequence_attention_mask, + } + + return batch + + def __len__(self): + return len(self.protein_sequence_list) diff --git a/ProteinDT/datasets/dataset_RepresentationPair.py b/ProteinDT/datasets/dataset_RepresentationPair.py new file mode 100644 index 0000000..d03edb8 --- /dev/null +++ b/ProteinDT/datasets/dataset_RepresentationPair.py @@ -0,0 +1,103 @@ +import os +import torch +from torch.utils.data import Dataset +import numpy as np + + +def load_file(file_path): + uniprot_id2record_dict = {} + f = open(file_path, 'r') + seq_list = [] + for line_idx, line in enumerate(f.readlines()): + seq = line.strip() + seq_list.append(seq) + return seq_list + + +class RepresentationPairDataset(Dataset): + def __init__(self, root): + self.root = root + + representation_file = os.path.join(self.root, "pairwise_representation.npz") + representation_data = np.load(representation_file) + print("representation_data", representation_data.keys) + + self.protein_repr_array = representation_data["protein_repr_array"] + self.description_repr_array = representation_data["description_repr_array"] + + print("shape of protein_repr_array: {}".format(self.protein_repr_array.shape)) + print("shape of description_repr_array: {}".format(self.description_repr_array.shape)) + + return + + def __getitem__(self, index): + protein_repr = self.protein_repr_array[index] + text_repr = self.description_repr_array[index] + + batch = { + "protein_repr": protein_repr, + "text_repr": text_repr, + } + + return batch + + def __len__(self): + return len(self.protein_repr_array) + + +class RepresentationPairWithRawDataDataset(Dataset): + def __init__(self, root, prob_unconditional): + self.root = root + self.prob_unconditional = prob_unconditional + + representation_file = os.path.join(self.root, "empty_sequence.npz") + representation_data = np.load(representation_file) + self.empty_description = representation_data["protein_repr"][0] + print("empty_description", self.empty_description.shape) + + representation_file = os.path.join(self.root, "pairwise_representation.npz") + representation_data = np.load(representation_file) + print("representation_data", representation_data.keys) + + self.protein_repr_array = representation_data["protein_repr_array"] + self.description_repr_array = representation_data["description_repr_array"] + + print("shape of protein_repr_array: {}".format(self.protein_repr_array.shape)) + print("shape of description_repr_array: {}".format(self.description_repr_array.shape)) + + protein_sequence_file = os.path.join(self.root, "protein_sequence.txt") + text_sequence_file = os.path.join(self.root, "text_sequence.txt") + + self.protein_sequence_list = load_file(protein_sequence_file) + print("len of protein_sequence {}".format(len(self.protein_sequence_list))) + + self.text_sequence_list = load_file(text_sequence_file) + print("len of text_sequence {}".format(len(self.text_sequence_list))) + + return + + def __getitem__(self, index): + protein_sequence = self.protein_sequence_list[index] + text_sequence = self.text_sequence_list[index] + protein_repr = self.protein_repr_array[index] + text_repr = self.description_repr_array[index] + + if self.prob_unconditional > 0: + roll_dice = np.random.uniform(0, 1) + if roll_dice <= self.prob_unconditional: + text_repr = self.empty_description + protein_repr = self.empty_description + text_sequence = '' + protein_sequence = '' + + batch = { + "protein_sequence": protein_sequence, + "text_sequence": text_sequence, + "protein_repr": protein_repr, + "text_repr": text_repr, + } + + return batch + + def __len__(self): + return len(self.protein_repr_array) diff --git a/ProteinDT/datasets/dataset_SecondaryStructure.py b/ProteinDT/datasets/dataset_SecondaryStructure.py new file mode 100644 index 0000000..15c662d --- /dev/null +++ b/ProteinDT/datasets/dataset_SecondaryStructure.py @@ -0,0 +1,110 @@ +import os +import re +import lmdb +import pickle as pkl +import numpy as np +import torch +from torch.utils.data import Dataset + + +def pad_sequences(sequences, constant_value=0, dtype=None) -> np.ndarray: + batch_size = len(sequences) + shape = [batch_size] + np.max([seq.shape for seq in sequences], 0).tolist() + + if dtype is None: + dtype = sequences[0].dtype + + if isinstance(sequences[0], np.ndarray): + array = np.full(shape, constant_value, dtype=dtype) + elif isinstance(sequences[0], torch.Tensor): + array = torch.full(shape, constant_value, dtype=dtype) + array = array.numpy() + + for arr, seq in zip(array, sequences): + arrslice = tuple(slice(dim) for dim in seq.shape) + arr[arrslice] = seq + return array + + +class SecondaryStructureDataset(Dataset): + def __init__(self, data_file_path, protein_tokenizer, target='ss3'): + self.protein_tokenizer = protein_tokenizer + self.target = target + self.ignore_index = -100 + + env = lmdb.open(data_file_path, max_readers=1, readonly=True, lock=False, readahead=False, meminit=False) + + with env.begin(write=False) as txn: + num_examples = pkl.loads(txn.get(b'num_examples')) + + self.protein_sequence_list = [] + self.ss3_label_list = [] + self.ss8_label_list = [] + + for index in range(num_examples): + with env.begin(write=False) as txn: + item = pkl.loads(txn.get(str(index).encode())) + # print(item.keys()) + protein_sequence = item["primary"] + ss3_labels = item["ss3"] + ss8_labels = item["ss8"] + protein_length = item["protein_length"] + + if len(protein_sequence) > 1024: + protein_sequence = protein_sequence[:1024] + ss3_labels = ss3_labels[:1024] + ss8_labels = ss8_labels[:1024] + + protein_sequence = re.sub(r"[UZOB]", "X", protein_sequence) + protein_sequence = " ".join(protein_sequence) + + self.protein_sequence_list.append(protein_sequence) + self.ss3_label_list.append(ss3_labels) + self.ss8_label_list.append(ss8_labels) + + if self.target == "ss3": + self.label_list = self.ss3_label_list + self.num_labels = 3 + else: + self.label_list = self.ss8_label_list + self.num_labels = 8 + return + + def __len__(self): + return len(self.label_list) + + def __getitem__(self, index): + protein_sequence = self.protein_sequence_list[index] + label = self.label_list[index] + # protein_sequence_encode = self.protein_tokenizer(protein_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + # protein_sequence_input_ids = protein_sequence_encode.input_ids#.squeeze() + # protein_sequence_attention_mask = protein_sequence_encode.attention_mask#.squeeze() + + protein_sequence_encode = self.protein_tokenizer(list(protein_sequence), is_split_into_words=True, truncation=False, padding=True) + protein_sequence_input_ids = np.array(protein_sequence_encode['input_ids']) + protein_sequence_attention_mask = np.ones_like(protein_sequence_input_ids) + + label = np.asarray(label, np.int64) + label = np.pad(label, (1, 1), 'constant', constant_values=self.ignore_index) + + # print("protein_sequence", len(protein_sequence)) + # print("protein_sequence_input_ids", len(protein_sequence_input_ids)) + # print("protein_sequence_attention_mask", len(protein_sequence_attention_mask)) + # print("label", len(label)) + + return protein_sequence, protein_sequence_input_ids, protein_sequence_attention_mask, label + + def collate_fn(self, batch): + protein_sequence, protein_sequence_input_ids, protein_sequence_attention_mask, label = tuple(zip(*batch)) + + protein_sequence_input_ids = torch.from_numpy(pad_sequences(protein_sequence_input_ids, constant_value=self.protein_tokenizer.pad_token_id)) + protein_sequence_attention_mask = torch.from_numpy(pad_sequences(protein_sequence_attention_mask, constant_value=0)) + label = torch.from_numpy(pad_sequences(label, constant_value=self.ignore_index)) + + output = { + "protein_sequence": protein_sequence, + "protein_sequence_input_ids": protein_sequence_input_ids, + "protein_sequence_attention_mask": protein_sequence_attention_mask, + "label": label, + } + return output diff --git a/ProteinDT/datasets/dataset_Stability.py b/ProteinDT/datasets/dataset_Stability.py new file mode 100644 index 0000000..1ce7a65 --- /dev/null +++ b/ProteinDT/datasets/dataset_Stability.py @@ -0,0 +1,71 @@ +import os +import re +from torch.utils.data import Dataset +from sklearn.utils import shuffle + + +class StabilityDataset(Dataset): + def __init__(self, root, seed, mode, split_size, protein_tokenizer, protein_max_sequence_len): + self.labels, self.seqs = [], [] + + for p in ['1', '2', '3', '4']: + file_path = os.path.join(root, 'rd{}_stability_scores'.format(p)) + + with open(file_path) as f: + lines = f.readlines()[1:] + for line in lines: + items = line.split("\t") + seq, score = items[1], items[-1][:-2] + if '_' not in seq and score != '': + seq = re.sub(r"[UZOB]", "X", seq) + seq = " ".join(seq) + score = float(score) + self.seqs.append(seq) + self.labels.append(score) + + self.seqs, self.labels = shuffle(self.seqs, self.labels, random_state=seed) + + train_size = int(split_size[0] * len(self.labels)) + train_val_size = int((split_size[0] + split_size[1]) * len(self.labels)) + if mode == "train": + self.seqs = self.seqs[:train_size] + self.labels = self.labels[:train_size] + elif mode == "val": + self.seqs = self.seqs[train_size:train_val_size] + self.labels = self.labels[train_size:train_val_size] + elif mode == "test": + self.seqs = self.seqs[train_val_size:] + self.labels = self.labels[train_val_size:] + else: + raise ValueError('Invalid split mode') + + self.protein_tokenizer = protein_tokenizer + self.protein_max_sequence_len = protein_max_sequence_len + return + + def __getitem__(self, index): + protein_sequence = self.seqs[index] + label = self.labels[index] + protein_sequence_encode = self.protein_tokenizer(protein_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze() + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze() + + output = { + "protein_sequence": protein_sequence, + "protein_sequence_input_ids": protein_sequence_input_ids, + "protein_sequence_attention_mask": protein_sequence_attention_mask, + "label": label, + } + return output + + def __len__(self): + return len(self.labels) + + +if __name__ == "__main__": + protein_dataset = StabilityDataset(root="../../data/stability/", seed=100, subset=False, mode="train", split_size=[0.8, 0.1, 0.1]) + print("Total number of seq: ", len(protein_dataset.labels)) + protein_dataset = StabilityDataset(root="../../data/stability/", seed=100, subset=False, mode="val", split_size=[0.8, 0.1, 0.1]) + print("Total number of seq: ", len(protein_dataset.labels)) + protein_dataset = StabilityDataset(root="../../data/stability/", seed=100, subset=False, mode="test", split_size=[0.8, 0.1, 0.1]) + print("Total number of seq: ", len(protein_dataset.labels)) diff --git a/ProteinDT/datasets/dataset_SwissProtCLAP.py b/ProteinDT/datasets/dataset_SwissProtCLAP.py new file mode 100644 index 0000000..8ebbfdf --- /dev/null +++ b/ProteinDT/datasets/dataset_SwissProtCLAP.py @@ -0,0 +1,105 @@ +import os +import torch +from torch.utils.data import Dataset + + +def load_protein_sequence_or_text_sequence_file(file_path): + uniprot_id2record_dict = {} + f = open(file_path, 'r') + for line_idx, line in enumerate(f.readlines()): + line = line.strip() + if line_idx % 2 == 0: + uniprot = line + else: + protein_sequence = line + uniprot_id2record_dict[uniprot] = protein_sequence + return uniprot_id2record_dict + + +class SwissProtCLAPDataset(Dataset): + def __init__(self, root, protein_tokenizer, text_tokenizer, protein_max_sequence_len, text_max_sequence_len): + self.root = root + self.protein_tokenizer = protein_tokenizer + self.text_tokenizer = text_tokenizer + self.protein_max_sequence_len = protein_max_sequence_len + self.text_max_sequence_len = text_max_sequence_len + + protein_sequence_file = os.path.join(root, "protein_sequence.txt") + text_sequence_file = os.path.join(root, "text_sequence.txt") + + uniprot_id2protein_sequence = load_protein_sequence_or_text_sequence_file(protein_sequence_file) + # print("len of protein_sequence {}".format(len(uniprot_id2protein_sequence))) + + uniprot_id2text_sequence = load_protein_sequence_or_text_sequence_file(text_sequence_file) + # print("len of protein_sequence {}".format(len(uniprot_id2text_sequence))) + + protein_sequence_list, text_sequence_list = [], [] + for uniprot_id, protein_sequence in uniprot_id2protein_sequence.items(): + if len(protein_sequence) > self.protein_max_sequence_len: + continue + text_sequence = uniprot_id2text_sequence[uniprot_id] + + # already done in preprocessing + # protein_sequence = re.sub(r"[UZOB]", "X", protein_sequence) + protein_sequence = " ".join(protein_sequence) + protein_sequence_list.append(protein_sequence) + text_sequence_list.append(text_sequence) + + self.protein_sequence_list = protein_sequence_list + self.text_sequence_list = text_sequence_list + print("num of (protein-sequence, text) pair: {}".format(len(self.protein_sequence_list))) + + return + + def __getitem__(self, index): + protein_sequence = self.protein_sequence_list[index] + text_sequence = self.text_sequence_list[index] + + protein_sequence_encode = self.protein_tokenizer(protein_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze() + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze() + + text_sequence_encode = self.text_tokenizer(text_sequence, truncation=True, max_length=self.text_max_sequence_len, padding='max_length', return_tensors='pt') + text_sequence_input_ids = text_sequence_encode.input_ids.squeeze() + text_sequence_attention_mask = text_sequence_encode.attention_mask.squeeze() + + batch = { + "protein_sequence": protein_sequence, + "protein_sequence_input_ids": protein_sequence_input_ids, + "protein_sequence_attention_mask": protein_sequence_attention_mask, + "text_sequence": text_sequence, + "text_sequence_input_ids": text_sequence_input_ids, + "text_sequence_attention_mask": text_sequence_attention_mask, + } + + return batch + + def __len__(self): + return len(self.protein_sequence_list) + + +if __name__ == "__main__": + from transformers import AutoModel, AutoTokenizer, BertModel, BertTokenizer + from torch.utils.data import DataLoader + + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../../data/temp_pretrained_ProtBert") + + text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + + dataset = SwissProtCLAPDataset( + root="../../data/SwissProtCLAP", + protein_tokenizer=protein_tokenizer, + text_tokenizer=text_tokenizer, + protein_max_sequence_len=512, + text_max_sequence_len=512 + ) + print("len of dataset", len(dataset)) + dataloader = DataLoader(dataset, batch_size=16, shuffle=True, num_workers=0) + for batch in dataloader: + protein_sequence_list = batch["protein_sequence"] + text_sequence_list = batch["text_sequence"] + for protein_sequence, text_sequence in zip(protein_sequence_list, text_sequence_list): + print(protein_sequence.replace(" ", "")) + print(text_sequence) + print() + break diff --git a/ProteinDT/datasets/dataset_Villin.py b/ProteinDT/datasets/dataset_Villin.py new file mode 100644 index 0000000..abea9c5 --- /dev/null +++ b/ProteinDT/datasets/dataset_Villin.py @@ -0,0 +1,46 @@ +import os +import re +from torch.utils.data import Dataset +from sklearn.utils import shuffle + + +class VillinDataset(Dataset): + def __init__(self, data_file_path, protein_tokenizer, protein_max_sequence_len): + self.labels, self.seqs = [], [] + + self.protein_sequnece_list, self.label_list = [], [] + f = open(data_file_path, 'r') + for line in f.readlines(): + line = line.strip() + line = line.split(",") + + protein_sequence = line[0] + assert len(protein_sequence) == 35 + protein_sequence = re.sub(r"[UZOB]", "X", protein_sequence) + protein_sequence = " ".join(protein_sequence) + + label = float(line[1]) + self.protein_sequnece_list.append(protein_sequence) + self.label_list.append(label) + + self.protein_tokenizer = protein_tokenizer + self.protein_max_sequence_len = protein_max_sequence_len + return + + def __getitem__(self, index): + protein_sequence = self.protein_sequnece_list[index] + label = self.label_list[index] + protein_sequence_encode = self.protein_tokenizer(protein_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze() + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze() + + output = { + "protein_sequence": protein_sequence, + "protein_sequence_input_ids": protein_sequence_input_ids, + "protein_sequence_attention_mask": protein_sequence_attention_mask, + "label": label, + } + return output + + def __len__(self): + return len(self.label_list) diff --git a/ProteinDT/model_ColdDiffusionDecoder.py b/ProteinDT/model_ColdDiffusionDecoder.py new file mode 100644 index 0000000..7b0a42c --- /dev/null +++ b/ProteinDT/model_ColdDiffusionDecoder.py @@ -0,0 +1,131 @@ +import torch +import torch.nn as nn +import torch.nn.functional as F +from transformers import BertConfig +from ProteinDT.models.model_SDE import VESDE, VPSDE +from ProteinDT.models.model_Sampler import ReverseDiffusionPredictor, LangevinCorrector +from ProteinDT.models.score_networks import ToyScoreNetwork, RNNScoreNetwork, BertScoreNetwork + +EPS = 1e-6 + + +class ColdDiffusionDecoder(nn.Module): + def __init__( + self, hidden_dim, condition_dim, beta_min, beta_max, num_diffusion_timesteps, num_classes, score_network_type + ): + super().__init__() + self.hidden_dim = hidden_dim + self.condition_dim = condition_dim + self.beta_min = beta_min + self.beta_max = beta_max + self.num_diffusion_timesteps = num_diffusion_timesteps + self.num_classes = num_classes + + self.SDE_func = VPSDE(beta_min=self.beta_min, beta_max=self.beta_max, N=self.num_diffusion_timesteps) + + output_dim = hidden_dim + if score_network_type == "Toy": + word_embedding_dim = self.hidden_dim + self.score_network = ToyScoreNetwork(hidden_dim=hidden_dim, output_dim=output_dim) + + elif score_network_type == "RNN": + word_embedding_dim = self.hidden_dim + self.score_network = RNNScoreNetwork(hidden_dim=hidden_dim, output_dim=output_dim) + + elif score_network_type == "BertBase": + config = BertConfig.from_pretrained( + "bert-base-uncased", + cache_dir="../data/temp_Bert_base", + vocab_size=self.num_classes, + hidden_size=hidden_dim, + num_attention_heads=8 + ) + word_embedding_dim = self.hidden_dim + self.score_network = BertScoreNetwork(config=config, output_dim=output_dim) + + self.word_embedding_dim = word_embedding_dim + self.embedding_layer = nn.Linear(self.num_classes, self.word_embedding_dim, bias=False) + self.decoder_layer = nn.Linear(word_embedding_dim, self.num_classes) + self.condition_proj_layer = nn.Linear(self.condition_dim, self.word_embedding_dim) + + self.CE_criterion = nn.CrossEntropyLoss(reduction='none') + return + + def forward(self, protein_seq_input_ids, protein_seq_attention_mask, condition): + B = protein_seq_input_ids.size()[0] + device = protein_seq_input_ids.device + + # TODO: need double-check range of timesteps + timesteps = torch.rand(B, device=device) * (1 - EPS) + EPS # (B) + + condition = self.condition_proj_layer(condition) # (B, max_seq_len, condition_dim) ---> (B, max_seq_len, hidden_dim) + + protein_seq_onehot = F.one_hot(protein_seq_input_ids, num_classes=self.num_classes) # (B, max_seq_len, num_class) + protein_seq_onehot = protein_seq_onehot.float() + + #### cold diffusion can add noise either in the one-hot level + epsilon = torch.randn_like(protein_seq_onehot.float()) # (B, max_seq_len, num_class) + mean_noise, std_noise = self.SDE_func.marginal_prob(protein_seq_onehot, timesteps) # (B, max_seq_len, num_classes), (B) + protein_seq_onehot_noise = mean_noise + std_noise[:, None, None] * epsilon # (B, max_seq_len, num_classes) + protein_seq_repr_noise = self.embedding_layer(protein_seq_onehot_noise) # (B, max_seq_len, hidden_dim) + + # ##### TODO: or in the embedding level??? + # protein_seq_repr = self.embedding_layer(protein_seq_onehot) # (B, max_seq_len, hidden_dim) + # epsilon = torch.randn_like(protein_seq_repr.float()) # (B, max_seq_len, hidden_dim) + # protein_seq_repr = self.embedding_layer(protein_seq_onehot) # (B, max_seq_len, hidden_dim) + # mean_noise, std_noise = self.SDE_func.marginal_prob(protein_seq_repr, timesteps) # (B, max_seq_len, hidden_dim), (B) + # protein_seq_repr_noise = mean_noise + std_noise[:, None, None] * epsilon # (B, max_seq_len, hidden_dim) + + score = self.score_network(protein_seq_repr=protein_seq_repr_noise, protein_seq_attention_mask=protein_seq_attention_mask, condition=condition) # (B, max_seq_len, hidden_dim) or (B, max_seq_len, num_class) + score = self.decoder_layer(score) # (B*max_sequence_len, num_class) + + flattened_logits = score.view(-1, score.size(-1)) # (B*max_sequence_len, num_class) + flattened_ids = protein_seq_input_ids.view(-1) # (B*max_sequence_len) + flattened_mask = protein_seq_attention_mask.view(-1) # (B*max_sequence_len) + total_SDE_loss = self.CE_criterion(flattened_logits, flattened_ids) # (B*max_sequence_len) + masked_SDE_loss = total_SDE_loss * flattened_mask # (B*max_sequence_len) + total_SDE_loss = torch.mean(total_SDE_loss) + masked_SDE_loss = total_SDE_loss.sum() / flattened_mask.sum() + + SDE_loss = total_SDE_loss + masked_SDE_loss + decoding_loss = 0 + + return SDE_loss, decoding_loss + + @torch.no_grad() + def inference(self, condition, max_seq_len, protein_seq_attention_mask): + B = condition.size()[0] + device = condition.device + + shape = (B, max_seq_len, self.num_classes) + + X_one_hot = self.SDE_func.prior_sampling(shape).to(device) # (B, max_seq_len, word_embedding_dim) + + EPSILON = 1e-5 + + timesteps = torch.linspace(self.SDE_func.T, EPSILON, self.num_diffusion_timesteps, device=device) # (num_diffusion_timesteps) + + condition = condition.float() + condition = self.condition_proj_layer(condition) # (B, max_seq_len, condition_dim) ---> (B, max_seq_len, hidden_dim) + + x_one_hot_t = X_one_hot + for i in range(0, self.num_diffusion_timesteps-1): + x_repr_t = self.embedding_layer(x_one_hot_t) # (B, max_seq_len, hidden_dim) + score = self.score_network(protein_seq_repr=x_repr_t, protein_seq_attention_mask=protein_seq_attention_mask, condition=condition) # (B, max_seq_len, hidden_dim) + hat_x_one_hot_0 = self.decoder_layer(score) # (B, max_sequence_len, num_class) + + t = timesteps[i] + vec_t = torch.ones(shape[0], device=device) * t # (B) + t_1 = timesteps[i+1] + vec_t_1 = torch.ones(shape[0], device=device) * t_1 # (B) + epsilon = torch.randn_like(hat_x_one_hot_0) # (B, max_seq_len, num_class) + + mean_noise, std_noise = self.SDE_func.marginal_prob(hat_x_one_hot_0, vec_t) # (B, max_seq_len, num_classes), (B) + x_one_hot_t = mean_noise + std_noise[:, None, None] * epsilon # (B, max_seq_len, num_classes) + mean_noise, std_noise = self.SDE_func.marginal_prob(hat_x_one_hot_0, vec_t_1) # (B, max_seq_len, num_classes), (B) + x_one_hot_t_1 = mean_noise + std_noise[:, None, None] * epsilon # (B, max_seq_len, num_classes) + + x_one_hot_t = x_one_hot_t - x_one_hot_t - x_one_hot_t_1 # (B, max_sequence_len, num_class) + x = x_one_hot_t + + return x diff --git a/ProteinDT/model_GaussianSDEDecoder.py b/ProteinDT/model_GaussianSDEDecoder.py new file mode 100644 index 0000000..83ed0dc --- /dev/null +++ b/ProteinDT/model_GaussianSDEDecoder.py @@ -0,0 +1,238 @@ +import torch +import torch.nn as nn +import torch.nn.functional as F +from transformers import BertConfig +from ProteinDT.models.model_SDE import VESDE, VPSDE +from ProteinDT.models.model_Sampler import ReverseDiffusionPredictor, LangevinCorrector +from ProteinDT.models.score_networks import ToyScoreNetwork, RNNScoreNetwork, BertScoreNetwork + +EPS = 1e-6 + + +def get_score_fn(SDE_func, score_network, train=True, continuous=True): + if not train: + score_network.eval() + + if isinstance(SDE_func, VPSDE): + def score_fn(x, x_mask, condition, t): + if continuous: + score = score_network(protein_seq_repr=x, protein_seq_attention_mask=x_mask, condition=condition) + std = SDE_func.marginal_prob(x, t)[1] + else: + raise NotImplementedError(f"Discrete not supported") + score = -score / std[:, None, None] + return score + + elif isinstance(SDE_func, VESDE): + def score_fn(x, x_mask, condition, t): + if continuous: + score = score_network(protein_seq_repr=x, protein_seq_attention_mask=x_mask, condition=condition) + else: + raise NotImplementedError(f"Discrete not supported") + score = -score + return score + + else: + raise NotImplementedError(f"SDE class {SDE_func.__class__.__name__} not supported.") + + return score_fn + + +class GaussianSDEDecoderModel(nn.Module): + def __init__( + self, hidden_dim, condition_dim, beta_min, beta_max, num_diffusion_timesteps, SDE_mode, num_classes, + score_network_type + ): + super().__init__() + self.hidden_dim = hidden_dim + self.condition_dim = condition_dim + self.beta_min = beta_min + self.beta_max = beta_max + self.num_diffusion_timesteps = num_diffusion_timesteps + self.SDE_mode = SDE_mode + self.num_classes = num_classes + + if self.SDE_mode in ["VE", "ColdVE"]: + self.SDE_func = VESDE(sigma_min=self.beta_min, sigma_max=self.beta_max, N=self.num_diffusion_timesteps) + elif self.SDE_mode in ["VP", "ColdVP"]: + self.SDE_func = VPSDE(beta_min=self.beta_min, beta_max=self.beta_max, N=self.num_diffusion_timesteps) + + if score_network_type == "Toy": + word_embedding_dim = self.hidden_dim + if self.SDE_mode in ["ColdVE", "ColdVP"]: + output_dim = self.num_classes + else: + output_dim = word_embedding_dim + self.score_network = ToyScoreNetwork(hidden_dim=hidden_dim, output_dim=output_dim) + + elif score_network_type == "RNN": + word_embedding_dim = self.hidden_dim + if self.SDE_mode in ["ColdVE", "ColdVP"]: + output_dim = self.num_classes + else: + output_dim = word_embedding_dim + self.score_network = RNNScoreNetwork(hidden_dim=hidden_dim, output_dim=output_dim) + + elif score_network_type == "BertProtBFD": + word_embedding_dim = 1024 + if self.SDE_mode in ["ColdVE", "ColdVP"]: + output_dim = self.num_classes + else: + output_dim = word_embedding_dim + self.score_network = BertScoreNetwork.from_pretrained( + "Rostlab/prot_bert_bfd", + cache_dir="../data/temp_pretrained_ProtBert_BFD", + ignore_mismatched_sizes=True, + ) + + elif score_network_type == "BertBase": + config = BertConfig.from_pretrained( + "bert-base-uncased", + cache_dir="../data/temp_Bert_base", + vocab_size=self.num_classes, + hidden_size=hidden_dim, + num_attention_heads=8 + ) + word_embedding_dim = self.hidden_dim + if self.SDE_mode in ["ColdVE", "ColdVP"]: + output_dim = self.num_classes + else: + output_dim = word_embedding_dim + self.score_network = BertScoreNetwork(config=config, output_dim=output_dim) + + self.word_embedding_dim = word_embedding_dim + self.embedding_layer = nn.Linear(self.num_classes, self.word_embedding_dim, bias=False) + self.decoder_layer = nn.Linear(word_embedding_dim, self.num_classes) + self.condition_proj_layer = nn.Linear(self.condition_dim, self.word_embedding_dim) + + self.score_fn = get_score_fn(self.SDE_func, self.score_network, train=True, continuous=True) + self.predictor = ReverseDiffusionPredictor(self.SDE_func, self.score_fn) + self.corrector = LangevinCorrector(self.SDE_func, self.score_fn, snr=0.1, n_steps=100) + self.CE_criterion = nn.CrossEntropyLoss(reduction='none') + return + + def forward(self, protein_seq_input_ids, protein_seq_attention_mask, condition): + B = protein_seq_input_ids.size()[0] + device = protein_seq_input_ids.device + + # TODO: need double-check range of timesteps + timesteps = torch.rand(B, device=device) * (1 - EPS) + EPS # (B) + + condition = self.condition_proj_layer(condition) # (B, max_seq_len, condition_dim) ---> (B, max_seq_len, hidden_dim) + + protein_seq_onehot = F.one_hot(protein_seq_input_ids, num_classes=self.num_classes) # (B, max_seq_len, num_class) + protein_seq_onehot = protein_seq_onehot.float() + + if self.SDE_mode in ["ColdVE", "ColdVP"]: + # epsilon = torch.randn_like(protein_seq_onehot.float()) # (B, max_seq_len, num_class) + # mean_noise, std_noise = self.SDE_func.marginal_prob(protein_seq_onehot, timesteps) # (B, max_seq_len, num_classes), (B) + # protein_seq_onehot_noise = mean_noise + std_noise[:, None, None] * epsilon # (B, max_seq_len, num_classes) + # protein_seq_repr_noise = self.embedding_layer(protein_seq_onehot_noise) # (B, max_seq_len, hidden_dim) + + protein_seq_repr = self.embedding_layer(protein_seq_onehot) # (B, max_seq_len, hidden_dim) + epsilon = torch.randn_like(protein_seq_repr.float()) # (B, max_seq_len, hidden_dim) + protein_seq_repr = self.embedding_layer(protein_seq_onehot) # (B, max_seq_len, hidden_dim) + mean_noise, std_noise = self.SDE_func.marginal_prob(protein_seq_repr, timesteps) # (B, max_seq_len, hidden_dim), (B) + protein_seq_repr_noise = mean_noise + std_noise[:, None, None] * epsilon # (B, max_seq_len, hidden_dim) + else: + protein_seq_repr = self.embedding_layer(protein_seq_onehot) # (B, max_seq_len, hidden_dim) + epsilon = torch.randn_like(protein_seq_repr.float()) # (B, max_seq_len, hidden_dim) + protein_seq_repr = self.embedding_layer(protein_seq_onehot) # (B, max_seq_len, hidden_dim) + mean_noise, std_noise = self.SDE_func.marginal_prob(protein_seq_repr, timesteps) # (B, max_seq_len, hidden_dim), (B) + protein_seq_repr_noise = mean_noise + std_noise[:, None, None] * epsilon # (B, max_seq_len, hidden_dim) + + score = self.score_fn(protein_seq_repr_noise, protein_seq_attention_mask, condition, timesteps) # (B, max_seq_len, hidden_dim) or (B, max_seq_len, num_class) + + if self.SDE_mode in ["ColdVE", "ColdVP"]: + flattened_logits = score.view(-1, score.size(-1)) # (B*max_sequence_len, num_class) + flattened_ids = protein_seq_input_ids.view(-1) # (B*max_sequence_len) + flattened_mask = protein_seq_attention_mask.view(-1) # (B*max_sequence_len) + total_SDE_loss = self.CE_criterion(flattened_logits, flattened_ids) # (B*max_sequence_len) + masked_SDE_loss = total_SDE_loss * flattened_mask # (B*max_sequence_len) + total_SDE_loss = torch.mean(total_SDE_loss) + masked_SDE_loss = total_SDE_loss.sum() / flattened_mask.sum() + + SDE_loss = total_SDE_loss + masked_SDE_loss + decoding_loss = 0 + + else: + total_SDE_loss = torch.square(score * std_noise[:, None, None] + epsilon) # (B, max_seq_len, hidden_dim) + masked_SDE_loss = total_SDE_loss * protein_seq_attention_mask.unsqueeze(2) # (B, max_seq_len, hidden_dim) + total_SDE_loss = torch.mean(total_SDE_loss) + masked_SDE_loss = masked_SDE_loss.sum() / protein_seq_attention_mask.sum() + SDE_loss = total_SDE_loss + masked_SDE_loss + + # regenerate protein_seq_repr + protein_seq_ids_pred_logit = self.decoder_layer(protein_seq_repr) # (B, max_seq_len, num_class) + flattened_logits = protein_seq_ids_pred_logit.view(-1, protein_seq_ids_pred_logit.size(-1)) # (B*max_sequence_len, num_class) + flattened_ids = protein_seq_input_ids.view(-1) # (B*max_sequence_len) + flattened_mask = protein_seq_attention_mask.view(-1) # (B*max_sequence_len) + total_decoding_loss = self.CE_criterion(flattened_logits, flattened_ids) # (B*max_sequence_len) + masked_decoding_loss = total_decoding_loss * flattened_mask # (B*max_sequence_len) + total_decoding_loss = torch.mean(total_decoding_loss) + masked_decoding_loss = masked_decoding_loss.sum() / flattened_mask.sum() + decoding_loss = total_decoding_loss + masked_decoding_loss + return SDE_loss, decoding_loss + + @torch.no_grad() + def inference(self, condition, max_seq_len, protein_seq_attention_mask): + B = condition.size()[0] + device = condition.device + + if self.SDE_mode in ["ColdVE", "ColdVP"]: + shape = (B, max_seq_len, self.num_classes) + else: + shape = (B, max_seq_len, self.word_embedding_dim) + + X_T = self.SDE_func.prior_sampling(shape).to(device) # (B, max_seq_len, word_embedding_dim) + + EPSILON = 1e-5 + + timesteps = torch.linspace(self.SDE_func.T, EPSILON, self.num_diffusion_timesteps, device=device) # (num_diffusion_timesteps) + + condition = condition.float() + condition = self.condition_proj_layer(condition) # (B, max_seq_len, condition_dim) ---> (B, max_seq_len, hidden_dim) + + if self.SDE_mode in ["ColdVE", "ColdVP"]: + # TODO: this is wrong + onehot_x = X_T + for i in range(0, self.num_diffusion_timesteps-1): + repr_x = self.embedding_layer(onehot_x) + + t = timesteps[i] + vec_t = torch.ones(shape[0], device=device) * t + std_t = self.SDE_func.marginal_prob(torch.ones_like(vec_t), vec_t)[1] + score_t = self.score_fn(repr_x, protein_seq_attention_mask, condition, vec_t) + # score_t = -score_t / std_t[:, None, None] + + t_1 = timesteps[i+1] + vec_t_1 = torch.ones(shape[0], device=device) * t_1 + std_t_1 = self.SDE_func.marginal_prob(torch.ones_like(vec_t_1), vec_t_1)[1] + score_t_1 = self.score_fn(repr_x, protein_seq_attention_mask, condition, vec_t_1) + # score_t_1 = -score_t_1 / std_t_1[:, None, None] + + onehot_x = onehot_x + score_t - score_t_1 + x = onehot_x + + else: + x = X_T + for i in range(0, self.num_diffusion_timesteps): + t = timesteps[i] + vec_t = torch.ones(shape[0], device=device) * t + + x, x_mean = self.corrector.update_fn(x, protein_seq_attention_mask, condition, vec_t) + + x, x_mean = self.predictor.update_fn(x, protein_seq_attention_mask, condition, vec_t) # (B, max_seq_len, num_class), (B, max_seq_len, num_class) + + x = self.decoder_layer(x) + return x + + +if __name__ == "__main__": + B = 10 + timesteps = torch.rand(B) * (1 - EPS) + EPS + print(timesteps) + + EPS = 1e-3 + timesteps = torch.linspace(1, EPS, 1000) + print(timesteps) diff --git a/ProteinDT/model_LSTMDecoder.py b/ProteinDT/model_LSTMDecoder.py new file mode 100644 index 0000000..42782aa --- /dev/null +++ b/ProteinDT/model_LSTMDecoder.py @@ -0,0 +1,103 @@ +import numpy as np + +import torch +import torch.nn as nn +import torch.nn.functional as F +import random + +# from utils import * + + +class LSTMDecoder(nn.Module): + def __init__(self, hidden_dim, n_layer, embedding_dim, epsilon, num_classes, tokenizer): + super(LSTMDecoder, self).__init__() + self.hidden_dim = hidden_dim + self.n_layer = n_layer + self.embedding_dim = embedding_dim + self.num_classes = num_classes + self.epsilon = epsilon + + self.embedding_layer = nn.Embedding(num_embeddings=self.num_classes, embedding_dim=self.embedding_dim) + + self.lstm = nn.LSTM(input_size=self.hidden_dim+self.embedding_dim, hidden_size=self.hidden_dim, num_layers=self.n_layer, batch_first=True) + self.fc = nn.Linear(self.hidden_dim, self.num_classes) + self.CE_criterion = nn.CrossEntropyLoss() + self.tokenizer = tokenizer + return + + def forward(self, protein_seq_input_ids, protein_seq_attention_mask, condition): + input_seq_emb = self.embedding_layer(protein_seq_input_ids) # [B, max_seq_len, embedding_dim] + + batch_size, n_seq, _ = input_seq_emb.size() + + h_0 = torch.zeros(self.n_layer, batch_size, self.hidden_dim).detach() + c_0 = torch.zeros(self.n_layer, batch_size, self.hidden_dim).detach() + g_hidden = (h_0.cuda(), c_0.cuda()) + + condition = condition.unsqueeze(1) # [B, 1, hidde_dim] + prev_word = protein_seq_input_ids[:, 0:1] # [B, 1] + + output = [] + + for j in range(n_seq-1): + if random.random() < self.epsilon: + current_word_emb = self.embedding_layer(prev_word) # [B, 1, embedding_dim] + else: + current_word_emb = input_seq_emb[:, j:(j+1), :] # [B, 1, embedding_dim] + + x = torch.cat([condition, current_word_emb], dim=-1) # [B, 1, hidden_dim+embedding_dim] + logits, g_hidden = self.lstm(x, g_hidden) # [B, 1, hidden_dim], [[n_layer, B, hidden_dim], [n_layer, B, hidden_dim]] + logits = self.fc(logits) # [B, 1, num_classes] + prev_word = torch.argmax(logits, dim = -1) # [B, 1] + output.append(logits) + + output = torch.cat(output, dim=1) # [B, max_seq_len-1, num_classes] + target_protein_seq_input_ids = protein_seq_input_ids[:, 1:].contiguous() # [B, max_seq_len-1] + target_protein_seq_attention_mask = protein_seq_attention_mask[:, 1:].contiguous() # [B, max_seq_len-1] + flattened_logits = output.view(-1, output.size(-1)) # [B * (max_sequence_len-1), num_class] + flattened_ids = target_protein_seq_input_ids.view(-1) # [B * (max_sequence_len-1)] + flattened_mask = target_protein_seq_attention_mask.view(-1) # [B * (max_sequence_len-1)] + total_loss = self.CE_criterion(flattened_logits, flattened_ids) # [B * (max_sequence_len-1)] + masked_loss = total_loss * flattened_mask # [B * (max_sequence_len-1)] + total_loss = torch.mean(total_loss) + masked_loss = masked_loss.sum() / flattened_mask.sum() + + loss = total_loss + masked_loss + decoding_loss = 0 + + return loss, decoding_loss + + def inference(self, condition, protein_seq_attention_mask, max_seq_len, temperature=1, use_sample=False): + + device = condition.device + condition = condition.unsqueeze(1) # [B, 1, hidde_dim] + batch_size = condition.size()[0] + prev_word = torch.ones([batch_size]).long().to(device) * self.tokenizer.cls_token_id # [B] + prev_word = prev_word.unsqueeze(1) # [B, 1] + + h_0 = torch.zeros(self.n_layer, batch_size, self.hidden_dim).detach() + c_0 = torch.zeros(self.n_layer, batch_size, self.hidden_dim).detach() + g_hidden = (h_0.cuda(), c_0.cuda()) + + output = [] + for _ in range(max_seq_len): + current_word_emb = self.embedding_layer(prev_word) # [B, 1, embedding_dim] + x = torch.cat([condition, current_word_emb], dim=-1) # [B, 1, hidden_dim+embedding_dim] + logits, g_hidden = self.lstm(x, g_hidden) # [B, 1, hidden_dim], [[n_layer, B, hidden_dim], [n_layer, B, hidden_dim]] + logits = self.fc(logits) # [B, 1, num_classes] + + if use_sample: + probs = torch.softmax(logits / temperature, dim=-1) + prediction = [] + for data_idx in range(batch_size): + prediction_temp = torch.multinomial(probs[data_idx], num_samples=1) + prediction.append(prediction_temp) + prediction = torch.cat(prediction) # [B, 1] + prev_word = prediction # [B, 1] + else: + prev_word = torch.argmax(logits, dim=-1) # [B, 1] + + output.append(prev_word) + + output = torch.cat(output, dim=1) # [B, max_seq_len] + return output diff --git a/ProteinDT/model_LatentDiffusionDecoder.py b/ProteinDT/model_LatentDiffusionDecoder.py new file mode 100644 index 0000000..6076e41 --- /dev/null +++ b/ProteinDT/model_LatentDiffusionDecoder.py @@ -0,0 +1,152 @@ +import torch +import torch.nn as nn +import torch.nn.functional as F +from transformers import BertConfig +from ProteinDT.models.model_SDE import VESDE, VPSDE +from ProteinDT.models.model_Sampler import ReverseDiffusionPredictor, LangevinCorrector +from ProteinDT.models.score_networks import ToyScoreNetwork, RNNScoreNetwork, BertScoreNetwork + +EPS = 1e-6 + + +def get_score_fn(SDE_func, score_network, train=True, continuous=True): + if not train: + score_network.eval() + + if isinstance(SDE_func, VPSDE): + def score_fn(x, x_mask, condition, t): + if continuous: + score = score_network(protein_seq_repr=x, protein_seq_attention_mask=x_mask, condition=condition) + std = SDE_func.marginal_prob(x, t)[1] + else: + raise NotImplementedError(f"Discrete not supported") + score = -score / std[:, None, None] + return score + + elif isinstance(SDE_func, VESDE): + def score_fn(x, x_mask, condition, t): + if continuous: + score = score_network(protein_seq_repr=x, protein_seq_attention_mask=x_mask, condition=condition) + else: + raise NotImplementedError(f"Discrete not supported") + score = -score + return score + + else: + raise NotImplementedError(f"SDE class {SDE_func.__class__.__name__} not supported.") + + return score_fn + + +class LatentDiffusionDecoder(nn.Module): + def __init__( + self, hidden_dim, condition_dim, beta_min, beta_max, num_diffusion_timesteps, num_classes, score_network_type + ): + super().__init__() + self.hidden_dim = hidden_dim + self.condition_dim = condition_dim + self.beta_min = beta_min + self.beta_max = beta_max + self.num_diffusion_timesteps = num_diffusion_timesteps + self.num_classes = num_classes + + self.SDE_func = VPSDE(beta_min=self.beta_min, beta_max=self.beta_max, N=self.num_diffusion_timesteps) + + word_embedding_dim = self.hidden_dim + output_dim = word_embedding_dim + + if score_network_type == "Toy": + self.score_network = ToyScoreNetwork(hidden_dim=hidden_dim, output_dim=output_dim) + + elif score_network_type == "RNN": + self.score_network = RNNScoreNetwork(hidden_dim=hidden_dim, output_dim=output_dim) + + elif score_network_type == "BertBase": + config = BertConfig.from_pretrained( + "bert-base-uncased", + cache_dir="../data/temp_Bert_base", + vocab_size=self.num_classes, + hidden_size=hidden_dim, + num_attention_heads=8 + ) + self.score_network = BertScoreNetwork(config=config, output_dim=output_dim) + + self.word_embedding_dim = word_embedding_dim + self.embedding_layer = nn.Linear(self.num_classes, self.word_embedding_dim, bias=False) + self.decoder_layer = nn.Linear(word_embedding_dim, self.num_classes) + self.condition_proj_layer = nn.Linear(self.condition_dim, self.word_embedding_dim) + + self.score_fn = get_score_fn(self.SDE_func, self.score_network, train=True, continuous=True) + self.predictor = ReverseDiffusionPredictor(self.SDE_func, self.score_fn) + self.corrector = LangevinCorrector(self.SDE_func, self.score_fn, snr=0.1, n_steps=10) + self.CE_criterion = nn.CrossEntropyLoss(reduction='none') + return + + def forward(self, protein_seq_input_ids, protein_seq_attention_mask, condition): + B = protein_seq_input_ids.size()[0] + device = protein_seq_input_ids.device + + # TODO: need double-check range of timesteps + timesteps = torch.rand(B, device=device) * (1 - EPS) + EPS # (B) + + condition = self.condition_proj_layer(condition) # (B, max_seq_len, condition_dim) ---> (B, max_seq_len, hidden_dim) + + protein_seq_onehot = F.one_hot(protein_seq_input_ids, num_classes=self.num_classes) # (B, max_seq_len, num_class) + protein_seq_onehot = protein_seq_onehot.float() + + protein_seq_repr = self.embedding_layer(protein_seq_onehot) # (B, max_seq_len, hidden_dim) + epsilon = torch.randn_like(protein_seq_repr.float()) # (B, max_seq_len, hidden_dim) + protein_seq_repr = self.embedding_layer(protein_seq_onehot) # (B, max_seq_len, hidden_dim) + mean_noise, std_noise = self.SDE_func.marginal_prob(protein_seq_repr, timesteps) # (B, max_seq_len, hidden_dim), (B) + protein_seq_repr_noise = mean_noise + std_noise[:, None, None] * epsilon # (B, max_seq_len, hidden_dim) + + score = self.score_network(protein_seq_repr=protein_seq_repr_noise, protein_seq_attention_mask=protein_seq_attention_mask, condition=condition) # (B, max_seq_len, hidden_dim) + score = -score / std_noise[:, None, None] + + total_SDE_loss = torch.square(score * std_noise[:, None, None] + epsilon) # (B, max_seq_len, hidden_dim) + masked_SDE_loss = total_SDE_loss * protein_seq_attention_mask.unsqueeze(2) # (B, max_seq_len, hidden_dim) + total_SDE_loss = torch.mean(total_SDE_loss) + masked_SDE_loss = masked_SDE_loss.sum() / protein_seq_attention_mask.sum() + SDE_loss = total_SDE_loss + masked_SDE_loss + + # regenerate protein_seq_repr + protein_seq_ids_pred_logit = self.decoder_layer(protein_seq_repr) # (B, max_seq_len, num_class) + flattened_logits = protein_seq_ids_pred_logit.view(-1, protein_seq_ids_pred_logit.size(-1)) # (B*max_sequence_len, num_class) + flattened_ids = protein_seq_input_ids.view(-1) # (B*max_sequence_len) + flattened_mask = protein_seq_attention_mask.view(-1) # (B*max_sequence_len) + total_decoding_loss = self.CE_criterion(flattened_logits, flattened_ids) # (B*max_sequence_len) + masked_decoding_loss = total_decoding_loss * flattened_mask # (B*max_sequence_len) + total_decoding_loss = torch.mean(total_decoding_loss) + masked_decoding_loss = masked_decoding_loss.sum() / flattened_mask.sum() + decoding_loss = total_decoding_loss + masked_decoding_loss + + return SDE_loss, decoding_loss + + @torch.no_grad() + def inference(self, condition, max_seq_len, protein_seq_attention_mask): + B = condition.size()[0] + device = condition.device + + shape = (B, max_seq_len, self.word_embedding_dim) + + X_T = self.SDE_func.prior_sampling(shape).to(device) # (B, max_seq_len, word_embedding_dim) + + EPSILON = 1e-5 + + timesteps = torch.linspace(self.SDE_func.T, EPSILON, self.num_diffusion_timesteps, device=device) # (num_diffusion_timesteps) + + condition = condition.float() + condition = self.condition_proj_layer(condition) # (B, max_seq_len, condition_dim) ---> (B, max_seq_len, hidden_dim) + + x = X_T + for i in range(0, self.num_diffusion_timesteps): + t = timesteps[i] + vec_t = torch.ones(shape[0], device=device) * t + + x, x_mean = self.corrector.update_fn(x, protein_seq_attention_mask, condition, vec_t) + + x, x_mean = self.predictor.update_fn(x, protein_seq_attention_mask, condition, vec_t) # (B, max_seq_len, num_class), (B, max_seq_len, num_class) + + x = self.decoder_layer(x) + + return x diff --git a/ProteinDT/model_SDE.py b/ProteinDT/model_SDE.py new file mode 100644 index 0000000..45d0885 --- /dev/null +++ b/ProteinDT/model_SDE.py @@ -0,0 +1,228 @@ +import abc +import torch +import numpy as np + + +class SDE(abc.ABC): + """SDE abstract class. Functions are designed for a mini-batch of inputs.""" + + def __init__(self, N): + """Construct an SDE. + Args: + N: number of discretization time steps. + """ + super().__init__() + self.N = N + + @property + @abc.abstractmethod + def T(self): + """End time of the SDE.""" + pass + + @abc.abstractmethod + def sde(self, x, t): + pass + + @abc.abstractmethod + def marginal_prob(self, x, t): + """Parameters to determine the marginal distribution of the SDE, $p_t(x)$.""" + pass + + @abc.abstractmethod + def prior_sampling(self, shape): + """Generate one sample from the prior distribution, $p_T(x)$.""" + pass + + @abc.abstractmethod + def prior_logp(self, z): + """Compute log-density of the prior distribution. + Useful for computing the log-likelihood via probability flow ODE. + Args: + z: latent code + Returns: + log probability density + """ + pass + + def discretize(self, x, t): + """Discretize the SDE in the form: x_{i+1} = x_i + f_i(x_i) + G_i z_i. + Useful for reverse diffusion sampling and probabiliy flow sampling. + Defaults to Euler-Maruyama discretization. + Args: + x: a torch tensor + t: a torch float representing the time step (from 0 to `self.T`) + Returns: + f, G + """ + dt = 1 / self.N + drift, diffusion = self.sde(x, t) + f = drift * dt + G = diffusion * torch.sqrt(torch.tensor(dt, device=t.device)) + return f, G + + def reverse(self, score_fn, probability_flow=False): + """Create the reverse-time SDE/ODE. + Args: + score_fn: A time-dependent score-based model that takes x and t and returns the score. + probability_flow: If `True`, create the reverse-time ODE used for probability flow sampling. + """ + N = self.N + T = self.T + sde_fn = self.sde + discretize_fn = self.discretize + + # -------- Build the class for reverse-time SDE -------- + class RSDE(self.__class__): + def __init__(self): + self.N = N + self.probability_flow = probability_flow + + @property + def T(self): + return T + + # def sde(self, feature, x, x_mask, condition, t): + # """Create the drift and diffusion functions for the reverse SDE/ODE.""" + # drift, diffusion = sde_fn(x, t) + # score = score_fn(x, x_mask, condition, t) + # drift = drift - diffusion[:, None, None] ** 2 * score * (0.5 if self.probability_flow else 1.) + # # -------- Set the diffusion function to zero for ODEs. -------- + # diffusion = 0. if self.probability_flow else diffusion + # return drift, diffusion + + def discretize(self, x, x_mask, condition, t): + """Create discretized iteration rules for the reverse diffusion sampler.""" + f, G = discretize_fn(x, t) # (B, max_seq_len, num_class), (B) + score = score_fn(x, x_mask, condition, t) # (B, max_seq_len, num_class) + rev_f = f - G[:, None, None] ** 2 * score * (0.5 if self.probability_flow else 1.) # (B, max_seq_len, num_class) + rev_G = torch.zeros_like(G) if self.probability_flow else G # (B) + return rev_f, rev_G + + return RSDE() + + +class VPSDE(SDE): + def __init__(self, beta_min=0.1, beta_max=20, N=1000): + """Construct a Variance Preserving SDE. + Args: + beta_min: value of beta(0) + beta_max: value of beta(1) + N: number of discretization steps + """ + super().__init__(N) + self.beta_0 = beta_min + self.beta_1 = beta_max + self.N = N + self.discrete_betas = torch.linspace(beta_min / N, beta_max / N, N) # \beta_1, \beta_2, ..., \beta_T + self.alphas = 1. - self.discrete_betas # \alpha_1, \alpha_2, ..., \alpha_T + self.alphas_cumprod = torch.cumprod(self.alphas, dim=0) # \bar\alpha_1, \bar\alpha_2, ..., \bar\alpha_T + self.sqrt_alphas_cumprod = torch.sqrt(self.alphas_cumprod) + self.sqrt_1m_alphas_cumprod = torch.sqrt(1. - self.alphas_cumprod) + + @property + def T(self): + return 1 + + def sde(self, x, t): + beta_t = self.beta_0 + t * (self.beta_1 - self.beta_0) + drift = -0.5 * beta_t[:, None, None] * x + diffusion = torch.sqrt(beta_t) + return drift, diffusion + + # -------- mean, std of the perturbation kernel -------- + def marginal_prob(self, x, t): + log_mean_coeff = -0.25 * t ** 2 * (self.beta_1 - self.beta_0) - 0.5 * t * self.beta_0 + mean = torch.exp(log_mean_coeff[:, None, None]) * x + std = torch.sqrt(1. - torch.exp(2. * log_mean_coeff)) + return mean, std + + def prior_sampling(self, shape): + return torch.randn(*shape) + + def prior_sampling_sym(self, shape): + x = torch.randn(*shape).triu(1) + return x + x.transpose(-1,-2) + + def prior_logp(self, z): + shape = z.shape + N = np.prod(shape[1:]) + logps = -N / 2. * np.log(2 * np.pi) - torch.sum(z ** 2, dim=(1, 2)) / 2. + return logps + + def discretize(self, x, t): + """DDPM discretization.""" + timestep = (t * (self.N - 1) / self.T).long() + beta = self.discrete_betas.to(x.device)[timestep] + alpha = self.alphas.to(x.device)[timestep] + sqrt_beta = torch.sqrt(beta) + f = torch.sqrt(alpha)[:, None, None] * x - x + G = sqrt_beta + return f, G + + def transition(self, x, t, dt): + # -------- negative timestep dt -------- + log_mean_coeff = 0.25 * dt * (2*self.beta_0 + (2*t + dt)*(self.beta_1 - self.beta_0) ) + mean = torch.exp(-log_mean_coeff[:, None, None]) * x + std = torch.sqrt(1. - torch.exp(2. * log_mean_coeff)) + return mean, std + + +class VESDE(SDE): + def __init__(self, sigma_min=0.01, sigma_max=50, N=1000): + """Construct a Variance Exploding SDE. + Args: + sigma_min: smallest sigma. + sigma_max: largest sigma. + N: number of discretization steps + """ + super().__init__(N) + self.sigma_min = sigma_min + self.sigma_max = sigma_max + self.discrete_sigmas = torch.exp(torch.linspace(np.log(self.sigma_min), np.log(self.sigma_max), N)) + self.N = N + + @property + def T(self): + return 1 + + def sde(self, x, t): + sigma = self.sigma_min * (self.sigma_max / self.sigma_min) ** t + drift = torch.zeros_like(x) + diffusion = sigma * torch.sqrt(torch.tensor(2 * (np.log(self.sigma_max) - np.log(self.sigma_min)), device=t.device)) + return drift, diffusion + + def marginal_prob(self, x, t): + std = self.sigma_min * (self.sigma_max / self.sigma_min) ** t + mean = x + return mean, std + + def prior_sampling(self, shape): + return torch.randn(*shape) + + def prior_sampling_sym(self, shape): + x = torch.randn(*shape).triu(1) + x = x + x.transpose(-1,-2) + return x + + def prior_logp(self, z): + shape = z.shape + N = np.prod(shape[1:]) + return -N / 2. * np.log(2 * np.pi * self.sigma_max ** 2) - torch.sum(z ** 2, dim=(1, 2, 3)) / (2 * self.sigma_max ** 2) + + def discretize(self, x, t): + """SMLD(NCSN) discretization.""" + timestep = (t * (self.N - 1) / self.T).long() + sigma = self.discrete_sigmas.to(t.device)[timestep] + adjacent_sigma = torch.where(timestep == 0, torch.zeros_like(t), self.discrete_sigmas.to(t.device)[timestep - 1]) + f = torch.zeros_like(x) + G = torch.sqrt(sigma ** 2 - adjacent_sigma ** 2) + return f, G + + def transition(self, x, t, dt): + # -------- negative timestep dt -------- + std = torch.square(self.sigma_min * (self.sigma_max / self.sigma_min) ** t) - \ + torch.square(self.sigma_min * (self.sigma_max / self.sigma_min) ** (t + dt)) + std = torch.sqrt(std) + mean = x + return mean, std diff --git a/ProteinDT/model_Sampler.py b/ProteinDT/model_Sampler.py new file mode 100644 index 0000000..d38a807 --- /dev/null +++ b/ProteinDT/model_Sampler.py @@ -0,0 +1,89 @@ +import abc +import torch +from .model_SDE import VPSDE, VESDE + + +class Predictor(abc.ABC): + """The abstract class for a predictor algorithm.""" + + def __init__(self, sde, score_fn, probability_flow=False): + super().__init__() + self.sde = sde + # Compute the reverse SDE/ODE + self.rsde = sde.reverse(score_fn, probability_flow) + self.score_fn = score_fn + + @abc.abstractmethod + def update_fn(self, x, t): + """One update of the predictor. + Args: + x: A PyTorch tensor representing the current state + t: A Pytorch tensor representing the current time step. + Returns: + x: A PyTorch tensor of the next state. + x_mean: A PyTorch tensor. The next state without random noise. Useful for denoising. + """ + pass + + +class Corrector(abc.ABC): + """The abstract class for a corrector algorithm.""" + + def __init__(self, sde, score_fn, snr, n_steps): + super().__init__() + self.sde = sde + self.score_fn = score_fn + self.snr = snr + self.n_steps = n_steps + + @abc.abstractmethod + def update_fn(self, x, t): + """One update of the corrector. + Args: + x: A PyTorch tensor representing the current state + t: A PyTorch tensor representing the current time step. + Returns: + x: A PyTorch tensor of the next state. + x_mean: A PyTorch tensor. The next state without random noise. Useful for denoising. + """ + pass + + +class ReverseDiffusionPredictor(Predictor): + def __init__(self, sde, score_fn, probability_flow=False): + super().__init__(sde, score_fn, probability_flow) + + def update_fn(self, x, x_mask, condition, t): + f, G = self.rsde.discretize(x, x_mask, condition, t) # (B, max_seq_len, num_class), (B) + z = torch.randn_like(x) # (B, max_seq_len, num_class) + x_mean = x - f # (B, max_seq_len, num_class) + x = x_mean + G[:, None, None] * z # (B, max_seq_len, num_class) + return x, x_mean + + +class LangevinCorrector(Corrector): + def __init__(self, sde, score_fn, snr, n_steps): + super().__init__(sde, score_fn, snr, n_steps) + if not isinstance(sde, VPSDE) and not isinstance(sde, VESDE): + raise NotImplementedError(f"SDE class {sde.__class__.__name__} not yet supported.") + + def update_fn(self, x, x_mask, condition, t): + sde = self.sde + score_fn = self.score_fn + n_steps = self.n_steps + target_snr = self.snr + if isinstance(sde, VPSDE): + timestep = (t * (sde.N - 1) / sde.T).long() + alpha = sde.alphas.to(t.device)[timestep] + else: + alpha = torch.ones_like(t) + + for i in range(n_steps): + grad = score_fn(x, x_mask, condition, t) # (B, max_seq_len, num_class) + noise = torch.randn_like(x) # (B, max_seq_len, num_class) + grad_norm = torch.norm(grad.reshape(grad.shape[0], -1), dim=-1).mean() # 1 + noise_norm = torch.norm(noise.reshape(noise.shape[0], -1), dim=-1).mean() # 1 + step_size = (target_snr * noise_norm / grad_norm) ** 2 * 2 * alpha # (B) + x_mean = x + step_size[:, None, None] * grad # (B, max_seq_len, num_class) + x = x_mean + torch.sqrt(step_size * 2)[:, None, None] * noise # (B, max_seq_len, num_class) + return x, x_mean diff --git a/ProteinDT/models/__init__.py b/ProteinDT/models/__init__.py new file mode 100644 index 0000000..4cd4122 --- /dev/null +++ b/ProteinDT/models/__init__.py @@ -0,0 +1,9 @@ +from ProteinDT.models.model_ProteinText import ProteinTextModel +from ProteinDT.models.model_GaussianFacilitator import GaussianFacilitatorModel + +from ProteinDT.models.model_TransformerDecoder import T5Decoder +from ProteinDT.models.model_MultinomialDiffusionDecoder import MultinomialDiffusion +from ProteinDT.models.model_RNNPrediction import RNNPrediction + +from ProteinDT.models.model_BindingModel import BindingModel +from ProteinDT.models.model_FoldingBindingInferenceModel import FoldingBindingInferenceModel \ No newline at end of file diff --git a/ProteinDT/models/model_BindingModel.py b/ProteinDT/models/model_BindingModel.py new file mode 100644 index 0000000..4b42760 --- /dev/null +++ b/ProteinDT/models/model_BindingModel.py @@ -0,0 +1,47 @@ +import torch +import torch.nn as nn +from .model_CDConv import CD_Convolution + + +class BindingModel(nn.Module): + def __init__(self, args): + super(BindingModel, self).__init__() + + num_class = 1 + + geometric_radii = [x * args.CDConv_radius for x in args.CDConv_geometric_raddi_coeff] + + self.peptide_model = CD_Convolution( + geometric_radii=geometric_radii, + sequential_kernel_size=args.CDConv_kernel_size, + kernel_channels=args.CDConv_kernel_channels, channels=args.CDConv_channels, base_width=args.CDConv_base_width, + num_classes=num_class) + + self.protein_model = CD_Convolution( + geometric_radii=geometric_radii, + sequential_kernel_size=args.CDConv_kernel_size, + kernel_channels=args.CDConv_kernel_channels, channels=args.CDConv_channels, base_width=args.CDConv_base_width, + num_classes=num_class) + + return + + def forward( + self, + protein_residue, protein_pos_N, protein_pos_Ca, protein_pos_C, protein_batch, + peptide_residue, peptide_pos_N, peptide_pos_Ca, peptide_pos_C, peptide_batch, + ): + + protein_residue_repr = self.protein_model( + pos=protein_pos_Ca, + seq=protein_residue, + batch=protein_batch, + ) + + peptide_residue_repr = self.peptide_model( + pos=peptide_pos_Ca, + seq=peptide_residue, + batch=peptide_batch, + ) + binding_energy = protein_residue_repr + peptide_residue_repr + + return binding_energy diff --git a/ProteinDT/models/model_CDConv.py b/ProteinDT/models/model_CDConv.py new file mode 100644 index 0000000..fc0b9ea --- /dev/null +++ b/ProteinDT/models/model_CDConv.py @@ -0,0 +1,381 @@ +import math +from typing import Type, Any, Callable, Union, List, Optional +import numpy as np + +import torch +import torch.nn as nn +from torch import Tensor +import torch.nn.functional as F + +from torch_scatter import scatter_max, scatter_min, scatter_mean, scatter_sum +from torch_sparse import SparseTensor, set_diag +from torch_geometric.data import Data +from torch_geometric.nn.conv import MessagePassing +from torch_geometric.typing import Adj, OptTensor, PairOptTensor, PairTensor +from torch_geometric.utils import add_self_loops, remove_self_loops +import torch_geometric.transforms as T +from torch_geometric.nn import fps, global_max_pool, global_mean_pool, radius +from torch_geometric.nn.pool import avg_pool, max_pool +import torch.optim as optim +from torch_geometric.loader import DataLoader + + +def kaiming_uniform(tensor, size): + fan = 1 + for i in range(1, len(size)): + fan *= size[i] + gain = math.sqrt(2.0 / (1 + math.sqrt(5) ** 2)) + std = gain / math.sqrt(fan) + bound = math.sqrt(3.0) * std # Calculate uniform bounds from standard deviation + with torch.no_grad(): + return tensor.uniform_(-bound, bound) + +class WeightNet(nn.Module): + def __init__(self, l: int, kernel_channels): + super(WeightNet, self).__init__() + + self.l = l + self.kernel_channels = kernel_channels + + self.Ws = nn.ParameterList() + self.bs = nn.ParameterList() + + for i, channels in enumerate(kernel_channels): + if i == 0: + self.Ws.append(torch.nn.Parameter(torch.empty(l, 3 + 3 + 1, channels))) + self.bs.append(torch.nn.Parameter(torch.empty(l, channels))) + else: + self.Ws.append(torch.nn.Parameter(torch.empty(l, kernel_channels[i-1], channels))) + self.bs.append(torch.nn.Parameter(torch.empty(l, channels))) + + self.relu = nn.LeakyReLU(0.2) + + def reset_parameters(self): + for i, channels in enumerate(self.kernel_channels): + if i == 0: + kaiming_uniform(self.Ws[0].data, size=[self.l, 3 + 3 + 1, channels]) + else: + kaiming_uniform(self.Ws[i].data, size=[self.l, self.kernel_channels[i-1], channels]) + self.bs[i].data.fill_(0.0) + + def forward(self, input, idx): + for i in range(len(self.kernel_channels)): + W = torch.index_select(self.Ws[i], 0, idx) + b = torch.index_select(self.bs[i], 0, idx) + if i == 0: + weight = self.relu(torch.bmm(input.unsqueeze(1), W).squeeze(1) + b) + else: + weight = self.relu(torch.bmm(weight.unsqueeze(1), W).squeeze(1) + b) + + return weight + +class CDConv(MessagePassing): + def __init__(self, r: float, l: float, kernel_channels, in_channels: int, out_channels: int, add_self_loops: bool = True, **kwargs): + kwargs.setdefault('aggr', 'add') + super().__init__(**kwargs) + self.r = r + self.l = l + self.kernel_channels = kernel_channels + self.in_channels = in_channels + self.out_channels = out_channels + + self.WeightNet = WeightNet(l, kernel_channels) + self.W = torch.nn.Parameter(torch.empty(kernel_channels[-1] * in_channels, out_channels)) + + self.add_self_loops = add_self_loops + + self.reset_parameters() + + def reset_parameters(self): + self.WeightNet.reset_parameters() + kaiming_uniform(self.W.data, size=[self.kernel_channels * self.in_channels, self.out_channels]) + + def forward(self, x: OptTensor, pos: Tensor, seq: Tensor, ori: Tensor, batch: Tensor) -> Tensor: + row, col = radius(pos, pos, self.r, batch, batch, max_num_neighbors=9999) + edge_index = torch.stack([col, row], dim=0) + + if self.add_self_loops: + if isinstance(edge_index, Tensor): + edge_index, _ = remove_self_loops(edge_index) + edge_index, _ = add_self_loops(edge_index, num_nodes=min(pos.size(0), pos.size(0))) + + elif isinstance(edge_index, SparseTensor): + edge_index = set_diag(edge_index) + + out = self.propagate(edge_index, x=(x, None), pos=(pos, pos), seq=(seq, seq), ori=(ori.reshape((-1, 9)), ori.reshape((-1, 9))), size=None) + out = torch.matmul(out, self.W) + + return out + + def message(self, x_j: Optional[Tensor], pos_i: Tensor, pos_j: Tensor, seq_i: Tensor, seq_j: Tensor, ori_i: Tensor, ori_j: Tensor) -> Tensor: + # orientation + pos = pos_j - pos_i + distance = torch.norm(input=pos, p=2, dim=-1, keepdim=True) + pos /= (distance + 1e-9) + + pos = torch.matmul(ori_i.reshape((-1, 3, 3)), pos.unsqueeze(2)).squeeze(2) + ori = torch.sum(input=ori_i.reshape((-1, 3, 3)) * ori_j.reshape((-1, 3, 3)), dim=2, keepdim=False) + + # + normed_distance = distance / self.r + + seq = seq_j - seq_i + s = self.l//2 + seq = torch.clamp(input=seq, min=-s, max=s) + seq_idx = (seq + s).squeeze(1).to(torch.int64) + normed_length = torch.abs(seq) / s + + # generated kernel weight: PointConv or PSTNet + delta = torch.cat([pos, ori, distance], dim=1) + kernel_weight = self.WeightNet(delta, seq_idx) + + # smooth: IEConv II + smooth = 0.5 - torch.tanh(normed_distance*normed_length*16.0 - 14.0)*0.5 + + # convolution + msg = torch.matmul((kernel_weight*smooth).unsqueeze(2), x_j.unsqueeze(1)) + + msg = msg.reshape((-1, msg.size(1)*msg.size(2))) + + return msg + + def __repr__(self) -> str: + return (f'{self.__class__.__name__}(r={self.r}, ' + f'l={self.l},' + f'kernel_channels={self.kernel_channels},' + f'in_channels={self.in_channels},' + f'out_channels={self.out_channels})') + +class MaxPooling(nn.Module): + def __init__(self): + super().__init__() + + def forward(self, x, pos, seq, ori, batch): + idx = torch.div(seq.squeeze(1), 2, rounding_mode='floor') + idx = torch.cat([idx, idx[-1].view((1,))]) + + idx = (idx[0:-1] != idx[1:]).to(torch.float32) + idx = torch.cumsum(idx, dim=0) - idx + idx = idx.to(torch.int64) + x = scatter_max(src=x, index=idx, dim=0)[0] + pos = scatter_mean(src=pos, index=idx, dim=0) + seq = scatter_max(src=torch.div(seq, 2, rounding_mode='floor'), index=idx, dim=0)[0] + ori = scatter_mean(src=ori, index=idx, dim=0) + ori = torch.nn.functional.normalize(ori, 2, -1) + batch = scatter_max(src=batch, index=idx, dim=0)[0] + + return x, pos, seq, ori, batch + +class AvgPooling(nn.Module): + def __init__(self): + super().__init__() + + def forward(self, x, pos, seq, ori, batch): + idx = torch.div(seq.squeeze(1), 2, rounding_mode='floor') + idx = torch.cat([idx, idx[-1].view((1,))]) + + idx = (idx[0:-1] != idx[1:]).to(torch.float32) + idx = torch.cumsum(idx, dim=0) - idx + idx = idx.to(torch.int64) + x = scatter_mean(src=x, index=idx, dim=0) + pos = scatter_mean(src=pos, index=idx, dim=0) + seq = scatter_max(src=torch.div(seq, 2, rounding_mode='floor'), index=idx, dim=0)[0] + ori = scatter_mean(src=ori, index=idx, dim=0) + ori = torch.nn.functional.normalize(ori, 2, -1) + batch = scatter_max(src=batch, index=idx, dim=0)[0] + + return x, pos, seq, ori, batch + + +class Linear(nn.Module): + def __init__(self, + in_channels: int, + out_channels: int, + batch_norm: bool = True, + dropout: float = 0.0, + bias: bool = False, + leakyrelu_negative_slope: float = 0.1, + momentum: float = 0.2) -> nn.Module: + super(Linear, self).__init__() + + module = [] + if batch_norm: + module.append(nn.BatchNorm1d(in_channels, momentum=momentum)) + module.append(nn.LeakyReLU(leakyrelu_negative_slope)) + module.append(nn.Dropout(dropout)) + module.append(nn.Linear(in_channels, out_channels, bias = bias)) + self.module = nn.Sequential(*module) + + def forward(self, x): + return self.module(x) + +class MLP(nn.Module): + def __init__(self, + in_channels: int, + mid_channels: int, + out_channels: int, + batch_norm: bool, + dropout: float = 0.0, + bias: bool = True, + leakyrelu_negative_slope: float = 0.2, + momentum: float = 0.2) -> nn.Module: + super(MLP, self).__init__() + + module = [] + if batch_norm: + module.append(nn.BatchNorm1d(in_channels, momentum=momentum)) + module.append(nn.LeakyReLU(leakyrelu_negative_slope)) + module.append(nn.Dropout(dropout)) + if mid_channels is None: + module.append(nn.Linear(in_channels, out_channels, bias = bias)) + else: + module.append(nn.Linear(in_channels, mid_channels, bias = bias)) + if batch_norm: + if mid_channels is None: + module.append(nn.BatchNorm1d(out_channels, momentum=momentum)) + else: + module.append(nn.BatchNorm1d(mid_channels, momentum=momentum)) + module.append(nn.LeakyReLU(leakyrelu_negative_slope)) + if mid_channels is None: + module.append(nn.Dropout(dropout)) + else: + module.append(nn.Linear(mid_channels, out_channels, bias = bias)) + + self.module = nn.Sequential(*module) + + def forward(self, input): + return self.module(input) + +class BasicBlock(nn.Module): + def __init__(self, + r: float, + l: float, + kernel_channels, + in_channels: int, + out_channels: int, + base_width: float = 16.0, + batch_norm: bool = True, + dropout: float = 0.0, + bias: bool = False, + leakyrelu_negative_slope: float = 0.1, + momentum: float = 0.2) -> nn.Module: + + super(BasicBlock, self).__init__() + + if in_channels != out_channels: + self.identity = Linear(in_channels=in_channels, + out_channels=out_channels, + batch_norm=batch_norm, + dropout=dropout, + bias=bias, + leakyrelu_negative_slope=leakyrelu_negative_slope, + momentum=momentum) + else: + self.identity = nn.Sequential() + + width = int(out_channels * (base_width / 64.)) + self.input = MLP(in_channels=in_channels, + mid_channels=None, + out_channels=width, + batch_norm=batch_norm, + dropout=dropout, + bias=bias, + leakyrelu_negative_slope=leakyrelu_negative_slope, + momentum=momentum) + self.conv = CDConv(r=r, l=l, kernel_channels=kernel_channels, in_channels=width, out_channels=width) + self.output = Linear(in_channels=width, + out_channels=out_channels, + batch_norm=batch_norm, + dropout=dropout, + bias=bias, + leakyrelu_negative_slope=leakyrelu_negative_slope, + momentum=momentum) + + def forward(self, x, pos, seq, ori, batch): + identity = self.identity(x) + x = self.input(x) + x = self.conv(x, pos, seq, ori, batch) + out = self.output(x) + identity + return out + +class CD_Convolution(nn.Module): + def __init__(self, + geometric_radii: List[float], + sequential_kernel_size: float, + kernel_channels: List[int], + channels: List[int], + base_width: float = 16.0, + embedding_dim: int = 16, + batch_norm: bool = True, + dropout: float = 0.2, + bias: bool = False, + num_classes: int = 1195) -> nn.Module: + + super().__init__() + + assert (len(geometric_radii) == len(channels)), "Model: 'geometric_radii' and 'channels' should have the same number of elements!" + + self.embedding = torch.nn.Embedding(num_embeddings=26, embedding_dim=embedding_dim) + self.local_mean_pool = AvgPooling() + + layers = [] + in_channels = embedding_dim + for i, radius in enumerate(geometric_radii): + layers.append(BasicBlock(r = radius, + l = sequential_kernel_size, + kernel_channels = kernel_channels, + in_channels = in_channels, + out_channels = channels[i], + base_width = base_width, + batch_norm = batch_norm, + dropout = dropout, + bias = bias)) + layers.append(BasicBlock(r = radius, + l = sequential_kernel_size, + kernel_channels = kernel_channels, + in_channels = channels[i], + out_channels = channels[i], + base_width = base_width, + batch_norm = batch_norm, + dropout = dropout, + bias = bias)) + in_channels = channels[i] + + self.layers = nn.Sequential(*layers) + + self.classifier = MLP(in_channels=channels[-1], + mid_channels=max(channels[-1], num_classes), + out_channels=num_classes, + batch_norm=batch_norm, + dropout=dropout) + + def orientation_CDConv(self, pos): + u = torch.nn.functional.normalize(pos[1:,:] - pos[:-1,:], dim=1) + u1 = u[1:,:] + u2 = u[:-1, :] + b = torch.nn.functional.normalize(u2 - u1, dim=1) + n = torch.nn.functional.normalize(torch.cross(u2, u1, dim=1), dim=1) + o = torch.nn.functional.normalize(torch.cross(b, n, dim=1), dim=1) + ori = torch.stack([b, n, o], dim=1) + return torch.cat([ori[0].unsqueeze(0), ori, ori[-1].unsqueeze(0)], dim=0) + + def forward(self, pos, seq, batch): + device = pos.device + seq_idx = torch.arange(pos.shape[0], device=device).unsqueeze(1).float() + center = torch.sum(pos, dim=0, keepdim=True)/pos.shape[0] + pos = pos - center + ori = self.orientation_CDConv(pos) + + x, pos, seq, ori, batch = (self.embedding(seq), pos, seq_idx, ori, batch) + + for i, layer in enumerate(self.layers): + x = layer(x, pos, seq, ori, batch) + if i == len(self.layers) - 1: + x = global_mean_pool(x, batch) + elif i % 2 == 1: + x, pos, seq, ori, batch = self.local_mean_pool(x, pos, seq, ori, batch) + seq = seq.to(device) + + out = self.classifier(x) + + return out diff --git a/ProteinDT/models/model_FoldingBindingInferenceModel.py b/ProteinDT/models/model_FoldingBindingInferenceModel.py new file mode 100644 index 0000000..4ac15bd --- /dev/null +++ b/ProteinDT/models/model_FoldingBindingInferenceModel.py @@ -0,0 +1,85 @@ +import torch +import torch.nn as nn +from .model_BindingModel import BindingModel +from transformers import AutoTokenizer, EsmForProteinFolding +from transformers.models.esm.openfold_utils.protein import to_pdb, Protein as OFProtein +from transformers.models.esm.openfold_utils.feats import atom14_to_atom37 + + +class AttrDict(dict): + def __init__(self, *args, **kwargs): + super(AttrDict, self).__init__(*args, **kwargs) + self.__dict__ = self + + +def convert_outputs_to_pdb(outputs): + final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs) + outputs = {k: v.to("cpu").numpy() for k, v in outputs.items()} + final_atom_positions = final_atom_positions.cpu().numpy() + final_atom_mask = outputs["atom37_atom_exists"] + pdbs = [] + for i in range(outputs["aatype"].shape[0]): + aa = outputs["aatype"][i] + pred_pos = final_atom_positions[i] + mask = final_atom_mask[i] + resid = outputs["residue_index"][i] + 1 + pred = OFProtein( + aatype=aa, + atom_positions=pred_pos, + atom_mask=mask, + residue_index=resid, + b_factors=outputs["plddt"][i], + chain_index=outputs["chain_index"][i] if "chain_index" in outputs else None, + ) + pdb = to_pdb(pred) + pdbs.append(pdb) + return pdbs + + +class FoldingBindingInferenceModel(nn.Module): + def __init__(self, input_model_path=None): + + super(FoldingBindingInferenceModel, self).__init__() + + self.folding_tokenizer = AutoTokenizer.from_pretrained("facebook/esmfold_v1") + self.folding_model = EsmForProteinFolding.from_pretrained("facebook/esmfold_v1", low_cpu_mem_usage=True) + + config = { + "CDConv_radius": 4, + "CDConv_geometric_raddi_coeff": [2, 3, 4, 5], + "CDConv_kernel_size": 21, + "CDConv_kernel_channels": [24], + "CDConv_channels": [256, 512, 1024, 2048], + "CDConv_base_width": 64, + } + config = AttrDict(config) + + self.binding_model = BindingModel(config) + if input_model_path is not None: + from collections import OrderedDict + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu')["binding_model"] + self.binding_model.load_state_dict(state_dict) + + return + + def folding(self, protein_sequence): + tokenized_input = self.folding_tokenizer(protein_sequence, return_tensors="pt", add_special_tokens=False)['input_ids'] + tokenized_input = tokenized_input.cuda() + + with torch.no_grad(): + output = self.folding_model(tokenized_input) + + pdb_list = convert_outputs_to_pdb(output) + return pdb_list + + def binding( + self, + protein_residue, protein_pos_N, protein_pos_Ca, protein_pos_C, protein_batch, + peptide_residue, peptide_pos_N, peptide_pos_Ca, peptide_pos_C, peptide_batch, + ): + energy = self.binding_model( + protein_residue, protein_pos_N, protein_pos_Ca, protein_pos_C, protein_batch, + peptide_residue, peptide_pos_N, peptide_pos_Ca, peptide_pos_C, peptide_batch, + ) + return energy diff --git a/ProteinDT/models/model_GaussianFacilitator.py b/ProteinDT/models/model_GaussianFacilitator.py new file mode 100644 index 0000000..c75f112 --- /dev/null +++ b/ProteinDT/models/model_GaussianFacilitator.py @@ -0,0 +1,25 @@ +import torch.nn as nn + + +class GaussianFacilitatorModel(nn.Module): + def __init__(self, latent_dim): + super().__init__() + self.latent_dim = latent_dim + + self.MLP = nn.Sequential( + nn.Linear( self.latent_dim, self.latent_dim), + nn.SiLU(inplace=True), + nn.Linear(self.latent_dim, self.latent_dim) + ) + + self.criterion = nn.MSELoss() + return + + def forward(self, protein_repr, text_repr): + protein_repr_pred = self.MLP(text_repr) + loss = self.criterion(protein_repr, protein_repr_pred) + return loss + + def inerence(self, text_repr): + protein_repr_pred = self.MLP(text_repr) + return protein_repr_pred \ No newline at end of file diff --git a/ProteinDT/models/model_MultinomialDiffusionDecoder.py b/ProteinDT/models/model_MultinomialDiffusionDecoder.py new file mode 100644 index 0000000..1c74e43 --- /dev/null +++ b/ProteinDT/models/model_MultinomialDiffusionDecoder.py @@ -0,0 +1,226 @@ +import torch +import torch.nn as nn +import torch.nn.functional as F +import torch.distributions as dists +from transformers import BertConfig +from ProteinDT.models.score_networks import ToyScoreNetwork, RNNScoreNetwork, BertScoreNetwork + +EPS = 1e-6 + + +class MultinomialDiffusion(nn.Module): + def __init__( + self, hidden_dim, condition_dim, beta_min, beta_max, num_diffusion_timesteps, mask_id, num_classes, score_network_type + ): + super().__init__() + self.hidden_dim = hidden_dim + self.condition_dim = condition_dim + self.beta_min = beta_min + self.beta_max = beta_max + self.num_diffusion_timesteps = num_diffusion_timesteps + self.num_classes = num_classes + self.mask_id = mask_id + + output_dim = hidden_dim + if score_network_type == "Toy": + word_embedding_dim = self.hidden_dim + self.score_network = ToyScoreNetwork(hidden_dim=hidden_dim, output_dim=output_dim) + + elif score_network_type == "RNN": + word_embedding_dim = self.hidden_dim + self.score_network = RNNScoreNetwork(hidden_dim=hidden_dim, output_dim=output_dim) + + elif score_network_type == "BertBase": + config = BertConfig.from_pretrained( + "bert-base-uncased", + # cache_dir="../data/temp_Bert_base", + vocab_size=self.num_classes, + hidden_size=hidden_dim, + num_attention_heads=8 + ) + word_embedding_dim = self.hidden_dim + self.score_network = BertScoreNetwork(config=config, output_dim=output_dim) + + self.word_embedding_dim = word_embedding_dim + self.embedding_layer = nn.Linear(self.num_classes, self.word_embedding_dim, bias=False) + self.decoder_layer = nn.Linear(word_embedding_dim, self.num_classes) + self.condition_proj_layer = nn.Linear(self.condition_dim, self.word_embedding_dim) + + self.CE_criterion = nn.CrossEntropyLoss(reduction='none') + return + + def forward(self, protein_seq_input_ids, protein_seq_attention_mask, condition): + B = protein_seq_input_ids.size()[0] + device = protein_seq_input_ids.device + + # TODO: need double-check range of timesteps + timesteps = torch.rand(B, device=device) * (1 - EPS) + EPS # (B) + timesteps = torch.randint(1, 1+self.num_diffusion_timesteps, (B,), device=device) + # pt = torch.ones_like(timesteps).float() / self.num_diffusion_timesteps + + condition = condition.float() + condition = self.condition_proj_layer(condition) # (B, max_seq_len, condition_dim) ---> (B, max_seq_len, hidden_dim) + + protein_seq_onehot = F.one_hot(protein_seq_input_ids, num_classes=self.num_classes) # (B, max_seq_len, num_class) + + x_t, x_0_ignore = protein_seq_input_ids.clone(), protein_seq_input_ids.clone() + + mask = torch.rand_like(x_t.float()) < timesteps.float().unsqueeze(-1) / self.num_diffusion_timesteps # (B, max_seq_len) + x_t[mask] = self.mask_id # (B, max_seq_len) + x_0_ignore[torch.bitwise_not(mask)] = -1 # (B, max_seq_len) + + x_t_one_hot = F.one_hot(x_t, num_classes=self.num_classes) # (B, max_seq_len, num_class) + x_t_one_hot = x_t_one_hot.float() + x_t_repr = self.embedding_layer(x_t_one_hot) # (B, max_seq_len, hidden_dim) + + x_0_repr = self.score_network(protein_seq_repr=x_t_repr, protein_seq_attention_mask=protein_seq_attention_mask, condition=condition) # (B, max_seq_len, hidden_dim) + x_0_logits = self.decoder_layer(x_0_repr) # (B*max_sequence_len, num_class) + + flattened_logits = x_0_logits.view(-1, x_0_logits.size(-1)) # (B*max_sequence_len, num_class) + flattened_ids = protein_seq_input_ids.view(-1) # (B*max_sequence_len) + flattened_mask = protein_seq_attention_mask.view(-1) # (B*max_sequence_len) + total_SDE_loss = self.CE_criterion(flattened_logits, flattened_ids) # (B*max_sequence_len) + masked_SDE_loss = total_SDE_loss * flattened_mask # (B*max_sequence_len) + total_SDE_loss = torch.mean(total_SDE_loss) + masked_SDE_loss = masked_SDE_loss.sum() / flattened_mask.sum() + # previously: + # masked_SDE_loss = total_SDE_loss.sum() / flattened_mask.sum() + + SDE_loss = total_SDE_loss + masked_SDE_loss + decoding_loss = 0 + + return SDE_loss, decoding_loss + + @torch.no_grad() + def inference(self, condition, max_seq_len, protein_seq_attention_mask, mode="simplified"): + if mode == "simplified": + return self.simplified_inference(condition, max_seq_len, protein_seq_attention_mask) + elif mode == "weighted": + return self.weighted_inference(condition, max_seq_len, protein_seq_attention_mask) + return + + @torch.no_grad() + def simplified_inference(self, condition, max_seq_len, protein_seq_attention_mask): + """ + credit to https://github.com/samb-t/unleashing-transformers/blob/master/models/absorbing_diffusion.py#L134 + """ + B = condition.size()[0] + device = condition.device + + shape = (B, max_seq_len, self.num_classes) + + condition = condition.float() + condition = self.condition_proj_layer(condition) # (B, max_seq_len, condition_dim) ---> (B, max_seq_len, hidden_dim) + + x_t = torch.ones((B, max_seq_len), device=device).long() * self.mask_id + unmasked = torch.zeros_like(x_t, device=device).bool() + temperature = 1. + + for timestep in reversed(range(1, 1+self.num_diffusion_timesteps)): + # TODO: need to double-check + t = torch.full((B,), timestep, device=device).long() # (B) + # t = torch.full((B,), self.num_diffusion_timesteps-timestep+1, device=device).long() # (B) + + # where to unmask + changes = torch.rand(x_t.shape, device=device) < 1/t.float().unsqueeze(-1) # (B, max_seq_len) + # don't unmask somwhere already masked + changes = torch.bitwise_xor(changes, torch.bitwise_and(changes, unmasked)) # (B, max_seq_len) + # update mask with changes + unmasked = torch.bitwise_or(unmasked, changes) # (B, max_seq_len) + + x_t_one_hot = F.one_hot(x_t, num_classes=self.num_classes) # (B, max_seq_len, num_class) + x_t_one_hot = x_t_one_hot.float() + x_t_repr = self.embedding_layer(x_t_one_hot) # (B, max_seq_len, hidden_dim) + + x_0_repr = self.score_network(protein_seq_repr=x_t_repr, protein_seq_attention_mask=protein_seq_attention_mask, condition=condition) # (B, max_seq_len, hidden_dim) + x_0_logits = self.decoder_layer(x_0_repr) # (B, max_sequence_len, num_class) + + x_0_logits /= temperature + x_0_dist = dists.Categorical(logits=x_0_logits) + x_0_hat = x_0_dist.sample().long() + + x_t[changes] = x_0_hat[changes] + + x = x_t + x = F.one_hot(x, num_classes=self.num_classes) + + return x + + @torch.no_grad() + def weighted_inference(self, condition, max_seq_len, protein_seq_attention_mask): + B = condition.size()[0] + device = condition.device + + shape = (B, max_seq_len, self.num_classes) + + condition = condition.float() + condition = self.condition_proj_layer(condition) # (B, max_seq_len, condition_dim) ---> (B, max_seq_len, hidden_dim) + + x_t = torch.ones((B, max_seq_len), device=device).long() * self.mask_id + unmasked = torch.zeros_like(x_t, device=device).bool() + temperature = 1. + + def get_Qt(t): + # TODO: need to double-check this + # beta_t = 1. / (self.num_diffusion_timesteps - t + 1) + beta_t = 1. / t + Q = torch.eye(self.num_classes) * (1 - beta_t) + Q[:, self.mask_id] = beta_t + Q[self.mask_id, self.mask_id] = 1 + Q = Q.to(device) + return Q + + bar_Q_t = torch.eye(self.num_classes).to(device) + + def posterior(x_t, x_0, t, bar_Q_t): + """ + q(x_t-1 | x_t, x_0) + x_t: (B, max_seq_le, vocab_size) + x_0: (B, max_seq_le, vocab_size) + """ + Q_t = get_Qt(t) # (vocab_size, vocab_size) + bar_Q_t_minus_1 = bar_Q_t # (vocab_size, vocab_size) + bar_Q_t = bar_Q_t_minus_1 * Q_t # (vocab_size, vocab_size) + fact_1 = torch.matmul(x_t, Q_t.transpose(0,1)) # (B, max_seq_le, vocab_size) + fact_2 = torch.matmul(x_0, bar_Q_t_minus_1.transpose(0,1)) # (B, max_seq_le, vocab_size) + denominator = torch.matmul(x_0, bar_Q_t) * x_t # (B, max_seq_le, vocab_size) + denominator = denominator.sum(dim=-1, keepdim=True) # (B, max_seq_le, 1) + logits = torch.exp(torch.log(fact_1+EPS) + torch.log(fact_2+EPS) - torch.log(denominator+EPS)) # (B, max_seq_le, vocab_size) + return logits, bar_Q_t + + softmax = torch.nn.Softmax(-1) + + for timestep in reversed(range(1, 1+self.num_diffusion_timesteps)): + # t = torch.full((B,), timestep, device=device).long() # (B) + t = torch.full((B,), self.num_diffusion_timesteps-timestep+1, device=device).long() # (B) + + # where to unmask + changes = torch.rand(x_t.shape, device=device) < 1/t.float().unsqueeze(-1) # (B, max_seq_len) + # don't unmask somwhere already masked + changes = torch.bitwise_xor(changes, torch.bitwise_and(changes, unmasked)) # (B, max_seq_len) + # update mask with changes + unmasked = torch.bitwise_or(unmasked, changes) # (B, max_seq_len) + + x_t_one_hot = F.one_hot(x_t, num_classes=self.num_classes) # (B, max_seq_len, num_class) + x_t_one_hot = x_t_one_hot.float() + x_t_repr = self.embedding_layer(x_t_one_hot) # (B, max_seq_len, hidden_dim) + + x_0_repr = self.score_network(protein_seq_repr=x_t_repr, protein_seq_attention_mask=protein_seq_attention_mask, condition=condition) # (B, max_seq_len, hidden_dim) + x_0_logits = self.decoder_layer(x_0_repr) # (B, max_sequence_len, num_class) + + x_0_logits /= temperature + x_0_prob = softmax(x_0_logits) + + posterior_logits, bar_Q_t = posterior(x_t_one_hot, x_0_prob, timestep, bar_Q_t) + + x_0_prob = x_0_prob * posterior_logits + + x_0_dist = dists.Categorical(probs=x_0_prob) + x_0_hat = x_0_dist.sample().long() + + x_t[changes] = x_0_hat[changes] + + x = x_t + x = F.one_hot(x, num_classes=self.num_classes) + + return x diff --git a/ProteinDT/models/model_ProteinText.py b/ProteinDT/models/model_ProteinText.py new file mode 100644 index 0000000..9a2a05c --- /dev/null +++ b/ProteinDT/models/model_ProteinText.py @@ -0,0 +1,21 @@ +import torch.nn as nn + + +class ProteinTextModel(nn.Module): + def __init__(self, protein_model, text_model, protein2latent_model, text2latent_model): + super().__init__() + self.protein_model = protein_model + self.text_model = text_model + self.protein2latent_model = protein2latent_model + self.text2latent_model = text2latent_model + return + + def forward(self, protein_sequence_input_ids, protein_sequence_attention_mask, text_sequence_input_ids, text_sequence_attention_mask): + protein_output = self.protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + protein_repr = protein_output["pooler_output"] + protein_repr = self.protein2latent_model(protein_repr) + + description_output = self.text_model(text_sequence_input_ids, text_sequence_attention_mask) + description_repr = description_output["pooler_output"] + description_repr = self.text2latent_model(description_repr) + return protein_repr, description_repr \ No newline at end of file diff --git a/ProteinDT/models/model_RNNPrediction.py b/ProteinDT/models/model_RNNPrediction.py new file mode 100644 index 0000000..c5f162d --- /dev/null +++ b/ProteinDT/models/model_RNNPrediction.py @@ -0,0 +1,27 @@ +import torch +from torch import nn + + +class RNNPrediction(nn.Module): + def __init__(self, hidden_dim, output_dim, num_layers=2): + super().__init__() + self.hidden_dim = hidden_dim + self.output_dim = output_dim + self.num_layers = num_layers + self.rnn_layer = nn.RNN(self.hidden_dim, self.hidden_dim, self.num_layers) + self.mlp_layer = nn.Sequential( + # nn.Linear(self.hidden_dim, self.hidden_dim), + # nn.SiLU(inplace=True), + nn.Linear(self.hidden_dim, self.output_dim) + ) + return + + def forward(self, protein_seq_repr): + max_seq_len = protein_seq_repr.size()[1] + + device = protein_seq_repr.device + h0 = torch.randn(self.num_layers, max_seq_len, self.hidden_dim).to(device=device) # (num_layers, max_seq_len, hidden_dim) + + out, _ = self.rnn_layer(protein_seq_repr, h0) # (B, max_seq_len, hidden_dim), (num_layers, max_seq_len, hidden_dim) + out = self.mlp_layer(out) # (B, max_seq_len, 1) + return out diff --git a/ProteinDT/models/model_TransformerDecoder.py b/ProteinDT/models/model_TransformerDecoder.py new file mode 100644 index 0000000..c45b6b9 --- /dev/null +++ b/ProteinDT/models/model_TransformerDecoder.py @@ -0,0 +1,62 @@ +import torch.nn as nn +from transformers import T5ForConditionalGeneration, T5Config +from transformers.modeling_outputs import BaseModelOutput + + +class T5Decoder(nn.Module): + def __init__(self, hidden_dim, tokenizer, T5_model): + super().__init__() + self.num_classes = tokenizer.vocab_size + + if T5_model == "ProtT5": + self.config = T5Config.from_pretrained("Rostlab/prot_t5_xl_uniref50", chache_dir="../data/temp_pretrained_prot_t5_xl_uniref50") + self.T5_model = T5ForConditionalGeneration.from_pretrained("Rostlab/prot_t5_xl_uniref50") + + elif T5_model == "T5Base": + self.config = T5Config.from_pretrained( + "t5-base", + chache_dir="../data/temp_t5", + vocab_size=self.num_classes, + ) + self.T5_model = T5ForConditionalGeneration(self.config) + + self.rep_linear = nn.Linear(hidden_dim, self.config.d_model) + self.tokenizer = tokenizer + return + + def forward(self, protein_seq_input_ids, protein_seq_attention_mask, condition): + condition = condition.unsqueeze(1) + if condition.size(2) != self.config.d_model: + condition = self.rep_linear(condition) # (B, 1, d_model) + + labels = protein_seq_input_ids # (B, d_model) + labels[labels == self.tokenizer.pad_token_id] = -100 + + model_outputs = self.T5_model(encoder_outputs=(condition, ), labels=labels) + loss = model_outputs.loss + return loss, 0 + + def inference( + self, condition, max_seq_len, protein_seq_attention_mask, + temperature=1.0, k=40, p=0.9, repetition_penalty=1.0, num_return_sequences=1, + do_sample=True, num_beams=1 + ): + if condition.dim() == 2: + condition = condition.unsqueeze(1).float() # (B, 1, hidden_dim) + if condition.size(2) != self.config.d_model: + condition = self.rep_linear(condition) + + enccoder_outputs = BaseModelOutput(last_hidden_state=condition) + output_ids = self.T5_model.generate( + encoder_outputs=enccoder_outputs, + max_length=max_seq_len, + temperature=temperature, + top_k=k, + top_p=p, + repetition_penalty=repetition_penalty, + num_beams=num_beams, + do_sample=do_sample, + num_return_sequences=num_return_sequences, + ) + # https://huggingface.co/docs/transformers/v4.25.1/en/main_classes/text_generation#transformers.GenerationMixin + return output_ids diff --git a/ProteinDT/models/score_networks/BertScoreNetwork.py b/ProteinDT/models/score_networks/BertScoreNetwork.py new file mode 100644 index 0000000..5fd5645 --- /dev/null +++ b/ProteinDT/models/score_networks/BertScoreNetwork.py @@ -0,0 +1,118 @@ +import torch +import torch.nn as nn +from transformers.models.bert import BertModel +from transformers.models.bert.modeling_bert import BertEncoder + + +class BertEmbeddings(nn.Module): + """Construct the embeddings from word, position and token_type embeddings.""" + + def __init__(self, config): + super().__init__() + self.position_embeddings = nn.Embedding(config.max_position_embeddings, config.hidden_size) + + self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps) + self.dropout = nn.Dropout(config.hidden_dropout_prob) + self.position_embedding_type = getattr(config, "position_embedding_type", "absolute") + self.register_buffer("position_ids", torch.arange(config.max_position_embeddings).expand((1, -1))) + self.register_buffer("token_type_ids", torch.zeros(self.position_ids.size(), dtype=torch.long), persistent=False) + + def forward( + self, + input_ids=None, + token_type_ids=None, + position_ids=None, + inputs_embeds=None, + past_key_values_length=0, + ) -> torch.Tensor: + if input_ids is not None: + input_shape = input_ids.size() + else: + input_shape = inputs_embeds.size()[:-1] + + seq_length = input_shape[1] + + if position_ids is None: + position_ids = self.position_ids[:, past_key_values_length : seq_length + past_key_values_length] + + if token_type_ids is None: + if hasattr(self, "token_type_ids"): + buffered_token_type_ids = self.token_type_ids[:, :seq_length] + buffered_token_type_ids_expanded = buffered_token_type_ids.expand(input_shape[0], seq_length) + token_type_ids = buffered_token_type_ids_expanded + else: + token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=self.position_ids.device) + + embeddings = inputs_embeds + if self.position_embedding_type == "absolute": + position_embeddings = self.position_embeddings(position_ids) + embeddings += position_embeddings + embeddings = self.LayerNorm(embeddings) + embeddings = self.dropout(embeddings) + return embeddings + + +class BertScoreNetwork(BertModel): + def __init__(self, config, **kwargs): + super().__init__(config) + self.config = config + + self.embeddings = BertEmbeddings(config) + self.encoder = BertEncoder(config) + + print("config.hidden_size", config.hidden_size) + print("config.vocab_size", config.vocab_size) + + self.post_init() + + def forward(self, protein_seq_repr, protein_seq_attention_mask, condition): + if self.config.is_decoder: + use_cache = use_cache if use_cache is not None else self.config.use_cache + else: + use_cache = False + + inputs_embeds = protein_seq_repr + attention_mask = protein_seq_attention_mask + input_shape = inputs_embeds.size()[:2] + + batch_size, seq_length = input_shape + device = inputs_embeds.device + + past_key_values_length = 0 + + if hasattr(self.embeddings, "token_type_ids"): + buffered_token_type_ids = self.embeddings.token_type_ids[:, :seq_length] + buffered_token_type_ids_expanded = buffered_token_type_ids.expand(batch_size, seq_length) + token_type_ids = buffered_token_type_ids_expanded + else: + token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=device) + + extended_attention_mask: torch.Tensor = self.get_extended_attention_mask(attention_mask, input_shape) + + encoder_extended_attention_mask = None + head_mask = None + + head_mask = self.get_head_mask(head_mask, self.config.num_hidden_layers) + + embedding_output = self.embeddings( + input_ids=None, + position_ids=None, + token_type_ids=token_type_ids, + inputs_embeds=inputs_embeds, + past_key_values_length=past_key_values_length, + ) + embedding_output[:, 0] += condition + encoder_outputs = self.encoder( + embedding_output, + attention_mask=extended_attention_mask, + head_mask=head_mask, + encoder_hidden_states=None, + encoder_attention_mask=encoder_extended_attention_mask, + past_key_values=None, + use_cache=use_cache, + output_attentions=None, + output_hidden_states=None, + return_dict=None, + ) + sequence_output = encoder_outputs[0] # 8, 512, hidden_dim + return sequence_output diff --git a/ProteinDT/models/score_networks/RNNScoreNetwork.py b/ProteinDT/models/score_networks/RNNScoreNetwork.py new file mode 100644 index 0000000..40aa7ac --- /dev/null +++ b/ProteinDT/models/score_networks/RNNScoreNetwork.py @@ -0,0 +1,41 @@ +import torch +import torch.nn as nn + + +class RNNScoreNetwork(nn.Module): + def __init__(self, hidden_dim, output_dim, num_layers=2): + super().__init__() + self.hidden_dim = hidden_dim + self.output_dim = output_dim + self.num_layers = num_layers + self.rnn_layer = nn.RNN(self.hidden_dim, self.hidden_dim, self.num_layers) + self.mlp_layer = nn.Sequential( + nn.Linear(self.hidden_dim, self.hidden_dim), + nn.SiLU(inplace=True), + nn.Linear(self.hidden_dim, self.output_dim) + ) + return + + def forward(self, protein_seq_repr, protein_seq_attention_mask, condition): + """ + Args: + protein_seq_repr: noised protein token-level representation, (B, max_seq_len, hidden_dim) + protein_seq_attention_mask: masking, (B, max_seq_len) + condition: the condition matrix, (B, hidden_dim) + Output: + gradient (score) + """ + max_seq_len = protein_seq_repr.size()[1] + protein_seq_attention_mask = protein_seq_attention_mask.unsqueeze(2) # (B, max_seq_len, 1) + condition = condition.unsqueeze(1).expand(-1, max_seq_len, -1) # (B, max_seq_len, hidden_dim) + condition = condition * protein_seq_attention_mask # (B, max_seq_len, hidden_dim) + + conditioned_protein_seq_repr = protein_seq_repr + condition # (B, max_seq_len, hidden_dim) + + max_seq_len = conditioned_protein_seq_repr.size()[1] + device = protein_seq_repr.device + h0 = torch.randn(self.num_layers, max_seq_len, self.hidden_dim).to(device=device) # (num_layers, max_seq_len, hidden_dim) + + conditioned_protein_seq_repr, _ = self.rnn_layer(conditioned_protein_seq_repr, h0) # (B, max_seq_len, hidden_dim), (num_layers, max_seq_len, hidden_dim) + score = self.mlp_layer(conditioned_protein_seq_repr) # (B, max_seq_len, 1) + return score \ No newline at end of file diff --git a/ProteinDT/models/score_networks/ToyScoreNetwork.py b/ProteinDT/models/score_networks/ToyScoreNetwork.py new file mode 100644 index 0000000..b45551f --- /dev/null +++ b/ProteinDT/models/score_networks/ToyScoreNetwork.py @@ -0,0 +1,34 @@ +import torch +import torch.nn as nn + + +class ToyScoreNetwork(nn.Module): + def __init__(self, hidden_dim, output_dim): + super().__init__() + self.hidden_dim = hidden_dim + self.output_dim = output_dim + + self.mlp_layer = nn.Sequential( + nn.Linear(2*self.hidden_dim, self.hidden_dim), + nn.SiLU(inplace=True), + nn.Linear(self.hidden_dim, self.output_dim) + ) + return + + def forward(self, protein_seq_repr, protein_seq_attention_mask, condition): + """ + Args: + protein_seq_repr: noised protein token-level representation, (B, max_seq_len, hidden_dim) + protein_seq_attention_mask: masking, (B, max_seq_len) + condition: the condition matrix, (B, hidden_dim) + Output: + gradient (score) + """ + max_seq_len = protein_seq_repr.size()[1] + protein_seq_attention_mask = protein_seq_attention_mask.unsqueeze(2) # (B, max_seq_len, 1) + condition = condition.unsqueeze(1).expand(-1, max_seq_len, -1) # (B, max_seq_len, hidden_dim) + condition = condition * protein_seq_attention_mask # (B, max_seq_len, hidden_dim) + + conditioned_protein_seq_repr = torch.cat([protein_seq_repr, condition], dim=-1) # (B, max_seq_len, 2*hidden_dim) + score = self.mlp_layer(conditioned_protein_seq_repr) # (B, max_seq_len, 1) + return score \ No newline at end of file diff --git a/ProteinDT/models/score_networks/__init__.py b/ProteinDT/models/score_networks/__init__.py new file mode 100644 index 0000000..c84c4ff --- /dev/null +++ b/ProteinDT/models/score_networks/__init__.py @@ -0,0 +1,3 @@ +from ProteinDT.models.score_networks.ToyScoreNetwork import ToyScoreNetwork +from ProteinDT.models.score_networks.RNNScoreNetwork import RNNScoreNetwork +from ProteinDT.models.score_networks.BertScoreNetwork import BertScoreNetwork \ No newline at end of file diff --git a/ProteinDT/utils/__init__.py b/ProteinDT/utils/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/ProteinDT/utils/tokenize.py b/ProteinDT/utils/tokenize.py new file mode 100644 index 0000000..8b62670 --- /dev/null +++ b/ProteinDT/utils/tokenize.py @@ -0,0 +1,48 @@ +# This script is merged into the dataset scripts. I.e., it is no longer used, only for backup. + +import re +import numpy as np +import torch + + +# This is for ProtBERT +def preprocess_each_protein_sequence(sentence, tokenizer, max_seq_len): + sentence = re.sub(r"[UZOB]", "X", sentence) + sentence = " ".join(sentence) + text_input = tokenizer(sentence, truncation=True, max_length=max_seq_len, padding='max_length', return_tensors='np') + + input_ids = text_input['input_ids'].squeeze() + attention_mask = text_input['attention_mask'].squeeze() + return [input_ids, attention_mask] + + +# This is for ProtBERT +def prepare_protein_sequence_tokens(description, tokenizer, max_seq_len): + B = len(description) + tokens_outputs = [preprocess_each_protein_sequence(description[idx], tokenizer, max_seq_len) for idx in range(B)] + tokens_ids = [o[0] for o in tokens_outputs] + masks = [o[1] for o in tokens_outputs] + tokens_ids = torch.Tensor(tokens_ids).long() + masks = torch.Tensor(masks).bool() + return tokens_ids, masks + + +# This is for SciBERT +def preprocess_each_text_sentence(sentence, tokenizer, max_seq_len): + text_input = tokenizer(sentence, truncation=True, max_length=max_seq_len, padding='max_length', return_tensors='np') + + input_ids = text_input['input_ids'].squeeze() + attention_mask = text_input['attention_mask'].squeeze() + + return [input_ids, attention_mask] + + +# This is for SciBERT +def prepare_text_sequence_tokens(description, tokenizer, max_seq_len): + B = len(description) + tokens_outputs = [preprocess_each_text_sentence(description[idx], tokenizer, max_seq_len) for idx in range(B)] + tokens_ids = [o[0] for o in tokens_outputs] + masks = [o[1] for o in tokens_outputs] + tokens_ids = torch.Tensor(tokens_ids).long() + masks = torch.Tensor(masks).bool() + return tokens_ids, masks \ No newline at end of file diff --git a/README.md b/README.md index 2220ebf..a86f777 100644 --- a/README.md +++ b/README.md @@ -1 +1,316 @@ -# ProteinDT \ No newline at end of file +# ProteinDT: A Text-guided Protein Design Framework + +Authors: Shengchao Liu, Yanjing Li, Zhuoxinran Li, Anthony Gitter, Yutao Zhu, Jiarui Lu, Zhao Xu, Weili Nie, Arvind Ramanathan, Chaowei Xiao\*, Jian Tang\*, Hongyu Guo\*, Anima Anandkumar\* + +\* jointly supervised + +[[Project Page](https://chao1224.github.io/ProteinDT)] [[ArXiv](https://arxiv.org/abs/2302.04611)] +[[Datasets on HuggingFace](https://huggingface.co/datasets/chao1224/ProteinDT/tree/main)] [[Checkpoints on HuggingFace](https://huggingface.co/chao1224/ProteinDT/tree/main)] + + +

+ +

+ +

+ +

+ +## 1 Environment + +``` +conda create -n ProteinDT python=3.7 +conda activate ProteinDT + +conda install -y numpy networkx scikit-learn + +pip install torch==1.10.* + +pip install transformers +pip install lxml + +# for TAPE +pip install lmdb +pip install seqeval + +# for baseline ChatGPT +pip install openai + +# for baseline Galactica +pip install accelerate + +# for visualization +pip install matplotlib + +# for binding editing +pip install h5py +pip install torch_geometric==2.0 torch_scatter torch_sparse torch_cluster +pip install biopython + +# for ESM folding +pip install "fair-esm[esmfold]" +pip install dm-tree omegaconf ml-collections einops +pip install fair-esm[esmfold]==2.0.0 --no-dependencies # Override deepspeed==0.5 +pip install 'dllogger @ git+https://github.com/NVIDIA/dllogger.git' +pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307' + +conda install mdtraj biopython -c conda-forge -yq + +# for ProteinDT +pip install . +``` + + +## 2 Pretraining Datasets (SwissProtCLAP) Preparation + +Please check folder `preprocess/SwissProtCLAP` for SwissProtCLAP construction from UniProt. + +We also provide a copy of SwissProtCLAP at [this HuggingFace link](https://huggingface.co/datasets/chao1224/ProteinDT/tree/main). Or you can use the following script: +``` +from huggingface_hub import HfApi, snapshot_download +api = HfApi() +snapshot_download(repo_id="chao1224/ProteinDT", repo_type="dataset", cache_dir='./') +``` + +Then move the data under `./data` folder. The data structure is +``` +./data/ +└── SwissProtCLAP + ├── protein_sequence.txt + └── text_sequence.txt +``` + +## 3 Pretraining + +Go to folder `examples`, and do the pretraining in 5 steps. We summarize the logics of these 5 steps as below: +

+ +

+ +The pretrained checkpoints can be found at [this HuggingFace link](https://huggingface.co/chao1224/ProteinDT/tree/main). +Before getting started, first we need to define our output home folder, e.g., `export OUTPUT_DIR=../output/ProteinDT/hyper_01`. + +- Step 1. Conduct CLAP pretraining + - On a single GPU card: + ``` + python pretrain_step_01_CLAP.py \ + --protein_lr=1e-5 --protein_lr_scale=1 \ + --text_lr=1e-5 --text_lr_scale=1 \ + --protein_backbone_model=ProtBERT_BFD \ + --epochs=10 --batch_size=9 --num_workers=0 \ + --output_model_dir="$OUTPUT_DIR" + ``` + + - We also support distribution learning with DDP. Example of using a server with 8 GPU cards: + ``` + CUDA_VISIBLE_DEVICES=0,1,2,3,4,5,6,7 \ + python pretrain_step_01_CLAP.py \ + --protein_lr=1e-5 --protein_lr_scale=1 \ + --text_lr=1e-5 --text_lr_scale=1 \ + --protein_backbone_model=ProtBERT_BFD \ + --epochs=10 --batch_size=9 --num_workers=0 \ + --output_model_dir="$OUTPUT_DIR" + ``` + +- Step 2. Obtain frozen representation: + ``` + python pretrain_step_02_empty_sequence.py \ + --protein_backbone_model=ProtBERT_BFD \ + --batch_size=16 --num_workers=0 \ + --pretrained_folder="$OUTPUT_DIR" + + python pretrain_step_02_pairwise_representation.py \ + --protein_backbone_model=ProtBERT_BFD \ + --batch_size=16 --num_workers=0 \ + --pretrained_folder="$OUTPUT_DIR" + ``` + +- Step 3. Learn the facilitator distribution: + ``` + python pretrain_step_03_facilitator.py \ + --protein_lr=1e-5 --protein_lr_scale=1 \ + --text_lr=1e-5 --text_lr_scale=1 \ + --protein_backbone_model=ProtBERT_BFD \ + --epochs=10 --batch_size=9 --num_workers=0 \ + --pretrained_folder="$OUTPUT_DIR" \ + --output_model_folder="$OUTPUT_DIR"/step_03_Gaussian_10 + ``` + +- Step 4. Learn the decoder distribution. Notice that we have three types of decoder distribution models: + - A Transformer-based auto-regressive decoder. Here we adopt the T5 architecture. + ``` + python pretrain_step_04_decoder.py \ + --num_workers=0 --lr=1e-4 --epochs=50 \ + --decoder_distribution=T5Decoder \ + --score_network_type=T5Base \ + --hidden_dim=16 \ + --pretrained_folder="$OUTPUT_DIR" \ + --output_folder="$OUTPUT_DIR"/step_04_T5 + ``` + - A discrete denoising diffusion model (multinomial diffusion). + - Using RNN as score network: + ``` + python pretrain_step_04_decoder.py \ + --num_workers=0 --lr=1e-4 --epochs=50 \ + --decoder_distribution=MultinomialDiffusion \ + --score_network_type=RNN \ + --hidden_dim=16 \ + --pretrained_folder="$OUTPUT_DIR" \ + --output_folder="$OUTPUT_DIR"/step_04_MultiDiffusion_RNN + ``` + + - Using BERT as score network: + ``` + python pretrain_step_04_decoder.py \ + --num_workers=0 --lr=1e-4 --epochs=50 \ + --decoder_distribution=MultinomialDiffusion \ + --score_network_type=BertBase \ + --hidden_dim=16 \ + --pretrained_folder="$OUTPUT_DIR" \ + --output_folder="$OUTPUT_DIR"/step_04_MultiDiffusion_BERT + ``` + +- Step 5. learn an auto-encoder that is specifically designed for text-guided editing task. You can also treat this as a downstream task. + ``` + python pretrain_step_05_AE.py \ + --num_workers=0 --lr=1e-4 --epochs=50 \ + --pretrained_folder="$OUTPUT_DIR" \ + --output_folder="$OUTPUT_DIR"/step_05 + ``` + +## 4 Downstream Tasks + +We include three types of downstream tasks, as will be introduced below. You can find the scripts for first two downstream tasks under folder `scripts`. + +### 4.1 Text-to-Protein Generation + +First let's go to the folder `examples/downstream_Text2Protein`. + +Then we sample text sequences for text-to-protein generation: +``` +python step_01_text_retrieval.py +``` +We also provide the sampled text data in `step_01_text_retrieval.txt`. You can replace it with the text sequences you want to use. + +Now we can do the text-to-sequence generation, e.g., if we use T5 as the decoder: +``` +export OUTPUT_DIR=../../output/ProteinDT/hyper_01 + +python step_02_inference_ProteinDT.py \ +--decoder_distribution=T5Decoder --score_network_type=T5Base \ +--num_workers=0 --hidden_dim=16 --batch_size=8 \ +--pretrained_folder="$OUTPUT_DIR" \ +--step_04_folder="$OUTPUT_DIR"/step_04_T5 \ +--num_repeat=16 --use_facilitator --AR_generation_mode=01 \ +--output_text_file_path="$OUTPUT_DIR"/step_04_T5/downstream_Text2Protein/step_02_inference.txt +``` + + +### 4.2 Zero-shot Text-guided Protein Editing + +First let's go to the folder `examples/downstream_Editing`. + +The dataset preparation can be found at `examples/downstream_Edting/README.md`. You can also find it on [this HuggingFace link](https://huggingface.co/datasets/chao1224/ProteinDT/tree/main/downstream_Editing/datasets_and_checkpoints). We include three types of editing tasks: stability, structure, and peptide binding. In terms of the methods, we have two types: latent optimization and latent interpolation. The demo scripts are explained below. + +#### 4.2.1 Latent Optimization +- Structure / Stability: `editing_task: alpha, beta, Villin, Pin1`. + ``` + export OUTPUT_DIR=../../output/ProteinDT/hyper_01 + + python step_01_editing_latent_optimization.py \ + --num_workers=0 --batch_size=8 \ + --lambda_value=0.9 --num_repeat=16 --oracle_mode=text --temperature=2 \ + --editing_task=alpha --text_prompt_id=101 \ + --pretrained_folder="$OUTPUT_DIR" \ + --step_05_folder="$OUTPUT_DIR"/step_05_AE \ + --output_folder="$OUTPUT_DIR"/step_05_AE/downstream_Editing_latent_optimization/alpha_prompt_101_lambda_0.9_num_repeat_16_oracle_text_T_2 \ + --output_text_file_path="$OUTPUT_DIR"/step_05_AE/downstream_Editing_latent_optimization/alpha_prompt_101_lambda_0.9_num_repeat_16_oracle_text_T_2/step_01_editing.txt + + python step_01_evaluate_structure.py \ + --num_workers=0 --batch_size=8 --editing_task=alpha --text_prompt_id=101 \ + --output_folder="$OUTPUT_DIR"/step_05_AE/downstream_Editing_latent_optimization/alpha_prompt_101_lambda_0.9_num_repeat_16_oracle_text_T_2 \ + --output_text_file_path="$OUTPUT_DIR"/step_05_AE/downstream_Editing_latent_optimization/alpha_prompt_101_lambda_0.9_num_repeat_16_oracle_text_T_2/step_01_editing.txt + ``` +- Peptide binding + ``` + export OUTPUT_DIR=../../output/ProteinDT/hyper_01 + + python step_01_editing_latent_optimization.py \ + --num_workers=0 --batch_size=4 \ + --lambda_value=0.9 --num_repeat=16 --oracle_mode=text --temperature=2 \ + --editing_task=peptide_binding --text_prompt_id=101 \ + --pretrained_folder="$OUTPUT_DIR" \ + --step_05_folder="$OUTPUT_DIR"/step_05_AE \ + --output_folder="$OUTPUT_DIR"/step_05_AE/downstream_Editing_latent_optimization/peptide_binding_prompt_101_lambda_0.9_num_repeat_16_oracle_text_T_2 \ + --output_text_file_path="$OUTPUT_DIR"/step_05_AE/downstream_Editing_latent_optimization/peptide_binding_prompt_101_lambda_0.9_num_repeat_16_oracle_text_T_2/step_02_editing.txt + ``` + + +#### 4.2.2 Latent Interpolation +Notice that for latent interpolation, we have three models: auto-regressive (T5), denoising diffusion model (RNN and BERT). We provide demos scripts using T5. +- Structure / Stability: `editing_task: alpha, beta, Villin, Pin1`. + ``` + export OUTPUT_DIR=../../output/ProteinDT/hyper_01 + + python step_01_editing_latent_interpolation.py \ + --editing_task=alpha --text_prompt_id=101 \ + --decoder_distribution=T5Decoder --score_network_type=T5Base \ + --num_workers=0 --hidden_dim=16 --batch_size=2 \ + --theta=0.9 --num_repeat=16 --oracle_mode=text --AR_generation_mode=01 --AR_condition_mode=expanded \ + --pretrained_folder="$OUTPUT_DIR" --step_04_folder="$OUTPUT_DIR"/step_04_T5 \ + --output_folder="$OUTPUT_DIR"/step_04_T5/downstream_Editing_latent_interpolation_alpha/prompt_101_theta_0.9_num_repeat_16_oracle_text_inference_01_expanded \ + --output_text_file_path="$OUTPUT_DIR"/step_04_T5/downstream_Editing_latent_interpolation_alpha/prompt_101_theta_0.9_num_repeat_16_oracle_text_inference_01_expanded/step_01_editing.txt + + python step_01_evaluate_structure.py \ + --num_workers=0 --batch_size=1 \ + --editing_task=alpha --text_prompt_id=101 \ + --output_folder="$OUTPUT_DIR"/step_04_T5/downstream_Editing_latent_interpolation_alpha/prompt_101_theta_0.9_num_repeat_16_oracle_text_inference_01_expanded \ + --output_text_file_path="$OUTPUT_DIR"/step_04_T5/downstream_Editing_latent_interpolation_alpha/prompt_101_theta_0.9_num_repeat_16_oracle_text_inference_01_expanded/step_01_editing.txt + ``` +- Peptide binding + ``` + export OUTPUT_DIR=../../output/ProteinDT/hyper_01 + + python step_02_binding_editing_latent_interpolation.py \ + --editing_task=peptide_binding --text_prompt_id=101 \ + --decoder_distribution=T5Decoder --score_network_type=T5Base \ + --num_workers=0 --hidden_dim=16 --batch_size=1 \ + --theta=0.9 --num_repeat=16 --oracle_mode=text --AR_generation_mode=01 --AR_condition_mode=expanded \ + --pretrained_folder="$OUTPUT_DIR" --step_04_folder="$OUTPUT_DIR"/step_04_T5 \ + --output_folder="$OUTPUT_DIR"/step_04_T5/downstream_Editing_latent_interpolation_peptide_binding/prompt_101_theta_0.9_num_repeat_16_oracle_text_inference_01_expanded \ + --output_text_file_path="$OUTPUT_DIR"/step_04_T5/downstream_Editing_latent_interpolation_peptide_binding/prompt_101_theta_0.9_num_repeat_16_oracle_text_inference_01_expanded/step_02_editing.txt + ``` + + + +### 4.3 Protein Property Prediction + +First please download the TAPE data following instructions [here](https://github.com/songlab-cal/tape?tab=readme-ov-file#lmdb-data). We also provide it at [this HuggingFace link](https://huggingface.co/datasets/chao1224/ProteinDT/tree/main). + +Under `examples`, and the script is `downstream_TAPE.py`. We follow the exactly same hyper-parameter as [OntoProtein](https://github.com/zjunlp/OntoProtein). + +``` +python downstream_TAPE.py \ +--task_name=ss3 \ +--seed=3 \ +--learning_rate=3e-5 \ +--num_train_epochs=5 \ +--per_device_train_batch_size=2 \ +--gradient_accumulation_steps=8 \ +--warmup_ratio=0.08 \ +--pretrained_model=ProteinDT \ +--pretrained_folder="$OUTPUT_DIR" \ +--output_dir="$OUTPUT_DIR"/downstream_TAPE +``` + + +## Cite Us +Feel free to cite this work if you find it useful to you! +``` +@article{liu2023text, + title={A Text-guided Protein Design Framework}, + author={Shengchao Liu, Yanjing Li, Zhuoxinran Li, Anthony Gitter, Yutao Zhu, Jiarui Lu, Zhao Xu, Weili Nie, Arvind Ramanathan, Chaowei Xiao, Jian Tang, Hongyu Guo, Anima Anandkumar}, + journal={arXiv preprint arXiv:2302.04611}, + year={2023} +} +``` diff --git a/README_checkpoints.md b/README_checkpoints.md new file mode 100644 index 0000000..72558d6 --- /dev/null +++ b/README_checkpoints.md @@ -0,0 +1 @@ +# Checkpoints for ProteinDT \ No newline at end of file diff --git a/README_data.md b/README_data.md new file mode 100644 index 0000000..3ff9f1b --- /dev/null +++ b/README_data.md @@ -0,0 +1 @@ +# Data for ProteinDT \ No newline at end of file diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 0000000..3224801 --- /dev/null +++ b/examples/README.md @@ -0,0 +1,27 @@ +Most of the checkpoints perform quite stable performance, yet here we provide details on exactly which we use in the manuscript. The checkpoint can be found at [this HuggingFace link](https://huggingface.co/chao1224/ProteinDT/tree/main). + +## 1 Downstream: Text-to-Protein Generation + +| | Checkpoints | Tables/Figures in Manuscript| +| -- | -- | -- | +| Autoregressive (T5) | `ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10/step_04_T5Decoder_T5Base_lr_1e-4_hidden_16_e_10_unconditional_0.1/downstream_Text2Protein` | Table 1 | +| Multinomial Diffusion (RNN) | `ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_04_MultinomialDiffusion_RNN_lr_1e-4_hidden_32_e_10_unconditional_0/downstream_Text2Protein` | Table 1 | +| Multinomial Diffusion (BERT) | `ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10/step_04_MultinomialDiffusion_BertBase_lr_1e-4_hidden_32_e_10_unconditional_0/downstream_Text2Protein` | Table 1 | + + +## 2 Downstream: Zero-shot Text-guided Protein Editing + +| | | Checkpoints | Tables/Figures in Manuscript| +| -- | -- | -- | -- | +| Latent Interpolation | Autoregressive (T5) | `ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10/step_04_T5Decoder_T5Base_lr_1e-4_hidden_16_e_10_unconditional_0` | Table 2 | +| | Multinomial Diffusion (RNN) | `ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_04_MultinomialDiffusion_RNN_lr_1e-5_hidden_16_e_10_unconditional_0` | Table 2 | +| | Multinomial Diffusion (BERT) | `ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_04_MultinomialDiffusion_BertBase_lr_1e-5_hidden_32_e_10_unconditional_0` | Table 2 | +| Latent Optimization | | `ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_05_AE_1e-3_3` | Table 2 | + + +## 3 Downstream: Protein Property Prediction + +| | Checkpoints | Tables/Figures in Manuscript| +| -- | -- | -- | +| InfoNCE | `ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-InfoNCE-0.1-batch-9-gpu-8-epoch-5` | Table 3 | +| EBM-NCE | `ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5` | Table 3 | diff --git a/examples/downstream_Editing/README.md b/examples/downstream_Editing/README.md new file mode 100644 index 0000000..b7ca1e3 --- /dev/null +++ b/examples/downstream_Editing/README.md @@ -0,0 +1,90 @@ +# Datasets and Checkpoints Preparation + +## 1 Structure Editing + +### 1.1 Dataset +This follows the [ChatDrug](https://github.com/chao1224/ChatDrug). + +``` +mkdir -p datasets_and_checkpoints/structure +cp -r ../../data/downstream_datasets/secondary_structure/*.lmdb datasets_and_checkpoints/structure/ + +python prepare_02_processed_data.py --editing_task=alpha +``` + +### 1.2 Oracle Evaluator +We can use this checkpoint: +``` +mkdir -p datasets_and_checkpoints/structure/oracle/ +cp ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/downstream_TAPE/ss3/3-3e-5-5-2-8-0.08/pytorch_model.bin \ + datasets_and_checkpoints/structure/oracle/pytorch_model_ss3.bin +``` + +Or use the following huggingface link: +``` +from huggingface_hub import hf_hub_download + +hf_hub_download( + repo_id="chao1224/ProteinCLAP_pretrain_EBM_NCE_downstream_property_prediction", + repo_type="model", + filename="pytorch_model_ss3.bin", + local_dir="datasets_and_checkpoints/structure/oracle") +``` + +## 2 Stability Editing + +### 2.1 Dataset +``` +mkdir -p datasets_and_checkpoints/stability +cp ../../data/downstream_datasets/stability/*.json datasets_and_checkpoints/stability/ + +python prepare_01_stability_raw_data_Villin.py +python prepare_01_stability_raw_data_Pin1.py + +python prepare_02_processed_data.py --editing_task=Villin +python prepare_02_processed_data.py --editing_task=Pin1 +``` + +### 2.2 Oracle Evaluator +We can use this checkpoint: +``` +mkdir -p datasets_and_checkpoints/stability/oracle/ + +cp ../../output/downstream_TAPE/stability/ProtBERT_BFD/3-3e-5-5-2-16-0.08/pytorch_model.bin \ + datasets_and_checkpoints/stability/oracle/pytorch_model_stability.bin +``` + +## 3 Peptide Editing + +### 3.1 Dataset + +Refer to this [GitHub link](https://github.com/t7morgen/misato-dataset). + +``` +cd .../../data + +mkdir -r MISATO/raw +cd MISATO/raw + +wget https://zenodo.org/record/7711953/files/MD.hdf5?download=1 +mv 'MD.hdf5?download=1' MD.hdf5 +wget https://zenodo.org/record/7711953/files/train_MD.txt?download=1 +mv 'train_MD.txt?download=1' train_MD.txt +wget https://zenodo.org/record/7711953/files/val_MD.txt?download=1 +mv 'val_MD.txt?download=1' val_MD.txt +wget https://zenodo.org/record/7711953/files/test_MD.txt?download=1 +mv 'test_MD.txt?download=1' test_MD.txt +``` + +Back to this folder, and do the following: +``` +python prepare_01_peptide_editing_raw_and_processed_data.py +``` + +### 3.2 Oracle Evaluator + +We will have to train an oracle model by ourselves + docking. + +``` +python prepare_03_train_peptide_editing_evaluator.py --epochs=1000 --lr=1e-4 --output_model_dir=datasets_and_checkpoints/peptide_binding/MISATO +``` diff --git a/examples/downstream_Editing/prepare_01_peptide_editing_raw_and_processed_data.py b/examples/downstream_Editing/prepare_01_peptide_editing_raw_and_processed_data.py new file mode 100644 index 0000000..0b39c80 --- /dev/null +++ b/examples/downstream_Editing/prepare_01_peptide_editing_raw_and_processed_data.py @@ -0,0 +1,75 @@ +import os +import random +random.seed(42) +from ProteinDT.datasets import MISATODataset +import requests +import json + + +text_file = "datasets_and_checkpoints/uniprot_sprot_xml_text.txt" +uniprot_id2text = {} +f = open(text_file, 'r') +for line_idx, line in enumerate(f.readlines()): + line = line.strip() + if line_idx % 2 == 0: + uniprot = line + else: + text = line + uniprot_id2text[uniprot] = text +print("len of text {}".format(len(uniprot_id2text))) + + +if __name__ == "__main__": + data_folder = "../../data/MISATO" + dataset = MISATODataset(data_folder) + + PDB_idx_list = dataset.PDB_idx_list + peptide_sequence_list = dataset.peptide_sequence_list + protein_sequence_list = dataset.protein_sequence_list + print("peptide_sequence_list", len(peptide_sequence_list)) + print("PDB_idx_list", len(PDB_idx_list)) + print("protein_sequence_list", len(protein_sequence_list)) + + output_dir = "datasets_and_checkpoints/peptide_binding/MISATO" + os.makedirs(output_dir, exist_ok = True) + + idx_list = [x for x in range(len(PDB_idx_list))] + print("idx_list", idx_list) + random.shuffle(idx_list) + print("idx_list", idx_list) + + PDB_idx2text = {} + for PDB_idx in PDB_idx_list: + description_url = "https://data.rcsb.org/rest/v1/core/uniprot/{entry_id}/1".format(entry_id=PDB_idx) + description_data = requests.get(description_url).json() + + try: + description_data = description_data[0] + uniprot_idx = description_data["rcsb_uniprot_accession"][0] + PDB_idx2text[PDB_idx] = uniprot_id2text[uniprot_idx] + except: + print("error with PDB: {}".format(PDB_idx)) + continue + print("PDB_idx2text: {}".format(len(PDB_idx2text))) + + f = open("{}/PDB_idx2text.json".format(output_dir), "w") + json.dump(PDB_idx2text, f) + + f = open("{}/PDB_mapping_data.txt".format(output_dir), "w") + for i in idx_list: + PDB_idx, peptide_sequence, protein_sequence = PDB_idx_list[i], peptide_sequence_list[i], protein_sequence_list[i] + if PDB_idx not in PDB_idx2text: + continue + print("{},{},{}".format(PDB_idx, peptide_sequence, protein_sequence), file=f) + f.flush() + f.close() + + f = open("{}/preprocessed_data.csv".format(output_dir), "w") + for i in idx_list: + peptide_sequence = peptide_sequence_list[i] + PDB_idx, peptide_sequence, protein_sequence = PDB_idx_list[i], peptide_sequence_list[i], protein_sequence_list[i] + if PDB_idx not in PDB_idx2text: + continue + print("{}".format(peptide_sequence), file=f) + f.flush() + f.close() \ No newline at end of file diff --git a/examples/downstream_Editing/prepare_01_stability_raw_data_Pin1.py b/examples/downstream_Editing/prepare_01_stability_raw_data_Pin1.py new file mode 100644 index 0000000..d428d7b --- /dev/null +++ b/examples/downstream_Editing/prepare_01_stability_raw_data_Pin1.py @@ -0,0 +1,53 @@ +import os +import json +from random import shuffle + + +if __name__ == "__main__": + input_json_file = "datasets_and_checkpoints/stability/stability_test.json" + f = open(input_json_file, 'r') + data = json.load(f) + + record_list = [] + for idx, record in enumerate(data): + if 'Pin1' not in record['topology']: + continue + protein_sequence = record["primary"] + assert protein_sequence[:1] == "G" + assert protein_sequence[-3:] == "GSS" + protein_sequence = protein_sequence[1:-3] + assert len(protein_sequence) == 39 + value = record["stability_score"][0] + record_list.append([protein_sequence, value]) + print("len of valid record", len(record_list)) + + shuffle(record_list) + N = len(record_list) + + split_size = [0.8, 0.1, 0.1] + train_size = int(split_size[0] * N) + train_val_size = int((split_size[0] + split_size[1]) * N) + + output_dir = "datasets_and_checkpoints/stability/Pin1" + os.makedirs(output_dir, exist_ok = True) + + f = open("{}/train_data.txt".format(output_dir), "w") + for idx in range(0, train_size): + protein_sequence, label = record_list[idx] + print("{},{}".format(protein_sequence, label), file=f) + f.flush() + f.close() + + f = open("{}/val_data.txt".format(output_dir), "w") + for idx in range(train_size, train_val_size): + protein_sequence, label = record_list[idx] + print("{},{}".format(protein_sequence, label), file=f) + f.flush() + f.close() + + f = open("{}/test_data.txt".format(output_dir), "w") + for idx in range(train_val_size, N): + protein_sequence, label = record_list[idx] + print("{},{}".format(protein_sequence, label), file=f) + f.flush() + f.close() diff --git a/examples/downstream_Editing/prepare_01_stability_raw_data_Villin.py b/examples/downstream_Editing/prepare_01_stability_raw_data_Villin.py new file mode 100644 index 0000000..3b7ce77 --- /dev/null +++ b/examples/downstream_Editing/prepare_01_stability_raw_data_Villin.py @@ -0,0 +1,53 @@ +import os +import json +from random import shuffle + + +if __name__ == "__main__": + input_json_file = "datasets_and_checkpoints/stability/stability_test.json" + f = open(input_json_file, 'r') + data = json.load(f) + + record_list = [] + for idx, record in enumerate(data): + if 'villin' not in record['topology']: + continue + protein_sequence = record["primary"] + assert protein_sequence[:5] == "GSSGS" + assert protein_sequence[-3:] == "GSS" + protein_sequence = protein_sequence[5:-3] + assert len(protein_sequence) == 35 + value = record["stability_score"][0] + record_list.append([protein_sequence, value]) + print("len of valid record", len(record_list)) + + shuffle(record_list) + N = len(record_list) + + split_size = [0.8, 0.1, 0.1] + train_size = int(split_size[0] * N) + train_val_size = int((split_size[0] + split_size[1]) * N) + + output_dir = "datasets_and_checkpoints/stability/Villin" + os.makedirs(output_dir, exist_ok = True) + + f = open("{}/train_data.txt".format(output_dir), "w") + for idx in range(0, train_size): + protein_sequence, label = record_list[idx] + print("{},{}".format(protein_sequence, label), file=f) + f.flush() + f.close() + + f = open("{}/val_data.txt".format(output_dir), "w") + for idx in range(train_size, train_val_size): + protein_sequence, label = record_list[idx] + print("{},{}".format(protein_sequence, label), file=f) + f.flush() + f.close() + + f = open("{}/test_data.txt".format(output_dir), "w") + for idx in range(train_val_size, N): + protein_sequence, label = record_list[idx] + print("{},{}".format(protein_sequence, label), file=f) + f.flush() + f.close() diff --git a/examples/downstream_Editing/prepare_02_processed_data.py b/examples/downstream_Editing/prepare_02_processed_data.py new file mode 100644 index 0000000..d94b70c --- /dev/null +++ b/examples/downstream_Editing/prepare_02_processed_data.py @@ -0,0 +1,111 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm + +import torch +import torch.nn as nn + +from transformers import BertModel, BertTokenizer + +from utils import text_prompt_dict, load_oracle_evaluator, load_editing_dataset_and_loader + + +@torch.no_grad() +def select(dataloader): + eval_prediction_model.eval() + + protein_sequence_list = [] + logits_list = [] + target_list = [] + eval_list = [] + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + for batch_idx, batch in enumerate(L): + protein_sequence = batch["protein_sequence"] + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + target = batch["label"].to(device) + + output = eval_prediction_model(protein_sequence_input_ids, protein_sequence_attention_mask) + logits = output.logits + + if args.editing_task in ["alpha", "beta"]: + pred = logits.argmax(dim=-1, keepdim=False) + pred = torch.where(protein_sequence_attention_mask==1, pred, -1) + eval_result = pred.eq(target) + + total = protein_sequence_attention_mask.sum(-1) + eval_result = eval_result * protein_sequence_attention_mask + eval_result = eval_result.sum(-1) + logits = eval_result # pseudo logits, without any specific meanings + target = eval_result + else: + logits = logits.squeeze(1) + eval_result = criterion_eval(logits, target) + + protein_sequence_list.extend(protein_sequence) + logits_list.append(logits.detach().cpu().numpy()) + target_list.append(target.detach().cpu().numpy()) + eval_list.append(eval_result.detach().cpu().numpy()) + + logits_list = np.concatenate(logits_list) + target_list = np.concatenate(target_list) + eval_list = np.concatenate(eval_list) + print("len of protein_sequence_list", len(protein_sequence_list)) + print("logits_list: {}".format(logits_list.shape)) + print("target_list: {}".format(target_list.shape)) + print("eval_list: {}".format(eval_list.shape)) + + output_path = os.path.join(output_folder, "preprocessed_data.csv") + f = open(output_path, 'w') + for protein_sequence, logits, target, eval in zip(protein_sequence_list, logits_list, target_list, eval_list): + protein_sequence = protein_sequence.replace(" ", "") + print("{},{},{},{}".format(protein_sequence, target, logits, eval), file=f) + + return + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=8) + parser.add_argument("--num_workers", type=int, default=8) + parser.add_argument("--lr", type=float, default=1e-5) + parser.add_argument("--decay", type=float, default=0) + parser.add_argument("--epochs", type=int, default=100) + parser.add_argument("--dataset_size", type=int, default=200) + parser.add_argument("--output_model_dir", type=str, default=None) + + parser.add_argument("--editing_task", type=str, default="Villin") + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=True) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + args = parser.parse_args() + print("arguments", args) + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Create prediction head + eval_prediction_model, eval_protein_tokenizer = load_oracle_evaluator(args.editing_task, device) + test_dataset, test_dataloader, criterion_eval = load_editing_dataset_and_loader(args, eval_protein_tokenizer) + print("len of test: {}".format(len(test_dataset))) + + output_folder = text_prompt_dict[args.editing_task]["data_folder"] + select(test_dataloader) diff --git a/examples/downstream_Editing/prepare_03_train_peptide_editing_evaluator.py b/examples/downstream_Editing/prepare_03_train_peptide_editing_evaluator.py new file mode 100644 index 0000000..e219b2a --- /dev/null +++ b/examples/downstream_Editing/prepare_03_train_peptide_editing_evaluator.py @@ -0,0 +1,134 @@ +import os +import random +import argparse +import numpy as np +import time +from tqdm import tqdm +import torch +import torch.nn as nn +import torch.optim as optim +from ProteinDT.datasets import MISATODataset, MISATODataLoader +from ProteinDT.models import BindingModel + + +def save_model(save_best): + if not args.output_model_dir == "": + if save_best: + print("save model with optimal loss") + output_model_path = os.path.join(args.output_model_dir, "model.pth") + saved_model_dict = {} + saved_model_dict["binding_model"] = binding_model.state_dict() + torch.save(saved_model_dict, output_model_path) + + else: + print("save model in the last epoch") + output_model_path = os.path.join(args.output_model_dir, "model_final.pth") + saved_model_dict = {} + saved_model_dict["binding_model"] = binding_model.state_dict() + torch.save(saved_model_dict, output_model_path) + return + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--batch_size", type=int, default=32) + parser.add_argument("--num_workers", type=int, default=0) + + # for CDConv + parser.add_argument("--CDConv_radius", type=float, default=4) + parser.add_argument("--CDConv_kernel_size", type=int, default=21) + parser.add_argument("--CDConv_kernel_channels", type=int, nargs="+", default=[24]) + parser.add_argument("--CDConv_geometric_raddi_coeff", type=int, nargs="+", default=[2, 3, 4, 5]) + parser.add_argument("--CDConv_channels", type=int, nargs="+", default=[256, 512, 1024, 2048]) + parser.add_argument("--CDConv_base_width", type=int, default=64) + + parser.add_argument("--loss", type=str, default="MAE", choices=["MSE", "MAE"]) + parser.add_argument("--epochs", type=int, default=32) + parser.add_argument("--optimizer", type=str, default="SGD", choices=["SGD", "Adam"]) + parser.add_argument("--lr", type=float, default=1e-4) + parser.add_argument("--lr_scheduler", type=str, default="None") + parser.add_argument("--decay", type=float, default=0) + parser.add_argument("--print_every_epoch", type=int, default=5) + parser.add_argument("--output_model_dir", type=str, default="") + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.add_argument("--no_verbose", dest="verbose", action="store_false") + parser.set_defaults(verbose=False) + + args = parser.parse_args() + print("args", args) + + torch.manual_seed(args.seed) + np.random.seed(args.seed) + random.seed(args.seed) + device = ( + torch.device("cuda:" + str(args.device)) + if torch.cuda.is_available() + else torch.device("cpu") + ) + if torch.cuda.is_available(): + torch.cuda.manual_seed_all(args.seed) + + data_folder = "../../data/MISATO" + dataset = MISATODataset(data_folder) + loader = MISATODataLoader(dataset, batch_size=args.batch_size, num_workers=args.num_workers, shuffle=True) + + binding_model = BindingModel(args).to(device) + binding_model.train() + + if args.loss == "MSE": + criterion = nn.MSELoss(reduction="mean") + elif args.loss == "MAE": + criterion = nn.L1Loss(reduction="mean") + + # set up optimizer + model_param_group = [ + {"params": binding_model.parameters(), "lr": args.lr}, + ] + if args.optimizer == "SGD": + optimizer = optim.SGD(model_param_group, lr=args.lr, weight_decay=args.decay) + elif args.optimizer == "Adam": + optimizer = optim.Adam(model_param_group, lr=args.lr, weight_decay=args.decay) + + for e in range(args.epochs): + if args.verbose: + L = tqdm(loader) + else: + L = loader + + start_time = time.time() + accum_loss, accum_count = 0, 0 + + for batch in L: + batch = batch.to(device) + + protein_residue = batch.protein_residue + protein_pos_N = batch.protein_pos[batch.protein_mask_n] + protein_pos_Ca = batch.protein_pos[batch.protein_mask_ca] + protein_pos_C = batch.protein_pos[batch.protein_mask_c] + + peptide_residue = batch.peptide_residue + peptide_pos_N = batch.peptide_pos[batch.peptide_mask_n] + peptide_pos_Ca = batch.peptide_pos[batch.peptide_mask_ca] + peptide_pos_C = batch.peptide_pos[batch.peptide_mask_c] + + y = batch.energy + + y_pred = binding_model( + protein_residue, protein_pos_N, protein_pos_Ca, protein_pos_C, batch.protein_batch, + peptide_residue, peptide_pos_N, peptide_pos_Ca, peptide_pos_C, batch.peptide_batch, + ) + + loss = criterion(y, y_pred) + + optimizer.zero_grad() + loss.backward() + optimizer.step() + + accum_loss += loss.item() + accum_count += 1 + + print("epoch: {}\tloss pos: {:.5f}\t{:.3f}s".format(e, accum_loss / accum_count, time.time() - start_time)) + + save_model(save_best=False) \ No newline at end of file diff --git a/examples/downstream_Editing/step_01_editing_Galactica.py b/examples/downstream_Editing/step_01_editing_Galactica.py new file mode 100644 index 0000000..538b802 --- /dev/null +++ b/examples/downstream_Editing/step_01_editing_Galactica.py @@ -0,0 +1,184 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import string +import re + +import torch +import torch.nn as nn + +from transformers import BertModel, BertTokenizer, AutoTokenizer, OPTForCausalLM +from torch.utils.data import DataLoader + +from utils import ProteinDataset, ProteinSeqDataset, text_prompt_dict, load_oracle_evaluator, evaluate, analyze + + +def parse_Galatica_result(text_prompt, result): + result = result.replace(text_prompt, "") + result = result.split("[END_AMINO]")[0].strip() + result = result.split("\n")[0].replace("?", "") + + pattern = re.compile('[A-Z]{5,}') + parsed_results = pattern.findall(result) + if len(parsed_results) == 0: + print("invalid") + return "" + + result = parsed_results[0] + result = re.sub(r"[UZOB]", "X", result) + return result + + +@torch.no_grad() +def inference_Galactica(dataloader, mutation_number): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + galactica_tokenizer = AutoTokenizer.from_pretrained("facebook/galactica-1.3b") + galactica_model = OPTForCausalLM.from_pretrained("facebook/galactica-1.3b", device_map="auto") + + input_protein_sequence_list, edited_protein_sequence_list = [], [] + for batch_idx, batch in enumerate(L): + protein_sequence_batch = batch["protein_sequence"] + for protein_sequence in protein_sequence_batch: + # protein_sequence = protein_sequence.split(" ") + protein_sequence = ''.join(protein_sequence).replace(" ", "") + + text_prompt = "Given an input amino acid sequence [START_AMINO]{}[END_AMINO]. Can you {}, which needs to be similar to the input sequence? [START_AMINO]".format( + protein_sequence, text_prompt_dict[args.editing_task][args.text_prompt_id]) + text_ids = galactica_tokenizer(text_prompt, return_tensors="pt").input_ids.to("cuda") + + outputs = galactica_model.generate( + text_ids, + max_new_tokens=len(protein_sequence)+10, + do_sample=True, + top_p=0.9, + temperature=1.0, + use_cache=True, + top_k=5, + repetition_penalty=1.0, + length_penalty=1, + num_return_sequences=1, + ) + + output = outputs[0] + protein_sequence_answer = galactica_tokenizer.decode(output) + edited_protein_sequence = parse_Galatica_result(text_prompt, protein_sequence_answer) + if len(edited_protein_sequence) == 0: + continue + + input_protein_sequence_list.append(protein_sequence) + edited_protein_sequence_list.append(edited_protein_sequence) + + return input_protein_sequence_list, edited_protein_sequence_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=8) + parser.add_argument("--mutation_number", type=int, default=1) + + parser.add_argument("--editing_task", type=str, default="Villin") + parser.add_argument("--dataset_size", type=int, default=None) + parser.add_argument("--text_prompt_id", type=int, default=101) + + parser.add_argument("--output_folder", type=str, default=None) + parser.add_argument("--output_text_file_path", type=str, default=None) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + + args = parser.parse_args() + print("arguments", args) + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False) + elif args.protein_backbone_model == "ProtBERT_BFD": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False) + protein_dim = 1024 + + ##### load protein sequence + dataset_file_path = os.path.join(text_prompt_dict[args.editing_task]["data_folder"], "preprocessed_data.csv") + dataset = ProteinDataset( + dataset_file_path=dataset_file_path, + dataset_size=args.dataset_size, + protein_tokenizer=CLAP_protein_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + input_protein_sequence_list, edited_protein_sequence_list = inference_Galactica(dataloader, mutation_number=args.mutation_number) + + if args.output_folder is None: + exit() + + ##### Load pretrained model + eval_prediction_model, eval_protein_tokenizer = load_oracle_evaluator(args.editing_task, device) + + print('input:') + input_dataset = ProteinSeqDataset(input_protein_sequence_list, eval_protein_tokenizer, args.protein_max_sequence_len) + input_dataloader = DataLoader(input_dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + input_eval_list = evaluate(input_dataloader, eval_prediction_model, device, args) + file_path = os.path.join(args.output_folder, "{editing_task}_input.png".format(editing_task=args.editing_task)) + analyze(input_eval_list, args, file_path) + + print("output") + output_dataset = ProteinSeqDataset(edited_protein_sequence_list, eval_protein_tokenizer, args.protein_max_sequence_len) + output_dataloader = DataLoader(output_dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + output_eval_list = evaluate(output_dataloader, eval_prediction_model, device, args) + file_path = os.path.join(args.output_folder, "{editing_task}_output_{mutation_number}.png".format(editing_task=args.editing_task, mutation_number=args.mutation_number)) + analyze(output_eval_list, args, file_path) + + + if args.output_text_file_path is None: + args.output_text_file_path = os.path.join(args.output_folder, "step_01_editing.txt") + + f = open(args.output_text_file_path, 'w') + hit, total = 0, 0 + for input_protein, input_eval, edited_protein, output_eval in zip(input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, output_eval_list): + print('input,{},{}'.format(input_protein, input_eval), file=f) + print('output,{},{}'.format(edited_protein, output_eval), file=f) + + total += 1 + + if args.editing_task in ["alpha", "beta"]: + if args.text_prompt_id in [101]: + if output_eval > input_eval: + hit += 1 + elif args.text_prompt_id in [201]: + if output_eval < input_eval: + hit += 1 + + elif args.editing_task in ["Villin", "Pin1", "hYAP65"]: + if args.text_prompt_id in [101, 102]: + if output_eval < input_eval: + hit += 1 + elif args.text_prompt_id in [201, 202]: + if output_eval > input_eval: + hit += 1 + + hit_ratio = 100. * hit / total + print("hit: {}".format(hit)) + print("total: {}".format(total)) + print("hit ratio: {}".format(hit_ratio)) diff --git a/examples/downstream_Editing/step_01_editing_latent_interpolation.py b/examples/downstream_Editing/step_01_editing_latent_interpolation.py new file mode 100644 index 0000000..f6634bc --- /dev/null +++ b/examples/downstream_Editing/step_01_editing_latent_interpolation.py @@ -0,0 +1,386 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import re +import string + +import torch +import torch.nn as nn + +from transformers import AutoModel, AutoTokenizer, BertModel, BertTokenizer, T5Tokenizer +from torch.utils.data import DataLoader + +from ProteinDT.models import MultinomialDiffusion, T5Decoder, GaussianFacilitatorModel +from utils import slerp, ProteinDataset, ProteinSeqDataset, text_prompt_dict, load_oracle_evaluator, evaluate, analyze + + +def select_protein_list(candidate_protein_sequence_list, oracle_repr, B, protein_sequence_batch): + assert B * args.num_repeat == len(candidate_protein_sequence_list) + assert oracle_repr.size()[0] == B + + input_protein_sequence_list, edited_protein_sequence_list = [], [] + ##### get protein representation + parsed_protein_sequence_list = [] + for protein_sequence in candidate_protein_sequence_list: + protein_sequence = re.sub(r"[UZOB]", "X", protein_sequence) + protein_sequence = " ".join(protein_sequence) + parsed_protein_sequence_list.append(protein_sequence) + protein_sequence_encode = CLAP_protein_tokenizer(parsed_protein_sequence_list, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.to(device) + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.to(device) + protein_output = CLAP_protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + protein_repr_test = protein_output["pooler_output"] + protein_repr_test = CLAP_protein2latent_model(protein_repr_test) + assert protein_repr_test.size()[0] == B * args.num_repeat + + ##### select the sequences most similar to the input protein sequences + for condition_id in range(B): + start, end = condition_id * args.num_repeat, (condition_id + 1) * args.num_repeat + oracle_protein_repr = oracle_repr[condition_id] # hidden_dim + candidate_protein_repr = protein_repr_test[start:end] # num_repeat, hidden_dim + + similarity = torch.matmul(oracle_protein_repr, candidate_protein_repr.transpose(0, 1)) # (num_repeat) + optimal_id = torch.argmax(similarity) + optimal_id = start + optimal_id + input_protein_sequence_list.append(protein_sequence_batch[condition_id].replace(" ", "")) + edited_protein_sequence_list.append(candidate_protein_sequence_list[optimal_id]) + return input_protein_sequence_list, edited_protein_sequence_list + + +@torch.no_grad() +def inference(dataloader, theta, text_condition_repr, device): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + input_protein_sequence_list, edited_protein_sequence_list = [], [] + for batch_idx, batch in enumerate(L): + protein_sequence_batch = batch["protein_sequence"] + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + B = len(protein_sequence_batch) + + protein_output = CLAP_protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + CLAP_protein_repr = protein_output["pooler_output"] + CLAP_protein_repr = CLAP_protein2latent_model(CLAP_protein_repr) # [B, hidden_dim] + + text_repr_batch = text_condition_repr.expand(B, -1) # [B, hidden_dim] + + condition_repr = slerp(theta, CLAP_protein_repr, text_repr_batch) # [B, hidden_dim] + + if args.AR_condition_mode == "aggregated": + repeated_condition_repr = condition_repr.unsqueeze(1).expand(-1, args.num_repeat, -1) # [B, num_repeat, hidden_dim] + repeated_condition_repr = repeated_condition_repr.reshape(-1, args.condition_dim) # [B*num_repeat, hidden_dim] + + else: # args.AR_condition_mode == "expanded": + protein_output = CLAP_protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + condition_repr = condition_repr.unsqueeze(1) # [B, 1, hidden_dim] + CLAP_protein_token_repr = protein_output["last_hidden_state"] # [B, max_seq_len, hidden_dim___] + CLAP_protein_token_repr = CLAP_protein_token_repr[:, 1:, :] # [B, max_seq_len-1, hidden_dim___] + CLAP_protein_token_repr = CLAP_protein2latent_model(CLAP_protein_token_repr) # [B, max_seq_len-1, hidden_dim] + + condition_repr = torch.concat([condition_repr, CLAP_protein_token_repr], dim=1) # [B, max_seq_len, hidden_dim] + repeated_condition_repr = condition_repr.unsqueeze(1).expand(-1, args.num_repeat, -1, -1) # [B, num_repeat, max_seq_len, hidden_dim] + assert args.protein_max_sequence_len == repeated_condition_repr.size()[2] + repeated_condition_repr = repeated_condition_repr.reshape(-1, args.protein_max_sequence_len, args.condition_dim) # [B*num_repeat, max_seq_len, hidden_dim] + + if args.decoder_distribution in ["T5Decoder"]: + max_len = max(protein_sequence_attention_mask.sum(1)).item() + if args.AR_generation_mode == "01": + temperature = 1.0 + k = 40 + p = 0.9 + repetition_penalty = 1.0 + num_return_sequences = 1 + do_sample = True + num_beams = 1 + elif args.AR_generation_mode == "02": + temperature = 1.0 + k = 40 + p = 0.9 + repetition_penalty = 1.0 + num_return_sequences = 1 + do_sample = False + num_beams = 10 + protein_sequence_pred_ids = decoder_distribution_model.inference( + condition=repeated_condition_repr, protein_seq_attention_mask=None, max_seq_len=max_len, + temperature=temperature, k=k, p=p, repetition_penalty=repetition_penalty, num_return_sequences=num_return_sequences, do_sample=do_sample, num_beams=num_beams + ) + + else: + ##### add variable length + min_len = min(protein_sequence_attention_mask.sum(1)).item() + max_len = max(protein_sequence_attention_mask.sum(1)).item() + protein_seq_attention_mask = torch.zeros((B*args.num_repeat, args.protein_max_sequence_len), device=device) + for protein_seq_attention_mask_each in protein_seq_attention_mask: + valid_length = random.randint(min_len, max_len) + protein_seq_attention_mask_each[:valid_length] = 1 + protein_seq_attention_mask = protein_seq_attention_mask.bool() + + protein_sequence_output = decoder_distribution_model.inference( + condition=repeated_condition_repr, protein_seq_attention_mask=protein_seq_attention_mask, max_seq_len=args.protein_max_sequence_len, mode=args.SDE_sampling_mode) + + protein_sequence_pred_ids = torch.argmax(protein_sequence_output, dim=-1) # (B*num_repeat, max_seq_len) + + ##### truncate after index + for protein_sequence_pred_id in protein_sequence_pred_ids: + index = None + for pid, pred_id in enumerate(protein_sequence_pred_id): + if pred_id != protein_decoder_tokenizer.pad_token_id: + continue + index = pid + break + if index is not None: + protein_sequence_pred_id[index:] = protein_decoder_tokenizer.pad_token_id + + ##### clean-ups + candidate_protein_sequence_list = protein_decoder_tokenizer.batch_decode(sequences=protein_sequence_pred_ids, skip_special_tokens=True) + candidate_protein_sequence_list = [protein_sequence.replace(" ", "") for protein_sequence in candidate_protein_sequence_list] + + if args.oracle_mode == "protein": + oracle_repr = CLAP_protein_repr + elif args.oracle_mode == "text": + oracle_repr = text_repr_batch + input_protein_sequence_list_, edited_protein_sequence_list_ = select_protein_list( + candidate_protein_sequence_list=candidate_protein_sequence_list, oracle_repr=oracle_repr, B=B, protein_sequence_batch=protein_sequence_batch) + input_protein_sequence_list.extend(input_protein_sequence_list_) + edited_protein_sequence_list.extend(edited_protein_sequence_list_) + + return input_protein_sequence_list, edited_protein_sequence_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=8) + + parser.add_argument("--editing_task", type=str, default="BotNTB") + parser.add_argument("--dataset_size", type=int, default=None) + parser.add_argument("--text_prompt_id", type=int, default=101) + parser.add_argument("--theta", type=float, default=0.01) + parser.add_argument("--num_repeat", type=int, default=2) + + parser.add_argument("--pretrained_folder", type=str, default=None) + parser.add_argument("--step_04_folder", type=str, default=None) + parser.add_argument("--output_folder", type=str, default=None) + parser.add_argument("--output_text_file_path", type=str, default=None) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--condition_dim", type=int, default=256) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--text_max_sequence_len", type=int, default=512) + + parser.add_argument("--facilitator_distribution", type=str, default="Gaussian", choices=["Gaussian"]) + + parser.add_argument("--decoder_distribution", type=str, default="MultinomialDiffusion", choices=["T5Decoder", "MultinomialDiffusion"]) + + ##### for AR ##### + parser.add_argument("--AR_generation_mode", type=str, default="01", choices=["01", "02"]) + parser.add_argument("--AR_condition_mode", type=str, default="aggregated", choices=["aggregated", "expanded"]) + + ##### for SDE ##### + parser.add_argument("--hidden_dim", type=int, default=16) + parser.add_argument("--beta_min", type=float, default=0.1) + parser.add_argument("--beta_max", type=float, default=30) + parser.add_argument("--num_diffusion_timesteps", type=int, default=1000) + parser.add_argument("--SDE_type", type=str, default="VP") + parser.add_argument("--score_network_type", type=str, default="BertProtBFD") + parser.add_argument("--SDE_sampling_mode", type=str, default="simplified", choices=["simplified", "weighted"]) + + ##### for post-selection ##### + parser.add_argument("--oracle_mode", type=str, default="protein", choices=["protein", "text", "condition"]) + + args = parser.parse_args() + print("arguments", args) + assert args.pretrained_folder is not None + assert args.step_04_folder is not None + step_01_folder = args.pretrained_folder + step_02_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + step_03_folder = os.path.join(args.pretrained_folder, "step_03_Gaussian_10") + step_04_folder = args.step_04_folder + + assert args.SSL_emb_dim == args.condition_dim + if args.AR_condition_mode == "expanded": + assert args.decoder_distribution == "T5Decoder" + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False) + CLAP_protein_model = BertModel.from_pretrained("Rostlab/prot_bert") + elif args.protein_backbone_model == "ProtBERT_BFD": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False) + CLAP_protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd") + protein_dim = 1024 + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_protein_model.load_state_dict(state_dict) + + ##### Load pretrained text model + CLAP_text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + CLAP_text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_dim = 768 + input_model_path = os.path.join(args.pretrained_folder, "text_model.pth") + print("Loading text model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_text_model.load_state_dict(state_dict) + + ##### Load pretrained protein2latent model + CLAP_protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_protein2latent_model.load_state_dict(state_dict) + + ##### Load pretrained text2latent model + CLAP_text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "text2latent_model.pth") + print("Loading text2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_text2latent_model.load_state_dict(state_dict) + + ##### Load pretrained facilitator model + if args.facilitator_distribution == "Gaussian": + facilitator_distribution_model = GaussianFacilitatorModel(args.SSL_emb_dim) + input_model_path = os.path.join(step_03_folder, "facilitator_distribution_model.pth") + print("Loading facilitator_distribution model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + facilitator_distribution_model.load_state_dict(state_dict) + + if args.decoder_distribution in ["T5Decoder"]: + protein_decoder_tokenizer = T5Tokenizer.from_pretrained("Rostlab/prot_t5_xl_uniref50", do_lower_case=False, chache_dir="../../data/temp_pretrained_t5_base") + else: + protein_decoder_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../../data/temp_pretrained_PotBert") + # print("protein_decoder_tokenizer pad_token_id", protein_decoder_tokenizer.pad_token_id) + # print("protein_decoder_tokenizer sep_token_id", protein_decoder_tokenizer.sep_token_id) + # print("protein_decoder_tokenizer eos_token_id", protein_decoder_tokenizer.eos_token_id) + # print(CLAP_protein_tokenizer.get_vocab()) + # print(protein_decoder_tokenizer.get_vocab()) + + ##### Load pretrained decoder model + if args.decoder_distribution == "MultinomialDiffusion": + mask_id = 4 + decoder_distribution_model = MultinomialDiffusion( + hidden_dim=args.hidden_dim, + condition_dim=args.condition_dim, mask_id=mask_id, + beta_min=args.beta_min, beta_max=args.beta_max, num_diffusion_timesteps=args.num_diffusion_timesteps, + num_classes=protein_decoder_tokenizer.vocab_size, score_network_type=args.score_network_type) + elif args.decoder_distribution == "T5Decoder": + decoder_distribution_model = T5Decoder( + hidden_dim=args.condition_dim, + tokenizer=protein_decoder_tokenizer, + T5_model=args.score_network_type) + + model_file_path = os.path.join(step_04_folder, "decoder_distribution_model.pth") + print("Loading decoder_distribution model from {}...".format(model_file_path)) + state_dict = torch.load(model_file_path, map_location='cpu') + decoder_distribution_model.load_state_dict(state_dict) + + CLAP_protein_model = CLAP_protein_model.to(device) + CLAP_protein_model.eval() + CLAP_text_model = CLAP_text_model.to(device) + CLAP_text_model.eval() + CLAP_protein2latent_model = CLAP_protein2latent_model.to(device) + CLAP_protein2latent_model.eval() + CLAP_text2latent_model = CLAP_text2latent_model.to(device) + CLAP_text2latent_model.eval() + facilitator_distribution_model = facilitator_distribution_model.to(device) + facilitator_distribution_model.eval() + decoder_distribution_model.to(device) + decoder_distribution_model.eval() + + ##### obtain text sequence representation + text_prompt = text_prompt_dict[args.editing_task][args.text_prompt_id] + print("===== the text prompt is : {} =====".format(text_prompt)) + text_prompt_sequence_list = [text_prompt] + text_prompt_sequence_encode = CLAP_text_tokenizer(text_prompt_sequence_list, truncation=True, max_length=args.text_max_sequence_len, padding='max_length', return_tensors='pt') + text_prompt_sequence_input_ids = text_prompt_sequence_encode.input_ids.to(device) + text_prompt_sequence_attention_mask = text_prompt_sequence_encode.attention_mask.to(device) + description_output = CLAP_text_model(text_prompt_sequence_input_ids, text_prompt_sequence_attention_mask) + text_prompt_repr = description_output["pooler_output"] + text_prompt_repr = CLAP_text2latent_model(text_prompt_repr) # [1, hidden_dim] + text_prompt_condition_repr = facilitator_distribution_model.inerence(text_repr=text_prompt_repr) # [1, hidden_dim] + + ##### load protein sequence + dataset_file_path = os.path.join(text_prompt_dict[args.editing_task]["data_folder"], "preprocessed_data.csv") + dataset = ProteinDataset( + dataset_file_path=dataset_file_path, + dataset_size=args.dataset_size, + protein_tokenizer=CLAP_protein_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + input_protein_sequence_list, edited_protein_sequence_list = inference(dataloader, args.theta, text_prompt_condition_repr, device) + + if args.output_folder is None: + exit() + + ##### Load pretrained model + eval_prediction_model, eval_protein_tokenizer = load_oracle_evaluator(args.editing_task, device) + + print('input:') + input_dataset = ProteinSeqDataset(input_protein_sequence_list, eval_protein_tokenizer, args.protein_max_sequence_len) + input_dataloader = DataLoader(input_dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + input_eval_list = evaluate(input_dataloader, eval_prediction_model, device, args).squeeze() + file_path = os.path.join(args.output_folder, "{editing_task}_input.png".format(editing_task=args.editing_task)) + analyze(input_eval_list, args, file_path) + + print("output: with theta {}".format(args.theta)) + output_dataset = ProteinSeqDataset(edited_protein_sequence_list, eval_protein_tokenizer, args.protein_max_sequence_len) + output_dataloader = DataLoader(output_dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + output_eval_list = evaluate(output_dataloader, eval_prediction_model, device, args).squeeze() + file_path = os.path.join(args.output_folder, "{editing_task}_output_{theta}.png".format(editing_task=args.editing_task, theta=args.theta)) + analyze(output_eval_list, args, file_path) + + if args.output_text_file_path is None: + args.output_text_file_path = os.path.join(args.output_folder, "step_01_editing.txt") + + f = open(args.output_text_file_path, 'w') + hit, total = 0, 0 + for input_protein, input_eval, edited_protein, output_eval in zip(input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, output_eval_list): + print('input,{},{}'.format(input_protein, input_eval), file=f) + print('output,{},{}'.format(edited_protein, output_eval), file=f) + + total += 1 + + if args.editing_task in ["alpha", "beta"]: + if args.text_prompt_id in [101]: + if output_eval > input_eval: + hit += 1 + elif args.text_prompt_id in [201]: + if output_eval < input_eval: + hit += 1 + + elif args.editing_task in ["Villin", "Pin1", "hYAP65"]: + if args.text_prompt_id in [101, 102]: + if output_eval < input_eval: + hit += 1 + elif args.text_prompt_id in [201, 202]: + if output_eval > input_eval: + hit += 1 + + hit_ratio = 100. * hit / total + print("hit: {}".format(hit)) + print("total: {}".format(total)) + print("hit ratio: {}".format(hit_ratio)) diff --git a/examples/downstream_Editing/step_01_editing_latent_optimization.py b/examples/downstream_Editing/step_01_editing_latent_optimization.py new file mode 100644 index 0000000..291e62b --- /dev/null +++ b/examples/downstream_Editing/step_01_editing_latent_optimization.py @@ -0,0 +1,431 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import re +import string +import math +import time + +import torch +import torch.nn as nn +import torch.optim as optim + +from transformers import AutoModel, AutoTokenizer, BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from ProteinDT.models import GaussianFacilitatorModel, RNNPrediction +from utils import ProteinDataset, ProteinSeqDataset, text_prompt_dict, load_oracle_evaluator, evaluate, analyze + + +def finetune_AE(dataloader, protein_model, CLAP_protein2latent_model, protein_tokenizer, optimizer, CE_criterion): + scaler = torch.cuda.amp.GradScaler() + auto_encoding_model.train() + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + start_time = time.time() + accum_AE_loss, accum_decoding_loss = 0, 0 + for batch_idx, batch in enumerate(L): + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + + with torch.no_grad(): + protein_output = protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + token_repr = protein_output["last_hidden_state"] # [B, max_seq_len, 1024] + token_repr = CLAP_protein2latent_model(token_repr) # [B, max_seq_len, SSL_emb_dim] + + with torch.cuda.amp.autocast(): + logit = auto_encoding_model(token_repr) # [B, max_seq_len, vocab_size] + + target_protein_seq_input_ids = protein_sequence_input_ids # [B, max_sequence_len] + target_protein_seq_attention_mask = protein_sequence_attention_mask # [B, max_sequence_len] + flattened_logits = torch.flatten(logit, start_dim=0, end_dim=1) # [B * max_sequence_len, vocab_size] + flattened_ids = torch.flatten(target_protein_seq_input_ids, start_dim=0, end_dim=1) # [B * max_sequence_len] + flattened_mask = torch.flatten(target_protein_seq_attention_mask, start_dim=0, end_dim=1) # [B * max_sequence_len] + total_loss = CE_criterion(flattened_logits, flattened_ids) # [B * max_sequence_len] + masked_loss = total_loss * flattened_mask # [B * max_sequence_len] + total_loss = torch.mean(total_loss) + masked_loss = masked_loss.sum() / flattened_mask.sum() + + loss = (total_loss + masked_loss) / 2 + + optimizer.zero_grad() + scaler.scale(loss).backward() + scaler.step(optimizer) + scaler.update() + + accum_AE_loss += loss.item() + + accum_AE_loss /= len(L) + accum_decoding_loss /= len(L) + global optimal_loss + temp_loss = accum_AE_loss + if temp_loss < optimal_loss: + optimal_loss = temp_loss + print("SDE Loss: {:.5f}\tDecoding Loss: {:.5f}\tTime: {:.5f}".format(accum_AE_loss, accum_decoding_loss, time.time() - start_time)) + return + + +def get_lr(t, initial_lr, rampdown=0.25, rampup=0.05): + lr_ramp = min(1, (1 - t) / rampdown) + lr_ramp = 0.5 - 0.5 * math.cos(lr_ramp * math.pi) + lr_ramp = lr_ramp * min(1, t / rampup) + return initial_lr * lr_ramp + + +@torch.no_grad() +def select_protein_list(candidate_protein_sequence_list, oracle_repr, B, protein_sequence_batch): + assert B * args.num_repeat == len(candidate_protein_sequence_list) + assert oracle_repr.size()[0] == B + + input_protein_sequence_list, edited_protein_sequence_list = [], [] + ##### get protein representation + parsed_protein_sequence_list = [] + for protein_sequence in candidate_protein_sequence_list: + protein_sequence = re.sub(r"[UZOB]", "X", protein_sequence) + protein_sequence = " ".join(protein_sequence) + parsed_protein_sequence_list.append(protein_sequence) + protein_sequence_encode = CLAP_protein_tokenizer(parsed_protein_sequence_list, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.to(device) + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.to(device) + protein_output = CLAP_protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + protein_repr_test = protein_output["pooler_output"] + protein_repr_test = CLAP_protein2latent_model(protein_repr_test) + assert protein_repr_test.size()[0] == B * args.num_repeat + + ##### select the sequences most similar to the input protein sequences + for condition_id in range(B): + start, end = condition_id * args.num_repeat, (condition_id + 1) * args.num_repeat + oracle_protein_repr = oracle_repr[condition_id] # hidden_dim + candidate_protein_repr = protein_repr_test[start:end] # num_repeat, hidden_dim + + similarity = torch.matmul(oracle_protein_repr, candidate_protein_repr.transpose(0, 1)) # (num_repeat) + optimal_id = torch.argmax(similarity) + optimal_id = start + optimal_id + input_protein_sequence_list.append(protein_sequence_batch[condition_id].replace(" ", "")) + edited_protein_sequence_list.append(candidate_protein_sequence_list[optimal_id]) + return input_protein_sequence_list, edited_protein_sequence_list + + +def latent_optimization(protein_sequence_input_ids, latent_code_init, text_CLAP_repr): + repeated_latent_code_init = latent_code_init.unsqueeze(0).expand(args.num_repeat, -1, -1, -1) # [B, num_repeat, max_seq_len, hidden_dim] + repeated_latent_code_init = repeated_latent_code_init.flatten(0, 1) # [num_repeat*B, max_seq_len, hidden_dim] + + repeated_protein_sequence_input_ids = protein_sequence_input_ids.unsqueeze(1).expand(-1, args.num_repeat, -1) # [B, num_repeat] + repeated_protein_sequence_input_ids = repeated_protein_sequence_input_ids.flatten(0, 1) # [num_repeat*B, max_seq_len] + + random_noise = torch.randn(repeated_latent_code_init.size()).to(device) / args.temperature # [num_repeat*B, max_seq_len, hidden_dim] + latent_code = repeated_latent_code_init.detach().clone() + random_noise + latent_code.requires_grad = True + optimizer = optim.Adam([latent_code], lr=args.lr) + + if args.verbose: + current_L = tqdm(range(args.epochs)) + else: + current_L = range(args.epochs) + + for i in current_L: + t = i / args.epochs + lr = get_lr(t, args.lr) + optimizer.param_groups[0]["lr"] = lr + + protein_repr = CLAP_protein_model.pooler(latent_code) # [num_repeat*B, hidden_dim] + protein_repr = CLAP_protein2latent_model(protein_repr) # [num_repeat*B, hidden_dim] + + loss_01 = ((protein_repr - text_CLAP_repr) ** 2).mean() + loss_02 = ((repeated_latent_code_init - latent_code) ** 2).mean() + + loss = (args.lambda_value) * loss_01 + (1 - args.lambda_value) * loss_02 + + optimizer.zero_grad() + loss.backward(retain_graph=True) + optimizer.step() + latent_code = latent_code.detach() + + # TODO + latent_code = CLAP_protein2latent_model(latent_code) # [num_repeat*B, max_seq_len, hidden_dim] + protein_sequence_output = auto_encoding_model(latent_code) # [num_repeat*B, max_seq_len, vocab_size] + return protein_sequence_output + + +def inference(dataloader, text_prompt_CLAP_repr, device): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + input_protein_sequence_list, edited_protein_sequence_list = [], [] + for batch_idx, batch in enumerate(L): + protein_sequence_batch = batch["protein_sequence"] + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + # print("protein_sequence_batch", protein_sequence_batch) + + B = protein_sequence_input_ids.size()[0] + text_CLAP_repr = text_prompt_CLAP_repr.expand(B*args.num_repeat, -1) # [B, hidden_dim] + text_CLAP_repr = text_CLAP_repr.detach() + + with torch.no_grad(): + protein_output = CLAP_protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + latent_code_init = protein_output["last_hidden_state"] # [B, max_seq_len, hidden_dim] + protein_CLAP_repr = protein_output["pooler_output"] + protein_CLAP_repr = CLAP_protein2latent_model(protein_CLAP_repr) # [B, hidden_dim] + + protein_sequence_output = latent_optimization(protein_sequence_input_ids, latent_code_init, text_CLAP_repr) + protein_sequence_output = protein_sequence_output.detach() + + protein_sequence_pred_ids = torch.argmax(protein_sequence_output, dim=-1) # (B*num_repeat, max_seq_len) + + # ##### truncate after index + # for protein_sequence_pred_id in protein_sequence_pred_ids: + # index = None + # for pid, pred_id in enumerate(protein_sequence_pred_id): + # if pred_id != protein_decoder_tokenizer.pad_token_id: + # continue + # index = pid + # break + # if index is not None: + # protein_sequence_pred_id[index:] = protein_decoder_tokenizer.pad_token_id + + ##### clean-ups + candidate_protein_sequence_list = protein_decoder_tokenizer.batch_decode(sequences=protein_sequence_pred_ids, skip_special_tokens=True) + candidate_protein_sequence_list = [protein_sequence.replace(" ", "") for protein_sequence in candidate_protein_sequence_list] + print("candidate_protein_sequence_list", len(candidate_protein_sequence_list)) + # print("candidate_protein_sequence_list", candidate_protein_sequence_list) + + if args.oracle_mode == "protein": + oracle_repr = protein_CLAP_repr + elif args.oracle_mode == "text": + oracle_repr = text_prompt_CLAP_repr.expand(B, -1) # [B, hidden_dim] + input_protein_sequence_list_, edited_protein_sequence_list_ = select_protein_list( + candidate_protein_sequence_list=candidate_protein_sequence_list, oracle_repr=oracle_repr, B=B, protein_sequence_batch=protein_sequence_batch) + input_protein_sequence_list.extend(input_protein_sequence_list_) + edited_protein_sequence_list.extend(edited_protein_sequence_list_) + + return input_protein_sequence_list, edited_protein_sequence_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=8) + parser.add_argument("--lr", type=float, default=0.1) + parser.add_argument("--epochs", type=int, default=100) + parser.add_argument("--temperature", type=float, default=0.5) + + parser.add_argument("--AE_lr", type=float, default=5e-4) + parser.add_argument("--AE_epochs", type=int, default=50) + parser.add_argument("--AE_decay", type=float, default=0) + + parser.add_argument("--editing_task", type=str, default="Villin") + parser.add_argument("--dataset_size", type=int, default=None) + parser.add_argument("--text_prompt_id", type=int, default=101) + parser.add_argument("--lambda_value", type=float, default=0.1) + parser.add_argument("--num_repeat", type=int, default=2) + + parser.add_argument("--pretrained_folder", type=str, default=None) + parser.add_argument("--output_folder", type=str, default=None) + parser.add_argument("--output_text_file_path", type=str, default=None) + parser.add_argument("--step_05_folder", type=str, default="step_05_AE_test") + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--condition_dim", type=int, default=256) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) #50 + parser.add_argument("--text_max_sequence_len", type=int, default=512) #50 + + parser.add_argument("--facilitator_distribution", type=str, default="Gaussian", choices=["Gaussian"]) + + ##### for post-selection ##### + parser.add_argument("--oracle_mode", type=str, default="protein", choices=["protein", "text"]) + + args = parser.parse_args() + print("arguments", args) + assert args.pretrained_folder is not None + assert args.step_05_folder is not None + step_01_folder = args.pretrained_folder + step_02_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + step_03_folder = os.path.join(args.pretrained_folder, "step_03_Gaussian_10") + step_05_folder = args.step_05_folder + + assert args.SSL_emb_dim == args.condition_dim + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False) + CLAP_protein_model = BertModel.from_pretrained("Rostlab/prot_bert") + elif args.protein_backbone_model == "ProtBERT_BFD": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False) + CLAP_protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd") + protein_dim = 1024 + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_protein_model.load_state_dict(state_dict) + + ##### Load pretrained text model + CLAP_text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + CLAP_text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_dim = 768 + input_model_path = os.path.join(args.pretrained_folder, "text_model.pth") + print("Loading text model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_text_model.load_state_dict(state_dict) + + ##### Load pretrained protein2latent model + CLAP_protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_protein2latent_model.load_state_dict(state_dict) + + ##### Load pretrained text2latent model + CLAP_text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "text2latent_model.pth") + print("Loading text2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_text2latent_model.load_state_dict(state_dict) + + ##### Load pretrained facilitator model + if args.facilitator_distribution == "Gaussian": + facilitator_distribution_model = GaussianFacilitatorModel(args.SSL_emb_dim) + input_model_path = os.path.join(step_03_folder, "facilitator_distribution_model.pth") + print("Loading facilitator_distribution model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + facilitator_distribution_model.load_state_dict(state_dict) + + protein_decoder_tokenizer = CLAP_protein_tokenizer + print("protein_decoder_tokenizer pad_token_id", protein_decoder_tokenizer.pad_token_id) + print("protein_decoder_tokenizer sep_token_id", protein_decoder_tokenizer.sep_token_id) + print("protein_decoder_tokenizer eos_token_id", protein_decoder_tokenizer.eos_token_id) + + ##### Load prediction head + auto_encoding_model = nn.Linear(args.SSL_emb_dim, CLAP_protein_tokenizer.vocab_size) + auto_encoding_model = RNNPrediction(args.SSL_emb_dim, CLAP_protein_tokenizer.vocab_size) + input_model_path = os.path.join(step_05_folder, "AE_model.pth") + print("Loading auto_encoding_model model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + auto_encoding_model.load_state_dict(state_dict) + + CLAP_protein_model = CLAP_protein_model.to(device) + CLAP_protein_model.eval() + CLAP_text_model = CLAP_text_model.to(device) + CLAP_text_model.eval() + CLAP_protein2latent_model = CLAP_protein2latent_model.to(device) + CLAP_protein2latent_model.eval() + CLAP_text2latent_model = CLAP_text2latent_model.to(device) + CLAP_text2latent_model.eval() + facilitator_distribution_model = facilitator_distribution_model.to(device) + facilitator_distribution_model.eval() + auto_encoding_model = auto_encoding_model.to(device) + auto_encoding_model.eval() + + ##### obtain text sequence representation + text_prompt = text_prompt_dict[args.editing_task][args.text_prompt_id] + print("===== the text prompt is : {} =====".format(text_prompt)) + text_prompt_sequence_list = [text_prompt] + text_prompt_sequence_encode = CLAP_text_tokenizer(text_prompt_sequence_list, truncation=True, max_length=args.text_max_sequence_len, padding='max_length', return_tensors='pt') + text_prompt_sequence_input_ids = text_prompt_sequence_encode.input_ids.to(device) + text_prompt_sequence_attention_mask = text_prompt_sequence_encode.attention_mask.to(device) + description_output = CLAP_text_model(text_prompt_sequence_input_ids, text_prompt_sequence_attention_mask) + text_prompt_repr = description_output["pooler_output"] + text_prompt_repr = CLAP_text2latent_model(text_prompt_repr) # [1, hidden_dim] + text_prompt_CLAP_repr = facilitator_distribution_model.inerence(text_repr=text_prompt_repr) # [1, hidden_dim] + + ##### load protein sequence + dataset_file_path = os.path.join(text_prompt_dict[args.editing_task]["data_folder"], "preprocessed_data.csv") + dataset = ProteinDataset( + dataset_file_path=dataset_file_path, + dataset_size=args.dataset_size, + protein_tokenizer=CLAP_protein_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=16, shuffle=True, num_workers=args.num_workers) + + optimal_loss = 1e10 + auto_encoding_model.train() + model_param_group = [{"params": auto_encoding_model.parameters(), "lr": args.AE_lr}] + CE_criterion = nn.CrossEntropyLoss() + optimizer = optim.Adam(model_param_group, weight_decay=args.AE_decay) + optimal_loss = 1e10 + print("========== start finetuning AE ==========") + for _ in range(args.AE_epochs): + finetune_AE(dataloader, CLAP_protein_model, CLAP_protein2latent_model, CLAP_protein_tokenizer, optimizer, CE_criterion) + print("========== done finetuning AE ==========") + auto_encoding_model.eval() + print("\n\n\n") + + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + input_protein_sequence_list, edited_protein_sequence_list = inference(dataloader, text_prompt_CLAP_repr, device) + + if args.output_folder is None: + exit() + + ##### Load pretrained model + eval_prediction_model, eval_protein_tokenizer = load_oracle_evaluator(args.editing_task, device) + + print('input:') + input_dataset = ProteinSeqDataset(input_protein_sequence_list, eval_protein_tokenizer, args.protein_max_sequence_len) + input_dataloader = DataLoader(input_dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + input_eval_list = evaluate(input_dataloader, eval_prediction_model, device, args).squeeze() + file_path = os.path.join(args.output_folder, "{editing_task}_input.png".format(editing_task=args.editing_task)) + analyze(input_eval_list, args, file_path) + + print("output: with lambda_value {}".format(args.lambda_value)) + output_dataset = ProteinSeqDataset(edited_protein_sequence_list, eval_protein_tokenizer, args.protein_max_sequence_len) + output_dataloader = DataLoader(output_dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + output_eval_list = evaluate(output_dataloader, eval_prediction_model, device, args).squeeze() + file_path = os.path.join(args.output_folder, "{editing_task}_output_{lambda_value}.png".format(editing_task=args.editing_task, lambda_value=args.lambda_value)) + analyze(output_eval_list, args, file_path) + + if args.output_text_file_path is None: + args.output_text_file_path = os.path.join(args.output_folder, "step_01_editing.txt") + + f = open(args.output_text_file_path, 'w') + hit, total = 0, 0 + for input_protein, input_eval, edited_protein, output_eval in zip(input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, output_eval_list): + print('input,{},{}'.format(input_protein, input_eval), file=f) + print('output,{},{}'.format(edited_protein, output_eval), file=f) + + total += 1 + + if args.editing_task in ["alpha", "beta"]: + if args.text_prompt_id in [101]: + if output_eval > input_eval: + hit += 1 + elif args.text_prompt_id in [201]: + if output_eval < input_eval: + hit += 1 + + elif args.editing_task in ["Villin", "Pin1", "hYAP65"]: + if args.text_prompt_id in [101, 102]: + if output_eval < input_eval: + hit += 1 + elif args.text_prompt_id in [201, 202]: + if output_eval > input_eval: + hit += 1 + + hit_ratio = 100. * hit / total + print("hit: {}".format(hit)) + print("total: {}".format(total)) + print("hit ratio: {}".format(hit_ratio)) diff --git a/examples/downstream_Editing/step_01_evaluate_stability.py b/examples/downstream_Editing/step_01_evaluate_stability.py new file mode 100644 index 0000000..a4f2f5d --- /dev/null +++ b/examples/downstream_Editing/step_01_evaluate_stability.py @@ -0,0 +1,229 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import string +import re + +import torch +import torch.nn as nn + +from transformers import BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from utils import ProteinDataset, ProteinSeqDataset, text_prompt_dict, load_oracle_evaluator, evaluate, analyze + + +from transformers import AutoTokenizer, EsmForProteinFolding +from transformers.models.esm.openfold_utils.protein import to_pdb, Protein as OFProtein +from transformers.models.esm.openfold_utils.feats import atom14_to_atom37 + + +@torch.no_grad() +def save_PDB_list(PDB_list, idx_list, PDB_output_folder): + for PDB, idx in zip(PDB_list, idx_list): + file_name = os.path.join(PDB_output_folder, "{}.txt".format(idx)) + f = open(file_name, "w") + f.write("".join(PDB)) + return + + +def convert_outputs_to_pdb(outputs): + final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs) + outputs = {k: v.to("cpu").numpy() for k, v in outputs.items()} + final_atom_positions = final_atom_positions.cpu().numpy() + final_atom_mask = outputs["atom37_atom_exists"] + pdbs = [] + for i in range(outputs["aatype"].shape[0]): + aa = outputs["aatype"][i] + pred_pos = final_atom_positions[i] + mask = final_atom_mask[i] + resid = outputs["residue_index"][i] + 1 + pred = OFProtein( + aatype=aa, + atom_positions=pred_pos, + atom_mask=mask, + residue_index=resid, + b_factors=outputs["plddt"][i], + chain_index=outputs["chain_index"][i] if "chain_index" in outputs else None, + ) + pdb = to_pdb(pred) + pdbs.append(pdb) + return pdbs + + +@torch.no_grad() +def evaluate_folding(protein_sequence_list): + PDB_data_list, idx_list, plddt_value_list = [], [], [] + for idx, protein_sequence in enumerate(protein_sequence_list): + print("protein_sequence", protein_sequence) + + tokenized_input = folding_tokenizer(protein_sequence, return_tensors="pt", add_special_tokens=False)['input_ids'] + tokenized_input = tokenized_input.cuda() + + output = folding_model(tokenized_input) + plddt_value = output["plddt"].squeeze(0) + tokenized_input = tokenized_input.squeeze(0) + + plddt_value_total = 0 + L = plddt_value.shape[0] + for i in range(L): + plddt_value_total += plddt_value[i][tokenized_input[i]] + plddt_value_mean = (plddt_value_total / L).item() + + PDB_list = convert_outputs_to_pdb(output) + + PDB_data_list.extend(PDB_list) + idx_list.append(idx) + plddt_value_list.append(plddt_value_mean) + + return PDB_data_list, idx_list, plddt_value_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=8) + parser.add_argument("--mutation_number", type=int, default=1) + + parser.add_argument("--editing_task", type=str, default="Villin") + parser.add_argument("--dataset_size", type=int, default=None) + parser.add_argument("--text_prompt_id", type=int, default=101) + + parser.add_argument("--output_folder", type=str, default=None) + parser.add_argument("--output_text_file_path", type=str, default=None) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + + args = parser.parse_args() + print("arguments", args) + + assert args.editing_task in ["Villin", "Pin1", "hYAP65"] + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + folding_tokenizer = AutoTokenizer.from_pretrained("facebook/esmfold_v1") + folding_model = EsmForProteinFolding.from_pretrained("facebook/esmfold_v1", low_cpu_mem_usage=True).to(device) + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False) + elif args.protein_backbone_model == "ProtBERT_BFD": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False) + protein_dim = 1024 + + ##### load protein sequence + dataset_file_path = os.path.join(text_prompt_dict[args.editing_task]["data_folder"], "preprocessed_data.csv") + dataset = ProteinDataset( + dataset_file_path=dataset_file_path, + dataset_size=args.dataset_size, + protein_tokenizer=CLAP_protein_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + if args.output_text_file_path is None: + args.output_text_file_path = os.path.join(args.output_folder, "step_01_editing.txt") + + f = open(args.output_text_file_path, "r") + input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, edited_eval_list = [], [], [], [] + for line in f.readlines(): + if line.startswith("input"): + line = line.strip().split(",") + input_protein_sequence_list.append(line[1]) + value = line[2].replace("[", "").replace("]", "") + input_eval_list.append(float(value)) + elif line.startswith("output"): + line = line.strip().split(",") + edited_protein_sequence = line[1] + edited_protein_sequence = re.sub(r"[UZOB]", "X", edited_protein_sequence) + edited_protein_sequence_list.append(edited_protein_sequence) + value = line[2].replace("[", "").replace("]", "") + edited_eval_list.append(float(value)) + + neo_input_protein_sequence_list, neo_input_eval_list, neo_edited_protein_sequence_list, neo_edited_eval_list = [], [], [], [] + for a,b,c,d in zip(input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, edited_eval_list): + if len(c) == 0: + continue + neo_input_protein_sequence_list.append(a) + neo_input_eval_list.append(b) + neo_edited_protein_sequence_list.append(c) + neo_edited_eval_list.append(d) + input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, edited_eval_list = neo_input_protein_sequence_list, neo_input_eval_list, neo_edited_protein_sequence_list, neo_edited_eval_list + + input_PDB_list, idx_list, input_plddt_list = evaluate_folding(input_protein_sequence_list) + PDB_output_folder = os.path.join(args.output_folder, "input_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + save_PDB_list(input_PDB_list, idx_list, PDB_output_folder) + + output_PDB_list, idx_list, output_plddt_list = evaluate_folding(edited_protein_sequence_list) + PDB_output_folder = os.path.join(args.output_folder, "output_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + save_PDB_list(output_PDB_list, idx_list, PDB_output_folder) + + ##### compare + evaluation_output_file_path = os.path.join(args.output_folder, "step_01_evaluate.txt") + f = open(evaluation_output_file_path, 'w') + eval_hit, plddt_hit, total = 0, 0, 0 + for input_protein, input_eval, input_plddt, edited_protein, output_eval, output_plddt in zip(input_protein_sequence_list, input_eval_list, input_plddt_list, edited_protein_sequence_list, edited_eval_list, output_plddt_list): + print('input,{},{},{}'.format(input_protein, input_eval, input_plddt), file=f) + print('output,{},{},{}'.format(edited_protein, output_eval, output_plddt), file=f) + + total += 1 + + if args.text_prompt_id in [101, 102]: + if output_eval > input_eval: + eval_hit += 1 + if output_plddt > input_plddt: + plddt_hit += 1 + elif args.text_prompt_id in [201, 202]: + if output_eval < input_eval: + eval_hit += 1 + if output_plddt < input_plddt: + plddt_hit += 1 + + if total > 0: + eval_hit_ratio = 100. * eval_hit / total + print("#1 eval hit: {}".format(eval_hit)) + print("#1 eval total: {}".format(total)) + print("#1 eval hit ratio: {}".format(eval_hit_ratio)) + + plddt_hit_ratio = 100. * plddt_hit / total + print("#1 pLDDT hit: {}".format(plddt_hit)) + print("#1 pLDDT total: {}".format(total)) + print("#1 pLDDT hit ratio: {}".format(plddt_hit_ratio)) + + total = len(dataset) + eval_hit_ratio = 100. * eval_hit / total + print("eval hit: {}".format(eval_hit)) + print("eval total: {}".format(total)) + print("eval hit ratio: {}".format(eval_hit_ratio)) + + plddt_hit_ratio = 100. * plddt_hit / total + print("pLDDT hit: {}".format(plddt_hit)) + print("pLDDT total: {}".format(total)) + print("pLDDT hit ratio: {}".format(plddt_hit_ratio)) + + """ + ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_06_AE_1e-3_3/downstream_Editing_latent_optimization/Villin_prompt_101_lambda_0.1_num_repeat_16_oracle_text_T_2 + + python step_01_evaluate_stability.py --num_workers=0 --batch_size=16 --editing_task=Villin --text_prompt_id=101 --output_folder=../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_06_AE_1e-3_3/downstream_Editing_latent_optimization/Villin_prompt_101_lambda_0.1_num_repeat_16_oracle_text_T_2 --output_text_file_path=../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_06_AE_1e-3_3/downstream_Editing_latent_optimization/Villin_prompt_101_lambda_0.1_num_repeat_16_oracle_text_T_2/step_01_editing.txt + + + python step_01_evaluate_stability.py --num_workers=0 --batch_size=16 --editing_task=hYAP65 --text_prompt_id=102 --output_folder=../../output/downstream_Editing/Galactica/hYAP65_text_prompt_id_102 --output_text_file_path=../../output/downstream_Editing/Galactica/hYAP65_text_prompt_id_102/step_01_editing.txt + """ diff --git a/examples/downstream_Editing/step_01_evaluate_structure.py b/examples/downstream_Editing/step_01_evaluate_structure.py new file mode 100644 index 0000000..b9da823 --- /dev/null +++ b/examples/downstream_Editing/step_01_evaluate_structure.py @@ -0,0 +1,257 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import string +import mdtraj +import re + +import torch +import torch.nn as nn + +from transformers import BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from utils import ProteinDataset, ProteinSeqDataset, text_prompt_dict, load_oracle_evaluator, evaluate, analyze + +from transformers import AutoTokenizer, EsmForProteinFolding +from transformers.models.esm.openfold_utils.protein import to_pdb, Protein as OFProtein +from transformers.models.esm.openfold_utils.feats import atom14_to_atom37 + + +@torch.no_grad() +def save_and_evaluate_PDB_list(PDB_list, idx_list, PDB_output_folder): + DSSP_list = [] + valid_idx_set = set() + for PDB, idx in zip(PDB_list, idx_list): + file_name = os.path.join(PDB_output_folder, "{}.pdb".format(idx)) + f = open(file_name, "w") + f.write("".join(PDB)) + f.flush() + f.close() + + try: + # MDtraj + traj = mdtraj.load(file_name) + # SS calculation + pdb_ss = mdtraj.compute_dssp(traj, simplified=True)[0] # (L, ) + + ss_count = { + 'alpha': np.sum(pdb_ss == 'H'), + 'beta': np.sum(pdb_ss == 'E'), + } + print("ss_count", ss_count) + DSSP_list.append(ss_count) + valid_idx_set.add(idx) + except Exception as e: + print(f'[Warning] Mdtraj failed with error {e}') + return DSSP_list, valid_idx_set + + +def convert_outputs_to_pdb(outputs): + final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs) + outputs = {k: v.to("cpu").numpy() for k, v in outputs.items()} + final_atom_positions = final_atom_positions.cpu().numpy() + final_atom_mask = outputs["atom37_atom_exists"] + pdbs = [] + for i in range(outputs["aatype"].shape[0]): + aa = outputs["aatype"][i] + pred_pos = final_atom_positions[i] + mask = final_atom_mask[i] + resid = outputs["residue_index"][i] + 1 + pred = OFProtein( + aatype=aa, + atom_positions=pred_pos, + atom_mask=mask, + residue_index=resid, + b_factors=outputs["plddt"][i], + chain_index=outputs["chain_index"][i] if "chain_index" in outputs else None, + ) + pdb = to_pdb(pred) + pdbs.append(pdb) + return pdbs + + +@torch.no_grad() +def evaluate_folding(protein_sequence_list): + PDB_data_list, idx_list = [], [] + for idx, protein_sequence in enumerate(tqdm(protein_sequence_list)): + + tokenized_input = folding_tokenizer(protein_sequence, return_tensors="pt", add_special_tokens=False)['input_ids'] + tokenized_input = tokenized_input.cuda() + + output = folding_model(tokenized_input) + + PDB_list = convert_outputs_to_pdb(output) + + PDB_data_list.extend(PDB_list) + idx_list.append(idx) + + return PDB_data_list, idx_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=8) + parser.add_argument("--mutation_number", type=int, default=1) + + parser.add_argument("--editing_task", type=str, default="alpha") + parser.add_argument("--dataset_size", type=int, default=None) + parser.add_argument("--text_prompt_id", type=int, default=101) + + parser.add_argument("--output_folder", type=str, default=None) + parser.add_argument("--output_text_file_path", type=str, default=None) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + + args = parser.parse_args() + print("arguments", args) + + assert args.editing_task in ["alpha", "beta"] + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + folding_tokenizer = AutoTokenizer.from_pretrained("facebook/esmfold_v1") + folding_model = EsmForProteinFolding.from_pretrained("facebook/esmfold_v1", low_cpu_mem_usage=True).to(device) + folding_model.trunk.set_chunk_size(512) + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False) + elif args.protein_backbone_model == "ProtBERT_BFD": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False) + protein_dim = 1024 + + ##### load protein sequence + dataset_file_path = os.path.join(text_prompt_dict[args.editing_task]["data_folder"], "preprocessed_data.csv") + dataset = ProteinDataset( + dataset_file_path=dataset_file_path, + dataset_size=args.dataset_size, + protein_tokenizer=CLAP_protein_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + if args.output_text_file_path is None: + args.output_text_file_path = os.path.join(args.output_folder, "step_01_editing.txt") + + f = open(args.output_text_file_path, "r") + input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, edited_eval_list = [], [], [], [] + for line in f.readlines(): + if line.startswith("input"): + line = line.strip().split(",") + input_protein_sequence_list.append(line[1]) + value = line[2].replace("[", "").replace("]", "") + input_eval_list.append(float(value)) + elif line.startswith("output"): + line = line.strip().split(",") + edited_protein_sequence = line[1] + edited_protein_sequence = re.sub(r"[UZOB]", "X", edited_protein_sequence) + edited_protein_sequence_list.append(edited_protein_sequence) + value = line[2].replace("[", "").replace("]", "") + edited_eval_list.append(float(value)) + + neo_input_protein_sequence_list, neo_input_eval_list, neo_edited_protein_sequence_list, neo_edited_eval_list = [], [], [], [] + for a,b,c,d in zip(input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, edited_eval_list): + if len(c) == 0: + continue + if len(a) >= 512: + continue + if len(c) >= 512: + continue + neo_input_protein_sequence_list.append(a) + neo_input_eval_list.append(b) + neo_edited_protein_sequence_list.append(c) + neo_edited_eval_list.append(d) + input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, edited_eval_list = neo_input_protein_sequence_list, neo_input_eval_list, neo_edited_protein_sequence_list, neo_edited_eval_list + + #################### compare #################### + eval_hit, total = 0, 0 + for input_protein, input_eval, edited_protein, output_eval in zip(input_protein_sequence_list, input_eval_list, edited_protein_sequence_list, edited_eval_list): + total += 1 + + if args.text_prompt_id in [101]: + if output_eval > input_eval: + eval_hit += 1 + elif args.text_prompt_id in [201]: + if output_eval < input_eval: + eval_hit += 1 + if total > 0: + eval_hit_ratio = 100. * eval_hit / total + print("#1 eval hit: {}".format(eval_hit)) + print("#1 eval total: {}".format(total)) + print("#1 eval hit ratio: {}".format(eval_hit_ratio)) + + total = len(dataset) + eval_hit_ratio = 100. * eval_hit / total + print("eval hit: {}".format(eval_hit)) + print("eval total: {}".format(total)) + print("eval hit ratio: {}".format(eval_hit_ratio)) + ################################################## + + input_PDB_list, idx_list = evaluate_folding(input_protein_sequence_list) + PDB_output_folder = os.path.join(args.output_folder, "input_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + input_DSSP_list, input_valid_idx_set = save_and_evaluate_PDB_list(input_PDB_list, idx_list, PDB_output_folder) + print("valid input (w/ secondary structure)", len(input_valid_idx_set)) + + output_PDB_list, idx_list = evaluate_folding(edited_protein_sequence_list) + PDB_output_folder = os.path.join(args.output_folder, "output_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + output_DSSP_list, output_valid_idx_set = save_and_evaluate_PDB_list(output_PDB_list, idx_list, PDB_output_folder) + print("valid output (w/ secondary structure)", len(output_valid_idx_set)) + + ##### compare + evaluation_output_file_path = os.path.join(args.output_folder, "step_01_evaluate.txt") + f = open(evaluation_output_file_path, 'w') + eval_hit, DSSP_hit, total = 0, 0, 0 + for input_protein, input_eval, input_DSSP, edited_protein, output_eval, output_DSSP, idx in zip(input_protein_sequence_list, input_eval_list, input_DSSP_list, edited_protein_sequence_list, edited_eval_list, output_DSSP_list, idx_list): + if not (idx in input_valid_idx_set and idx in output_valid_idx_set): + print("invalid", idx, input_valid_idx_set, output_valid_idx_set) + continue + print('input,{},{},{}'.format(input_protein, input_eval, input_DSSP), file=f) + print('output,{},{},{}'.format(edited_protein, output_eval, output_DSSP), file=f) + + total += 1 + + if args.text_prompt_id in [101]: + if output_DSSP[args.editing_task] > input_DSSP[args.editing_task]: + DSSP_hit += 1 + elif args.text_prompt_id in [201]: + if output_DSSP[args.editing_task] < input_DSSP[args.editing_task]: + DSSP_hit += 1 + + if total > 0: + DSSP_hit_ratio = 100. * DSSP_hit / total + print("#1 DSSP hit: {}".format(DSSP_hit)) + print("#1 DSSP total: {}".format(total)) + print("#1 DSSP hit ratio: {}".format(DSSP_hit_ratio)) + + total = len(dataset) + DSSP_hit_ratio = 100. * DSSP_hit / total + print("DSSP hit: {}".format(DSSP_hit)) + print("DSSP total: {}".format(total)) + print("DSSP hit ratio: {}".format(DSSP_hit_ratio)) + + """ + ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_06_AE_1e-3_3/downstream_Editing_latent_optimization/alpha_prompt_101_lambda_0.1_num_repeat_16_oracle_text_T_2 + cp ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_06_AE_1e-3_3/downstream_Editing_latent_optimization/alpha_prompt_101_lambda_0.1_num_repeat_16_oracle_text_T_2 . + + python step_01_evaluate_structure.py --num_workers=0 --batch_size=4 --editing_task=alpha --text_prompt_id=101 --output_folder=alpha_prompt_101_lambda_0.1_num_repeat_16_oracle_text_T_2 --output_text_file_path=alpha_prompt_101_lambda_0.1_num_repeat_16_oracle_text_T_2/step_01_editing.txt + """ diff --git a/examples/downstream_Editing/step_02_binding_editing_Galactica.py b/examples/downstream_Editing/step_02_binding_editing_Galactica.py new file mode 100644 index 0000000..3451319 --- /dev/null +++ b/examples/downstream_Editing/step_02_binding_editing_Galactica.py @@ -0,0 +1,188 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import string + +import torch +import torch.nn as nn + +from transformers import BertModel, BertTokenizer, AutoTokenizer, OPTForCausalLM +from torch.utils.data import DataLoader + +from ProteinDT.datasets import MISATODataset + +from utils import text_prompt_dict +from utils_peptide_editing import ProteinBindingDataset, load_oracle_evaluator, evaluate_folding, evaluate_binding, save_PDB_list + +import re + + +def parse_Galatica_result(text_prompt, result): + result = result.replace(text_prompt, "") + result = result.split("[END_AMINO]")[0].strip() + result = result.split("\n")[0].replace("?", "") + + pattern = re.compile('[A-Z]{5,}') + parsed_results = pattern.findall(result) + + result = parsed_results[0] + result = re.sub(r"[UZOB]", "X", result) + + return result + + +@torch.no_grad() +def inference_Galactica(dataloader): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + galactica_tokenizer = AutoTokenizer.from_pretrained("facebook/galactica-1.3b") + galactica_model = OPTForCausalLM.from_pretrained("facebook/galactica-1.3b", device_map="auto") + + input_protein_sequence_list, edited_protein_sequence_list, PDB_id_list = [], [], [] + for batch_idx, batch in enumerate(L): + peptide_sequence_batch, text_sequence_batch, PDB_id_batch = batch["peptide_sequence"], batch["text_sequence"], batch["PDB_id"] + for peptide_sequence, text_sequence, PDB_id in zip(peptide_sequence_batch, text_sequence_batch, PDB_id_batch): + peptide_sequence = ''.join(peptide_sequence).replace(" ", "") + text_sequence = ''.join(text_sequence).replace(" ", "") + + text_prompt = "Given an input peptide amino acid sequence [START_AMINO]{}[END_AMINO] and a target protein. The target protein satisfies the following property. {} Can you {}, which needs to be similar to the input sequence? [START_AMINO]".format( + peptide_sequence, text_sequence, text_prompt_dict[args.editing_task][args.text_prompt_id]) + text_ids = galactica_tokenizer(text_prompt, return_tensors="pt").input_ids.to("cuda") + print("text_prompt", text_prompt) + + outputs = galactica_model.generate( + text_ids, + max_new_tokens=len(peptide_sequence)+10, + do_sample=True, + top_p=0.9, + temperature=1.0, + use_cache=True, + top_k=5, + repetition_penalty=1.0, + length_penalty=1, + num_return_sequences=1, + ) + + output = outputs[0] + protein_sequence_answer = galactica_tokenizer.decode(output) + try: + edited_protein_sequence = parse_Galatica_result(text_prompt, protein_sequence_answer) + except: + print("invalid", protein_sequence_answer) + continue + + input_protein_sequence_list.append(peptide_sequence) + edited_protein_sequence_list.append(edited_protein_sequence) + PDB_id_list.append(PDB_id) + + return input_protein_sequence_list, edited_protein_sequence_list, PDB_id_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=8) + parser.add_argument("--num_workers", type=int, default=0) + parser.add_argument("--mutation_number", type=int, default=1) + + parser.add_argument("--editing_task", type=str, default="peptide_binding") + parser.add_argument("--dataset_size", type=int, default=200) + parser.add_argument("--text_prompt_id", type=int, default=101) + + parser.add_argument("--output_folder", type=str, default=None) + parser.add_argument("--output_text_file_path", type=str, default=None) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + + args = parser.parse_args() + print("arguments", args) + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False) + elif args.protein_backbone_model == "ProtBERT_BFD": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False) + protein_dim = 1024 + + ##### load protein sequence + dataset = ProteinBindingDataset( + data_folder=text_prompt_dict[args.editing_task]["data_folder"], + dataset_size=args.dataset_size, + protein_tokenizer=CLAP_protein_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + input_peptide_sequence_list, edited_peptide_sequence_list, PDB_id_list = inference_Galactica(dataloader) + + if args.output_folder is None: + exit() + + ##### Load pretrained model + eval_prediction_model = load_oracle_evaluator(device) + data_folder = "../../data/MISATO" + misato_dataset = MISATODataset(data_folder) + peptide_idx2data = misato_dataset.get_peptide_idx2data() + + print('input:') + input_peptide_PDB_id_list = evaluate_folding(input_peptide_sequence_list, eval_prediction_model) + PDB_output_folder = os.path.join(args.output_folder, "input_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + save_PDB_list(input_peptide_PDB_id_list, PDB_id_list, PDB_output_folder) + input_eval_list = evaluate_binding(input_peptide_PDB_id_list, PDB_id_list, peptide_idx2data, eval_prediction_model, device, args) + + print("output") + output_peptide_PDB_id_list = evaluate_folding(edited_peptide_sequence_list, eval_prediction_model) + PDB_output_folder = os.path.join(args.output_folder, "output_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + save_PDB_list(output_peptide_PDB_id_list, PDB_id_list, PDB_output_folder) + output_eval_list = evaluate_binding(output_peptide_PDB_id_list, PDB_id_list, peptide_idx2data, eval_prediction_model, device, args) + + if args.output_text_file_path is None: + args.output_text_file_path = os.path.join(args.output_folder, "step_01_editing.txt") + + f = open(args.output_text_file_path, 'w') + hit, total = 0, 0 + for input_peptide, input_eval, edited_peptide, output_eval in zip(input_peptide_sequence_list, input_eval_list, edited_peptide_sequence_list, output_eval_list): + print('input,{},{}'.format(input_peptide, input_eval), file=f) + print('output,{},{}'.format(edited_peptide, output_eval), file=f) + + total += 1 + + if args.editing_task in ["peptide_binding"]: + if args.text_prompt_id in [101]: + if output_eval < input_eval: + hit += 1 + elif args.text_prompt_id in [201]: + if output_eval > input_eval: + hit += 1 + + hit_ratio = 100. * hit / total + print("hit: {}".format(hit)) + print("#1 total: {}".format(total)) + print("#1 hit ratio: {}".format(hit_ratio)) + + total = len(dataset) + hit_ratio = 100. * hit / total + print("total: {}".format(total)) + print("hit ratio: {}".format(hit_ratio)) \ No newline at end of file diff --git a/examples/downstream_Editing/step_02_binding_editing_latent_interpolation.py b/examples/downstream_Editing/step_02_binding_editing_latent_interpolation.py new file mode 100644 index 0000000..be3e601 --- /dev/null +++ b/examples/downstream_Editing/step_02_binding_editing_latent_interpolation.py @@ -0,0 +1,401 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import re +import string + +import torch +import torch.nn as nn + +from transformers import AutoModel, AutoTokenizer, BertModel, BertTokenizer, T5Tokenizer +from torch.utils.data import DataLoader + +from ProteinDT.models import MultinomialDiffusion, T5Decoder, GaussianFacilitatorModel +from ProteinDT.datasets import MISATODataset + +from utils import text_prompt_dict, slerp +from utils_peptide_editing import ProteinBindingDataset, load_oracle_evaluator, evaluate_folding, evaluate_binding, save_PDB_list + + +def select_protein_list(candidate_peptide_sequence_list, oracle_repr, B, peptide_sequence_batch): + assert B * args.num_repeat == len(candidate_peptide_sequence_list) + assert oracle_repr.size()[0] == B + + input_peptide_sequence_list, edited_peptide_sequence_list = [], [] + ##### get protein representation + parsed_peptide_sequence_list = [] + for peptide_sequence in candidate_peptide_sequence_list: + peptide_sequence = re.sub(r"[UZOB]", "X", peptide_sequence) + peptide_sequence = " ".join(peptide_sequence) + parsed_peptide_sequence_list.append(peptide_sequence) + peptide_sequence_encode = CLAP_protein_tokenizer(parsed_peptide_sequence_list, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + peptide_sequence_input_ids = peptide_sequence_encode.input_ids.to(device) + peptide_sequence_attention_mask = peptide_sequence_encode.attention_mask.to(device) + protein_output = CLAP_protein_model(peptide_sequence_input_ids, peptide_sequence_attention_mask) + protein_repr_test = protein_output["pooler_output"] + protein_repr_test = CLAP_protein2latent_model(protein_repr_test) + assert protein_repr_test.size()[0] == B * args.num_repeat + + ##### select the sequences most similar to the input protein sequences + for condition_id in range(B): + start, end = condition_id * args.num_repeat, (condition_id + 1) * args.num_repeat + oracle_protein_repr = oracle_repr[condition_id] # hidden_dim + candidate_protein_repr = protein_repr_test[start:end] # num_repeat, hidden_dim + + similarity = torch.matmul(oracle_protein_repr, candidate_protein_repr.transpose(0, 1)) # (num_repeat) + optimal_id = torch.argmax(similarity) + optimal_id = start + optimal_id + input_peptide_sequence_list.append(peptide_sequence_batch[condition_id].replace(" ", "")) + edited_peptide_sequence_list.append(candidate_peptide_sequence_list[optimal_id]) + return input_peptide_sequence_list, edited_peptide_sequence_list + + +@torch.no_grad() +def inference(dataloader, theta, device): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + input_peptide_sequence_list, edited_peptide_sequence_list, PDB_id_list = [], [], [] + for batch_idx, batch in enumerate(L): + PDB_id_list_ = batch["PDB_id"] + + peptide_sequence_batch = batch["peptide_sequence"] + peptide_sequence_input_ids = batch["peptide_sequence_input_ids"].to(device) + peptide_sequence_attention_mask = batch["peptide_sequence_attention_mask"].to(device) + B = len(peptide_sequence_batch) + + protein_output = CLAP_protein_model(peptide_sequence_input_ids, peptide_sequence_attention_mask) + CLAP_protein_repr = protein_output["pooler_output"] + CLAP_protein_repr = CLAP_protein2latent_model(CLAP_protein_repr) # [B, hidden_dim] + + + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device).squeeze(1) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device).squeeze(1) + + description_output = CLAP_text_model(text_sequence_input_ids, text_sequence_attention_mask) + CLAP_text_repr = description_output["pooler_output"] + CLAP_text_repr = CLAP_text2latent_model(CLAP_text_repr) # [B, hidden_dim] + CLAP_text_repr = facilitator_distribution_model.inerence(text_repr=CLAP_text_repr) # [B, hidden_dim] + + condition_repr = slerp(theta, CLAP_protein_repr, CLAP_text_repr) # [B, hidden_dim] + + if args.AR_condition_mode == "aggregated": + repeated_condition_repr = condition_repr.unsqueeze(1).expand(-1, args.num_repeat, -1) # [B, num_repeat, hidden_dim] + repeated_condition_repr = repeated_condition_repr.reshape(-1, args.condition_dim) # [B*num_repeat, hidden_dim] + + else: # args.AR_condition_mode == "expanded": + protein_output = CLAP_protein_model(peptide_sequence_input_ids, peptide_sequence_attention_mask) + condition_repr = condition_repr.unsqueeze(1) # [B, 1, hidden_dim] + CLAP_protein_token_repr = protein_output["last_hidden_state"] # [B, max_seq_len, hidden_dim___] + CLAP_protein_token_repr = CLAP_protein_token_repr[:, 1:, :] # [B, max_seq_len-1, hidden_dim___] + CLAP_protein_token_repr = CLAP_protein2latent_model(CLAP_protein_token_repr) # [B, max_seq_len-1, hidden_dim] + + condition_repr = torch.concat([condition_repr, CLAP_protein_token_repr], dim=1) # [B, max_seq_len, hidden_dim] + repeated_condition_repr = condition_repr.unsqueeze(1).expand(-1, args.num_repeat, -1, -1) # [B, num_repeat, max_seq_len, hidden_dim] + assert args.protein_max_sequence_len == repeated_condition_repr.size()[2] + repeated_condition_repr = repeated_condition_repr.reshape(-1, args.protein_max_sequence_len, args.condition_dim) # [B*num_repeat, max_seq_len, hidden_dim] + + if args.decoder_distribution in ["T5Decoder"]: + max_len = max(peptide_sequence_attention_mask.sum(1)).item() + if args.AR_generation_mode == "01": + temperature = 1.0 + k = 40 + p = 0.9 + repetition_penalty = 1.0 + num_return_sequences = 1 + do_sample = True + num_beams = 1 + elif args.AR_generation_mode == "02": + temperature = 1.0 + k = 40 + p = 0.9 + repetition_penalty = 1.0 + num_return_sequences = 1 + do_sample = False + num_beams = 10 + peptide_sequence_pred_ids = decoder_distribution_model.inference( + condition=repeated_condition_repr, protein_seq_attention_mask=None, max_seq_len=max_len, + temperature=temperature, k=k, p=p, repetition_penalty=repetition_penalty, num_return_sequences=num_return_sequences, do_sample=do_sample, num_beams=num_beams + ) + + else: + ##### add variable length + min_len = min(peptide_sequence_attention_mask.sum(1)).item() + max_len = max(peptide_sequence_attention_mask.sum(1)).item() + protein_seq_attention_mask = torch.zeros((B*args.num_repeat, args.protein_max_sequence_len), device=device) + for protein_seq_attention_mask_each in protein_seq_attention_mask: + valid_length = random.randint(min_len, max_len) + protein_seq_attention_mask_each[:valid_length] = 1 + protein_seq_attention_mask = protein_seq_attention_mask.bool() + + peptide_sequence_output = decoder_distribution_model.inference( + condition=repeated_condition_repr, protein_seq_attention_mask=protein_seq_attention_mask, max_seq_len=args.protein_max_sequence_len, mode=args.SDE_sampling_mode) + + peptide_sequence_pred_ids = torch.argmax(peptide_sequence_output, dim=-1) # (B*num_repeat, max_seq_len) + + ##### truncate after index + for peptide_sequence_pred_id in peptide_sequence_pred_ids: + index = None + for pid, pred_id in enumerate(peptide_sequence_pred_id): + if pred_id != protein_decoder_tokenizer.pad_token_id: + continue + index = pid + break + if index is not None: + peptide_sequence_pred_id[index:] = protein_decoder_tokenizer.pad_token_id + + ##### clean-ups + candidate_peptide_sequence_list = protein_decoder_tokenizer.batch_decode(sequences=peptide_sequence_pred_ids, skip_special_tokens=True) + candidate_peptide_sequence_list = [peptide_sequence.replace(" ", "") for peptide_sequence in candidate_peptide_sequence_list] + + if args.oracle_mode == "protein": + oracle_repr = CLAP_protein_repr + elif args.oracle_mode == "text": + oracle_repr = CLAP_text_repr + input_peptide_sequence_list_, edited_peptide_sequence_list_ = select_protein_list( + candidate_peptide_sequence_list=candidate_peptide_sequence_list, oracle_repr=oracle_repr, B=B, peptide_sequence_batch=peptide_sequence_batch) + input_peptide_sequence_list.extend(input_peptide_sequence_list_) + edited_peptide_sequence_list.extend(edited_peptide_sequence_list_) + PDB_id_list.extend(PDB_id_list_) + + neo_input_peptide_sequence_list, neo_edited_peptide_sequence_list, neo_PDB_id_list = [], [], [] + for input_peptide, output_peptide, PDB_id in zip(input_peptide_sequence_list, edited_peptide_sequence_list, PDB_id_list): + if len(output_peptide) <= 2: + continue + neo_input_peptide_sequence_list.append(input_peptide) + output_peptide = re.sub(r"[UZOB]", "X", output_peptide) + neo_edited_peptide_sequence_list.append(output_peptide) + neo_PDB_id_list.append(PDB_id) + return neo_input_peptide_sequence_list, neo_edited_peptide_sequence_list, neo_PDB_id_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=0) + + parser.add_argument("--editing_task", type=str, default="peptide_binding") + parser.add_argument("--dataset_size", type=int, default=200) + parser.add_argument("--text_prompt_id", type=int, default=101) + parser.add_argument("--theta", type=float, default=0.01) + parser.add_argument("--num_repeat", type=int, default=2) + + parser.add_argument("--pretrained_folder", type=str, default=None) + parser.add_argument("--step_04_folder", type=str, default=None) + parser.add_argument("--output_folder", type=str, default=None) + parser.add_argument("--output_text_file_path", type=str, default=None) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--condition_dim", type=int, default=256) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--text_max_sequence_len", type=int, default=512) + + parser.add_argument("--facilitator_distribution", type=str, default="Gaussian", choices=["Gaussian"]) + + parser.add_argument("--decoder_distribution", type=str, default="MultinomialDiffusion", choices=["T5Decoder", "MultinomialDiffusion"]) + + ##### for AR ##### + parser.add_argument("--AR_generation_mode", type=str, default="01", choices=["01", "02"]) + parser.add_argument("--AR_condition_mode", type=str, default="aggregated", choices=["aggregated", "expanded"]) + + ##### for SDE ##### + parser.add_argument("--hidden_dim", type=int, default=16) + parser.add_argument("--beta_min", type=float, default=0.1) + parser.add_argument("--beta_max", type=float, default=30) + parser.add_argument("--num_diffusion_timesteps", type=int, default=1000) + parser.add_argument("--SDE_type", type=str, default="VP") + parser.add_argument("--score_network_type", type=str, default="BertProtBFD") + parser.add_argument("--SDE_sampling_mode", type=str, default="simplified", choices=["simplified", "weighted"]) + + ##### for post-selection ##### + parser.add_argument("--oracle_mode", type=str, default="protein", choices=["protein", "text", "condition"]) + + args = parser.parse_args() + print("arguments", args) + assert args.pretrained_folder is not None + assert args.step_04_folder is not None + step_01_folder = args.pretrained_folder + step_02_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + step_03_folder = os.path.join(args.pretrained_folder, "step_03_Gaussian_10") + step_04_folder = args.step_04_folder + + assert args.SSL_emb_dim == args.condition_dim + if args.AR_condition_mode == "expanded": + assert args.decoder_distribution == "T5Decoder" + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False) + CLAP_protein_model = BertModel.from_pretrained("Rostlab/prot_bert") + elif args.protein_backbone_model == "ProtBERT_BFD": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False) + CLAP_protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd") + protein_dim = 1024 + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_protein_model.load_state_dict(state_dict) + + ##### Load pretrained text model + CLAP_text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + CLAP_text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_dim = 768 + input_model_path = os.path.join(args.pretrained_folder, "text_model.pth") + print("Loading text model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_text_model.load_state_dict(state_dict) + + ##### Load pretrained protein2latent model + CLAP_protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_protein2latent_model.load_state_dict(state_dict) + + ##### Load pretrained text2latent model + CLAP_text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "text2latent_model.pth") + print("Loading text2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_text2latent_model.load_state_dict(state_dict) + + ##### Load pretrained facilitator model + if args.facilitator_distribution == "Gaussian": + facilitator_distribution_model = GaussianFacilitatorModel(args.SSL_emb_dim) + input_model_path = os.path.join(step_03_folder, "facilitator_distribution_model.pth") + print("Loading facilitator_distribution model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + facilitator_distribution_model.load_state_dict(state_dict) + + if args.decoder_distribution in ["T5Decoder"]: + protein_decoder_tokenizer = T5Tokenizer.from_pretrained("Rostlab/prot_t5_xl_uniref50", do_lower_case=False, chache_dir="../../data/temp_pretrained_t5_base") + else: + protein_decoder_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../../data/temp_pretrained_PotBert") + # print("protein_decoder_tokenizer pad_token_id", protein_decoder_tokenizer.pad_token_id) + # print("protein_decoder_tokenizer sep_token_id", protein_decoder_tokenizer.sep_token_id) + # print("protein_decoder_tokenizer eos_token_id", protein_decoder_tokenizer.eos_token_id) + # print(CLAP_protein_tokenizer.get_vocab()) + # print(protein_decoder_tokenizer.get_vocab()) + + ##### Load pretrained decoder model + if args.decoder_distribution == "MultinomialDiffusion": + mask_id = 4 + decoder_distribution_model = MultinomialDiffusion( + hidden_dim=args.hidden_dim, + condition_dim=args.condition_dim, mask_id=mask_id, + beta_min=args.beta_min, beta_max=args.beta_max, num_diffusion_timesteps=args.num_diffusion_timesteps, + num_classes=protein_decoder_tokenizer.vocab_size, score_network_type=args.score_network_type) + elif args.decoder_distribution == "T5Decoder": + decoder_distribution_model = T5Decoder( + hidden_dim=args.condition_dim, + tokenizer=protein_decoder_tokenizer, + T5_model=args.score_network_type) + + model_file_path = os.path.join(step_04_folder, "decoder_distribution_model.pth") + print("Loading decoder_distribution model from {}...".format(model_file_path)) + state_dict = torch.load(model_file_path, map_location='cpu') + decoder_distribution_model.load_state_dict(state_dict) + + CLAP_protein_model = CLAP_protein_model.to(device) + CLAP_protein_model.eval() + CLAP_text_model = CLAP_text_model.to(device) + CLAP_text_model.eval() + CLAP_protein2latent_model = CLAP_protein2latent_model.to(device) + CLAP_protein2latent_model.eval() + CLAP_text2latent_model = CLAP_text2latent_model.to(device) + CLAP_text2latent_model.eval() + facilitator_distribution_model = facilitator_distribution_model.to(device) + facilitator_distribution_model.eval() + decoder_distribution_model.to(device) + decoder_distribution_model.eval() + + ##### obtain text sequence representation + text_prompt = text_prompt_dict[args.editing_task][args.text_prompt_id] + print("===== the text prompt is : {} =====".format(text_prompt)) + + ##### load protein sequence + dataset = ProteinBindingDataset( + data_folder=text_prompt_dict[args.editing_task]["data_folder"], + dataset_size=args.dataset_size, + protein_tokenizer=CLAP_protein_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len, + text_tokenizer=CLAP_text_tokenizer, + text_max_sequence_len=args.text_max_sequence_len, + text_prompt=text_prompt) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + input_peptide_sequence_list, edited_peptide_sequence_list, PDB_id_list = inference(dataloader, args.theta, device) + + if args.output_folder is None: + exit() + + ##### Load pretrained model + eval_prediction_model = load_oracle_evaluator(device) + data_folder = "../../data/MISATO" + misato_dataset = MISATODataset(data_folder) + peptide_idx2data = misato_dataset.get_peptide_idx2data() + + print('input:') + input_peptide_PDB_id_list = evaluate_folding(input_peptide_sequence_list, eval_prediction_model) + PDB_output_folder = os.path.join(args.output_folder, "input_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + save_PDB_list(input_peptide_PDB_id_list, PDB_id_list, PDB_output_folder) + input_eval_list = evaluate_binding(input_peptide_PDB_id_list, PDB_id_list, peptide_idx2data, eval_prediction_model, device, args) + + print("output: with theta {}".format(args.theta)) + output_peptide_PDB_id_list = evaluate_folding(edited_peptide_sequence_list, eval_prediction_model) + PDB_output_folder = os.path.join(args.output_folder, "output_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + save_PDB_list(output_peptide_PDB_id_list, PDB_id_list, PDB_output_folder) + output_eval_list = evaluate_binding(output_peptide_PDB_id_list, PDB_id_list, peptide_idx2data, eval_prediction_model, device, args) + + if args.output_text_file_path is None: + args.output_text_file_path = os.path.join(args.output_folder, "step_01_editing.txt") + + f = open(args.output_text_file_path, 'w') + hit, total = 0, 0 + for input_peptide, input_eval, edited_peptide, output_eval in zip(input_peptide_sequence_list, input_eval_list, edited_peptide_sequence_list, output_eval_list): + print('input,{},{}'.format(input_peptide, input_eval), file=f) + print('output,{},{}'.format(edited_peptide, output_eval), file=f) + + total += 1 + + if args.editing_task in ["peptide_binding"]: + if args.text_prompt_id in [101]: + if output_eval < input_eval: + hit += 1 + elif args.text_prompt_id in [201]: + if output_eval > input_eval: + hit += 1 + + hit_ratio = 100. * hit / total + print("hit: {}".format(hit)) + print("#1 total: {}".format(total)) + print("#1 hit ratio: {}".format(hit_ratio)) + + total = len(dataset) + hit_ratio = 100. * hit / total + print("total: {}".format(total)) + print("hit ratio: {}".format(hit_ratio)) \ No newline at end of file diff --git a/examples/downstream_Editing/step_02_binding_editing_latent_optimization.py b/examples/downstream_Editing/step_02_binding_editing_latent_optimization.py new file mode 100644 index 0000000..3eae5aa --- /dev/null +++ b/examples/downstream_Editing/step_02_binding_editing_latent_optimization.py @@ -0,0 +1,446 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import re +import string +import math +import time + +import torch +import torch.nn as nn +import torch.optim as optim + +from transformers import AutoModel, AutoTokenizer, BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from ProteinDT.models import GaussianFacilitatorModel, RNNPrediction +from ProteinDT.datasets import MISATODataset + +from utils import text_prompt_dict +from utils_peptide_editing import ProteinBindingDataset, load_oracle_evaluator, evaluate_folding, evaluate_binding, save_PDB_list + + +def finetune_AE(dataloader, protein_model, CLAP_protein2latent_model, protein_tokenizer, optimizer, CE_criterion): + scaler = torch.cuda.amp.GradScaler() + auto_encoding_model.train() + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + start_time = time.time() + accum_AE_loss, accum_decoding_loss = 0, 0 + for batch_idx, batch in enumerate(L): + peptide_sequence_input_ids = batch["peptide_sequence_input_ids"].to(device) + peptide_sequence_attention_mask = batch["peptide_sequence_attention_mask"].to(device) + + with torch.no_grad(): + protein_output = protein_model(peptide_sequence_input_ids, peptide_sequence_attention_mask) + token_repr = protein_output["last_hidden_state"] # [B, max_seq_len, 1024] + token_repr = CLAP_protein2latent_model(token_repr) # [B, max_seq_len, SSL_emb_dim] + + with torch.cuda.amp.autocast(): + logit = auto_encoding_model(token_repr) # [B, max_seq_len, vocab_size] + + target_protein_seq_input_ids = peptide_sequence_input_ids # [B, max_sequence_len] + target_protein_seq_attention_mask = peptide_sequence_attention_mask # [B, max_sequence_len] + flattened_logits = torch.flatten(logit, start_dim=0, end_dim=1) # [B * max_sequence_len, vocab_size] + flattened_ids = torch.flatten(target_protein_seq_input_ids, start_dim=0, end_dim=1) # [B * max_sequence_len] + flattened_mask = torch.flatten(target_protein_seq_attention_mask, start_dim=0, end_dim=1) # [B * max_sequence_len] + total_loss = CE_criterion(flattened_logits, flattened_ids) # [B * max_sequence_len] + masked_loss = total_loss * flattened_mask # [B * max_sequence_len] + total_loss = torch.mean(total_loss) + masked_loss = masked_loss.sum() / flattened_mask.sum() + + loss = (total_loss + masked_loss) / 2 + + optimizer.zero_grad() + scaler.scale(loss).backward() + scaler.step(optimizer) + scaler.update() + + accum_AE_loss += loss.item() + + accum_AE_loss /= len(L) + accum_decoding_loss /= len(L) + global optimal_loss + temp_loss = accum_AE_loss + if temp_loss < optimal_loss: + optimal_loss = temp_loss + print("SDE Loss: {:.5f}\tDecoding Loss: {:.5f}\tTime: {:.5f}".format(accum_AE_loss, accum_decoding_loss, time.time() - start_time)) + return + + +def get_lr(t, initial_lr, rampdown=0.25, rampup=0.05): + lr_ramp = min(1, (1 - t) / rampdown) + lr_ramp = 0.5 - 0.5 * math.cos(lr_ramp * math.pi) + lr_ramp = lr_ramp * min(1, t / rampup) + return initial_lr * lr_ramp + + +def select_protein_list(candidate_peptide_sequence_list, oracle_repr, B, peptide_sequence_batch): + assert B * args.num_repeat == len(candidate_peptide_sequence_list) + assert oracle_repr.size()[0] == B + + input_peptide_sequence_list, edited_peptide_sequence_list = [], [] + ##### get protein representation + parsed_peptide_sequence_list = [] + for peptide_sequence in candidate_peptide_sequence_list: + peptide_sequence = re.sub(r"[UZOB]", "X", peptide_sequence) + peptide_sequence = " ".join(peptide_sequence) + parsed_peptide_sequence_list.append(peptide_sequence) + peptide_sequence_encode = CLAP_protein_tokenizer(parsed_peptide_sequence_list, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + peptide_sequence_input_ids = peptide_sequence_encode.input_ids.to(device) + peptide_sequence_attention_mask = peptide_sequence_encode.attention_mask.to(device) + protein_output = CLAP_protein_model(peptide_sequence_input_ids, peptide_sequence_attention_mask) + protein_repr_test = protein_output["pooler_output"] + protein_repr_test = CLAP_protein2latent_model(protein_repr_test) + assert protein_repr_test.size()[0] == B * args.num_repeat + + ##### select the sequences most similar to the input protein sequences + for condition_id in range(B): + start, end = condition_id * args.num_repeat, (condition_id + 1) * args.num_repeat + oracle_protein_repr = oracle_repr[condition_id] # hidden_dim + candidate_protein_repr = protein_repr_test[start:end] # num_repeat, hidden_dim + + similarity = torch.matmul(oracle_protein_repr, candidate_protein_repr.transpose(0, 1)) # (num_repeat) + optimal_id = torch.argmax(similarity) + optimal_id = start + optimal_id + input_peptide_sequence_list.append(peptide_sequence_batch[condition_id].replace(" ", "")) + edited_peptide_sequence_list.append(candidate_peptide_sequence_list[optimal_id]) + return input_peptide_sequence_list, edited_peptide_sequence_list + + +def latent_optimization(peptide_sequence_input_ids, latent_code_init, CLAP_text_repr): + repeated_latent_code_init = latent_code_init.unsqueeze(0).expand(args.num_repeat, -1, -1, -1) # [B, num_repeat, max_seq_len, hidden_dim] + repeated_latent_code_init = repeated_latent_code_init.flatten(0, 1) # [num_repeat*B, max_seq_len, hidden_dim] + + repeated_peptide_sequence_input_ids = peptide_sequence_input_ids.unsqueeze(1).expand(-1, args.num_repeat, -1) # [B, num_repeat] + repeated_peptide_sequence_input_ids = repeated_peptide_sequence_input_ids.flatten(0, 1) # [num_repeat*B, max_seq_len] + + random_noise = torch.randn(repeated_latent_code_init.size()).to(device) / args.temperature # [num_repeat*B, max_seq_len, hidden_dim] + latent_code = repeated_latent_code_init.detach().clone() + random_noise + latent_code.requires_grad = True + optimizer = optim.Adam([latent_code], lr=args.lr) + + if args.verbose: + current_L = tqdm(range(args.epochs)) + else: + current_L = range(args.epochs) + + for i in current_L: + t = i / args.epochs + lr = get_lr(t, args.lr) + optimizer.param_groups[0]["lr"] = lr + + protein_repr = CLAP_protein_model.pooler(latent_code) # [num_repeat*B, hidden_dim] + protein_repr = CLAP_protein2latent_model(protein_repr) # [num_repeat*B, hidden_dim] + + loss_01 = ((protein_repr - CLAP_text_repr) ** 2).mean() + loss_02 = ((repeated_latent_code_init - latent_code) ** 2).mean() + + loss = (args.lambda_value) * loss_01 + (1 - args.lambda_value) * loss_02 + + optimizer.zero_grad() + loss.backward(retain_graph=True) + optimizer.step() + latent_code = latent_code.detach() + + # TODO + latent_code = CLAP_protein2latent_model(latent_code) # [num_repeat*B, max_seq_len, hidden_dim] + peptide_sequence_output = auto_encoding_model(latent_code) # [num_repeat*B, max_seq_len, vocab_size] + return peptide_sequence_output + + +def inference(dataloader, device): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + input_peptide_sequence_list, edited_peptide_sequence_list, PDB_id_list = [], [], [] + for batch_idx, batch in enumerate(L): + PDB_id_list_ = batch["PDB_id"] + + peptide_sequence_batch = batch["peptide_sequence"] + peptide_sequence_input_ids = batch["peptide_sequence_input_ids"].to(device) + peptide_sequence_attention_mask = batch["peptide_sequence_attention_mask"].to(device) + + peptide_output = CLAP_protein_model(peptide_sequence_input_ids, peptide_sequence_attention_mask) + latent_code_init = peptide_output["last_hidden_state"] # [B, max_seq_len, hidden_dim] + CLAP_peptide_repr = peptide_output["pooler_output"] + CLAP_peptide_repr = CLAP_protein2latent_model(CLAP_peptide_repr) # [B, hidden_dim] + + + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device).squeeze(1) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device).squeeze(1) + + description_output = CLAP_text_model(text_sequence_input_ids, text_sequence_attention_mask) + CLAP_text_repr = description_output["pooler_output"] + CLAP_text_repr = CLAP_text2latent_model(CLAP_text_repr) # [B, hidden_dim] + CLAP_text_repr = prior_distribution_model.inerence(text_repr=CLAP_text_repr) # [B, hidden_dim] + + expanded_CLAP_text_repr = CLAP_text_repr.unsqueeze(0).repeat(args.num_repeat, 1, 1) + B = peptide_sequence_input_ids.size()[0] + expanded_CLAP_text_repr = expanded_CLAP_text_repr.reshape(B*args.num_repeat, -1) # [B*num_repeat, hidden_dim] + + + peptide_sequence_output = latent_optimization(peptide_sequence_input_ids, latent_code_init, expanded_CLAP_text_repr) + peptide_sequence_output = peptide_sequence_output.detach() + + peptide_sequence_pred_ids = torch.argmax(peptide_sequence_output, dim=-1) # (B*num_repeat, max_seq_len) + + # ##### truncate after index + # for peptide_sequence_pred_id in peptide_sequence_pred_ids: + # index = None + # for pid, pred_id in enumerate(peptide_sequence_pred_id): + # if pred_id != protein_decoder_tokenizer.pad_token_id: + # continue + # index = pid + # break + # if index is not None: + # peptide_sequence_pred_id[index:] = protein_decoder_tokenizer.pad_token_id + + ##### clean-ups + candidate_peptide_sequence_list = protein_decoder_tokenizer.batch_decode(sequences=peptide_sequence_pred_ids, skip_special_tokens=True) + candidate_peptide_sequence_list = [peptide_sequence.replace(" ", "") for peptide_sequence in candidate_peptide_sequence_list] + print("candidate_peptide_sequence_list", len(candidate_peptide_sequence_list)) + # print("candidate_peptide_sequence_list", candidate_peptide_sequence_list) + + if args.oracle_mode == "protein": + oracle_repr = CLAP_peptide_repr + elif args.oracle_mode == "text": + oracle_repr = CLAP_text_repr # [B, hidden_dim] + input_peptide_sequence_list_, edited_peptide_sequence_list_ = select_protein_list( + candidate_peptide_sequence_list=candidate_peptide_sequence_list, oracle_repr=oracle_repr, B=B, peptide_sequence_batch=peptide_sequence_batch) + input_peptide_sequence_list.extend(input_peptide_sequence_list_) + edited_peptide_sequence_list.extend(edited_peptide_sequence_list_) + PDB_id_list.extend(PDB_id_list_) + + neo_input_peptide_sequence_list, neo_edited_peptide_sequence_list, neo_PDB_id_list = [], [], [] + for input_peptide, output_peptide, PDB_id in zip(input_peptide_sequence_list, edited_peptide_sequence_list, PDB_id_list): + if len(output_peptide) <= 2: + continue + neo_input_peptide_sequence_list.append(input_peptide) + output_peptide = re.sub(r"[UZOB]", "X", output_peptide) + neo_edited_peptide_sequence_list.append(output_peptide) + neo_PDB_id_list.append(PDB_id) + return neo_input_peptide_sequence_list, neo_edited_peptide_sequence_list, neo_PDB_id_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=0) + parser.add_argument("--lr", type=float, default=0.1) + parser.add_argument("--epochs", type=int, default=100) + parser.add_argument("--temperature", type=float, default=0.5) + + parser.add_argument("--AE_lr", type=float, default=5e-4) + parser.add_argument("--AE_epochs", type=int, default=50) + parser.add_argument("--AE_decay", type=float, default=0) + + parser.add_argument("--editing_task", type=str, default="peptide_binding") + parser.add_argument("--dataset_size", type=int, default=200) + parser.add_argument("--text_prompt_id", type=int, default=101) + parser.add_argument("--lambda_value", type=float, default=0.1) + parser.add_argument("--num_repeat", type=int, default=2) + + parser.add_argument("--pretrained_folder", type=str, default=None) + parser.add_argument("--output_folder", type=str, default=None) + parser.add_argument("--output_text_file_path", type=str, default=None) + parser.add_argument("--step_06_folder", type=str, default="step_06_AE_test") + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--condition_dim", type=int, default=256) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=50) + parser.add_argument("--text_max_sequence_len", type=int, default=50) + + parser.add_argument("--prior_distribution", type=str, default="Gaussian", choices=["Gaussian"]) + + ##### for post-selection ##### + parser.add_argument("--oracle_mode", type=str, default="protein", choices=["protein", "text"]) + + args = parser.parse_args() + print("arguments", args) + assert args.pretrained_folder is not None + assert args.step_06_folder is not None + step_01_folder = args.pretrained_folder + step_02_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + step_03_folder = os.path.join(args.pretrained_folder, "step_03_Gaussian_10") + step_06_folder = args.step_06_folder + + assert args.SSL_emb_dim == args.condition_dim + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False) + CLAP_protein_model = BertModel.from_pretrained("Rostlab/prot_bert") + elif args.protein_backbone_model == "ProtBERT_BFD": + CLAP_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False) + CLAP_protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd") + protein_dim = 1024 + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_protein_model.load_state_dict(state_dict) + + ##### Load pretrained text model + CLAP_text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + CLAP_text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_dim = 768 + input_model_path = os.path.join(args.pretrained_folder, "text_model.pth") + print("Loading text model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_text_model.load_state_dict(state_dict) + + ##### Load pretrained protein2latent model + CLAP_protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_protein2latent_model.load_state_dict(state_dict) + + ##### Load pretrained text2latent model + CLAP_text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "text2latent_model.pth") + print("Loading text2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLAP_text2latent_model.load_state_dict(state_dict) + + ##### Load pretrained prior model + if args.prior_distribution == "Gaussian": + prior_distribution_model = GaussianFacilitatorModel(args.SSL_emb_dim) + input_model_path = os.path.join(step_03_folder, "prior_distribution_model.pth") + print("Loading prior_distribution model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + prior_distribution_model.load_state_dict(state_dict) + + protein_decoder_tokenizer = CLAP_protein_tokenizer + print("protein_decoder_tokenizer pad_token_id", protein_decoder_tokenizer.pad_token_id) + print("protein_decoder_tokenizer sep_token_id", protein_decoder_tokenizer.sep_token_id) + print("protein_decoder_tokenizer eos_token_id", protein_decoder_tokenizer.eos_token_id) + + ##### Load prediction head + auto_encoding_model = nn.Linear(args.SSL_emb_dim, CLAP_protein_tokenizer.vocab_size) + auto_encoding_model = RNNPrediction(args.SSL_emb_dim, CLAP_protein_tokenizer.vocab_size) + input_model_path = os.path.join(step_06_folder, "AE_model.pth") + print("Loading auto_encoding_model model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + auto_encoding_model.load_state_dict(state_dict) + + CLAP_protein_model = CLAP_protein_model.to(device) + CLAP_protein_model.eval() + CLAP_text_model = CLAP_text_model.to(device) + CLAP_text_model.eval() + CLAP_protein2latent_model = CLAP_protein2latent_model.to(device) + CLAP_protein2latent_model.eval() + CLAP_text2latent_model = CLAP_text2latent_model.to(device) + CLAP_text2latent_model.eval() + prior_distribution_model = prior_distribution_model.to(device) + prior_distribution_model.eval() + auto_encoding_model = auto_encoding_model.to(device) + auto_encoding_model.eval() + + ##### obtain text sequence representation + text_prompt = text_prompt_dict[args.editing_task][args.text_prompt_id] + print("===== the text prompt is : {} =====".format(text_prompt)) + + ##### load protein sequence + dataset = ProteinBindingDataset( + data_folder=text_prompt_dict[args.editing_task]["data_folder"], + dataset_size=args.dataset_size, + protein_tokenizer=CLAP_protein_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len, + text_tokenizer=CLAP_text_tokenizer, + text_max_sequence_len=args.text_max_sequence_len, + text_prompt=text_prompt) + dataloader = DataLoader(dataset, batch_size=16, shuffle=True, num_workers=args.num_workers) + + optimal_loss = 1e10 + auto_encoding_model.train() + model_param_group = [{"params": auto_encoding_model.parameters(), "lr": args.AE_lr}] + CE_criterion = nn.CrossEntropyLoss() + optimizer = optim.Adam(model_param_group, weight_decay=args.AE_decay) + optimal_loss = 1e10 + print("========== start finetuning AE ==========") + for _ in range(args.AE_epochs): + finetune_AE(dataloader, CLAP_protein_model, CLAP_protein2latent_model, CLAP_protein_tokenizer, optimizer, CE_criterion) + print("========== done finetuning AE ==========") + auto_encoding_model.eval() + print("\n\n\n") + + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + input_peptide_sequence_list, edited_peptide_sequence_list, PDB_id_list = inference(dataloader, device) + + if args.output_folder is None: + exit() + + ##### Load pretrained model + eval_prediction_model = load_oracle_evaluator(device) + data_folder = "../../data/MISATO" + misato_dataset = MISATODataset(data_folder) + peptide_idx2data = misato_dataset.get_peptide_idx2data() + + print('input:') + input_peptide_PDB_id_list = evaluate_folding(input_peptide_sequence_list, eval_prediction_model) + PDB_output_folder = os.path.join(args.output_folder, "input_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + save_PDB_list(input_peptide_PDB_id_list, PDB_id_list, PDB_output_folder) + input_eval_list = evaluate_binding(input_peptide_PDB_id_list, PDB_id_list, peptide_idx2data, eval_prediction_model, device, args) + + print("output: with lambda_value {}".format(args.lambda_value)) + output_peptide_PDB_id_list = evaluate_folding(edited_peptide_sequence_list, eval_prediction_model) + PDB_output_folder = os.path.join(args.output_folder, "output_PDB") + os.makedirs(PDB_output_folder, exist_ok = True) + save_PDB_list(output_peptide_PDB_id_list, PDB_id_list, PDB_output_folder) + output_eval_list = evaluate_binding(output_peptide_PDB_id_list, PDB_id_list, peptide_idx2data, eval_prediction_model, device, args) + + if args.output_text_file_path is None: + args.output_text_file_path = os.path.join(args.output_folder, "step_01_editing.txt") + + f = open(args.output_text_file_path, 'w') + hit, total = 0, 0 + for input_peptide, input_eval, edited_peptide, output_eval in zip(input_peptide_sequence_list, input_eval_list, edited_peptide_sequence_list, output_eval_list): + print('input,{},{}'.format(input_peptide, input_eval), file=f) + print('output,{},{}'.format(edited_peptide, output_eval), file=f) + + total += 1 + + if args.editing_task in ["peptide_binding"]: + if args.text_prompt_id in [101]: + if output_eval < input_eval: + hit += 1 + elif args.text_prompt_id in [201]: + if output_eval > input_eval: + hit += 1 + + hit_ratio = 100. * hit / total + print("hit: {}".format(hit)) + print("#1 total: {}".format(total)) + print("#1 hit ratio: {}".format(hit_ratio)) + + total = len(dataset) + hit_ratio = 100. * hit / total + print("total: {}".format(total)) + print("hit ratio: {}".format(hit_ratio)) \ No newline at end of file diff --git a/examples/downstream_Editing/test.py b/examples/downstream_Editing/test.py new file mode 100644 index 0000000..2c28f54 --- /dev/null +++ b/examples/downstream_Editing/test.py @@ -0,0 +1,28 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import string +import mdtraj as md + +import torch +import torch.nn as nn + +from transformers import BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from utils import ProteinDataset, ProteinSeqDataset, text_prompt_dict, load_oracle_evaluator, evaluate, analyze + +from transformers import AutoTokenizer, EsmForProteinFolding +from transformers.models.esm.openfold_utils.protein import to_pdb, Protein as OFProtein +from transformers.models.esm.openfold_utils.feats import atom14_to_atom37 + + + +# traj = md.load_pdb("0.pdb") +traj = md.load_pdb("../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_06_AE_1e-3_3/downstream_Editing_latent_optimization/alpha_prompt_101_lambda_0.1_num_repeat_16_oracle_text_T_2/input_PDB/0.pdb") +print(traj) + +pdb_ss = md.compute_dssp(traj, simplified=True)[0] # (L, ) +print(pdb_ss) diff --git a/examples/downstream_Editing/utils.py b/examples/downstream_Editing/utils.py new file mode 100644 index 0000000..dfa15b1 --- /dev/null +++ b/examples/downstream_Editing/utils.py @@ -0,0 +1,268 @@ +import numpy as np +import os +from collections import defaultdict +import torch +import torch.nn as nn +from torch.utils.data import Dataset +from tqdm import tqdm +from transformers import BertTokenizer +from ProteinDT.TAPE_benchmark.models import BertForTokenClassification2, BertForSequenceClassification2 +import matplotlib +import matplotlib.pyplot as plt +plt.switch_backend('agg') + + +text_prompt_dict = { + "alpha": { + 101: "modify the amino acid sequence to have more alpha helices in the secondary structure", + 201: "modify the amino acid sequence to have fewer alpha helices in the secondary structure", + "data_folder": "datasets_and_checkpoints/structure", + "target_label": 0, + }, + "beta": { + 101: "modify the amino acid sequence to have more beta sheets in the secondary structure", + 201: "modify the amino acid sequence to have fewer beta sheets in the secondary structure", + "data_folder": "datasets_and_checkpoints/structure", + "target_label": 1, + }, + "Villin": { + 101: "modify the amino acid sequence to have higher stability", + 102: "modify the amino acid sequence to have fewer intrinsically disordered regions", + 201: "modify the amino acid sequence to have lower stability", + 202: "modify the amino acid sequence to have more intrinsically disordered regions", + "data_folder": "datasets_and_checkpoints/stability/Villin", + }, + "Pin1": { + 101: "modify the amino acid sequence to have higher stability", + 102: "modify the amino acid sequence to have fewer intrinsically disordered regions", + 201: "modify the amino acid sequence to have lower stability", + 202: "modify the amino acid sequence to have more intrinsically disordered regions", + "data_folder": "datasets_and_checkpoints/stability/Pin1", + }, + "hYAP65": { + 101: "modify the amino acid sequence to have higher stability", + 102: "modify the amino acid sequence to have fewer intrinsically disordered regions", + 201: "modify the amino acid sequence to have lower stability", + 202: "modify the amino acid sequence to have more intrinsically disordered regions", + "data_folder": "datasets_and_checkpoints/stability/hYAP65", + }, + "stability": { + "data_folder": "datasets_and_checkpoints/stability_test" + }, + "peptide_binding": { + 101: "modify the peptide amino acid sequence to have higher binding affinity with the target protein. The target protein satisfies the following property. {}", + 201: "modify the peptide amino acid sequence to have lower binding affinity with the target protein. The target protein satisfies the following property. {}", + "data_folder": "datasets_and_checkpoints/peptide_binding/MISATO", + }, +} + + +class ProteinDataset(Dataset): + def __init__(self, dataset_file_path, protein_tokenizer, protein_max_sequence_len, dataset_size=None): + self.dataset_file_path = dataset_file_path + self.dataset_size = dataset_size + + f = open(self.dataset_file_path, 'r') + protein_sequence_list = [] + for line in f.readlines(): + line = line.strip().split(',') + protein_sequence = line[0] + protein_sequence = protein_sequence.replace(" ", "") + protein_sequence = " ".join(protein_sequence) + protein_sequence_list.append(protein_sequence) + self.protein_sequence_list = protein_sequence_list + if self.dataset_size is not None: + self.protein_sequence_list = self.protein_sequence_list[:self.dataset_size] + self.protein_tokenizer = protein_tokenizer + self.protein_max_sequence_len = protein_max_sequence_len + + return + + def __getitem__(self, index): + protein_sequence = self.protein_sequence_list[index] + + protein_sequence_encode = self.protein_tokenizer(protein_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze() + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze() + + batch = { + "protein_sequence": protein_sequence, + "protein_sequence_input_ids": protein_sequence_input_ids, + "protein_sequence_attention_mask": protein_sequence_attention_mask, + } + + return batch + + def __len__(self): + return len(self.protein_sequence_list) + + +class ProteinSeqDataset(Dataset): + def __init__(self, protein_sequence_list, protein_tokenizer, protein_max_sequence_len): + protein_sequence_list = [" ".join(seq) for seq in protein_sequence_list] + self.protein_sequence_list = protein_sequence_list + self.protein_tokenizer = protein_tokenizer + self.protein_max_sequence_len = protein_max_sequence_len + + return + + def __getitem__(self, index): + protein_sequence = self.protein_sequence_list[index] + + protein_sequence_encode = self.protein_tokenizer(protein_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze() + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze() + + batch = { + "protein_sequence": protein_sequence, + "protein_sequence_input_ids": protein_sequence_input_ids, + "protein_sequence_attention_mask": protein_sequence_attention_mask, + } + + return batch + + def __len__(self): + return len(self.protein_sequence_list) + + +def load_oracle_evaluator(editing_task, device, input_model_path=None): + if editing_task in ["alpha", "beta"]: + num_labels = 3 + eval_prediction_model = BertForTokenClassification2.from_pretrained( + "Rostlab/prot_bert_bfd", + mean_output=True, + num_labels=num_labels, + ) + if input_model_path is None: + input_model_path = os.path.join("datasets_and_checkpoints/structure/oracle/pytorch_model_ss3.bin") + + elif editing_task in ["Villin", "Pin1", "hYAP65"]: + num_labels = 1 + eval_prediction_model = BertForSequenceClassification2.from_pretrained( + "Rostlab/prot_bert_bfd", + mean_output=True, + num_labels=num_labels, + ) + if input_model_path is None: + input_model_path = os.path.join("datasets_and_checkpoints/stability/oracle/pytorch_model_stability.bin") + + elif editing_task == "stability": + # only for testing + num_labels = 1 + eval_prediction_model = BertForSequenceClassification2.from_pretrained( + "Rostlab/prot_bert_bfd", + mean_output=True, + num_labels=num_labels, + ) + if input_model_path is None: + input_model_path = os.path.join("datasets_and_checkpoints/stability/oracle/pytorch_model_stability.bin") + + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + eval_prediction_model.load_state_dict(state_dict) + eval_prediction_model = eval_prediction_model.to(device) + eval_protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False) + return eval_prediction_model, eval_protein_tokenizer + + +def load_editing_dataset_and_loader(args, eval_protein_tokenizer): + from torch.utils.data import DataLoader + from ProteinDT.datasets import SecondaryStructureDataset, VillinDataset, Pin1Dataset, hYAP65Dataset, StabilityDataset + + if args.editing_task in ["alpha", "beta"]: + test_dataset = SecondaryStructureDataset(data_file_path="./datasets_and_checkpoints/structure/secondary_structure_cb513.lmdb", protein_tokenizer=eval_protein_tokenizer) + test_dataloader = DataLoader(test_dataset, batch_size=args.batch_size, shuffle=True, num_workers=args.num_workers, collate_fn=test_dataset.collate_fn) + criterion_eval = None + + elif args.editing_task == "Villin": + test_dataset = VillinDataset(data_file_path="./datasets_and_checkpoints/stability/Villin/test_data.txt", protein_tokenizer=eval_protein_tokenizer, protein_max_sequence_len=args.protein_max_sequence_len) + test_dataloader = DataLoader(test_dataset, batch_size=args.batch_size*2, shuffle=True, num_workers=args.num_workers) + criterion_eval = nn.L1Loss(reduce=False) + + elif args.editing_task == "Pin1": + test_dataset = Pin1Dataset(data_file_path="./datasets_and_checkpoints/stability/Pin1/test_data.txt", protein_tokenizer=eval_protein_tokenizer, protein_max_sequence_len=args.protein_max_sequence_len) + test_dataloader = DataLoader(test_dataset, batch_size=args.batch_size*2, shuffle=True, num_workers=args.num_workers) + criterion_eval = nn.L1Loss(reduce=False) + + elif args.editing_task == "hYAP65": + test_dataset = hYAP65Dataset(data_file_path="./datasets_and_checkpoints/stability/hYAP65/test_data.txt", protein_tokenizer=eval_protein_tokenizer, protein_max_sequence_len=args.protein_max_sequence_len) + test_dataloader = DataLoader(test_dataset, batch_size=args.batch_size*2, shuffle=True, num_workers=args.num_workers) + criterion_eval = nn.L1Loss(reduce=False) + + elif args.editing_task == "stability": + split_size = [0.8, 0.1, 0.1] + test_dataset = StabilityDataset(root="../../data/stability/", seed=args.seed, mode="test", split_size=split_size, protein_tokenizer=eval_protein_tokenizer, protein_max_sequence_len=args.protein_max_sequence_len) + test_dataloader = DataLoader(test_dataset, batch_size=args.batch_size*2, shuffle=True, num_workers=args.num_workers) + criterion_eval = nn.L1Loss(reduce=False) + + return test_dataset, test_dataloader, criterion_eval + + +@torch.no_grad() +def evaluate(dataloader, eval_prediction_model, device, args): + eval_prediction_model.eval() + + L = tqdm(dataloader) + result_list = [] + for batch_id, batch in enumerate(L): + protein_sequence = batch["protein_sequence"] + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + + output = eval_prediction_model(protein_sequence_input_ids, protein_sequence_attention_mask) + logits = output.logits + + if args.editing_task in ["alpha", "beta"]: + pred = logits.argmax(dim=-1, keepdim=False) + pred = torch.where(protein_sequence_attention_mask==1, pred, -1) + pred = (pred == text_prompt_dict[args.editing_task]["target_label"]).sum(-1) + + else: + pred = logits + + result_list.append(pred.detach().cpu().numpy()) + + result_list = np.concatenate(result_list) + return result_list + + +def analyze(result_list, args, file_path=None): + if args.editing_task in ["alpha", "beta"]: + count = defaultdict(int) + for c in result_list: + count[c] += 1 + key_list = sorted(count.keys()) + for k in key_list: + print(k, count[k]) + else: + counts, bins = np.histogram(result_list, bins=20) + + plt.hist(bins[:-1], bins, weights=counts) + plt.savefig(file_path, dpi=300, bbox_inches='tight') + plt.clf() + return + + +def slerp(theta, start, end): + start_norm = start / torch.norm(start, dim=1, keepdim=True) + end_norm = end / torch.norm(end, dim=1, keepdim=True) + omega = torch.acos((start_norm*end_norm).sum(1)) + so = torch.sin(omega) + res = (torch.sin((1.0-theta)*omega)/so).unsqueeze(1) * start + (torch.sin(theta*omega)/so).unsqueeze(1) * end + return res + + +if __name__ == "__main__": + start = torch.Tensor([[0, 0, 0], [1, 1, 1]]) + end = torch.Tensor([[1, 1, 1], [2, 2, 2]]) + + start = torch.Tensor([[1, 1, 1], [2, 2, 2]]) + end = torch.Tensor([[3, 3, 3], [6, 6, 6]]) + + start = torch.Tensor([[1, 1, 1], [1, 2, 2]]) + end = torch.Tensor([[2, 2, 2], [6, 6, 6]]) + + theta_list = [0, 0.1, 0.5, 0.9, 1] + for theta in theta_list: + interpolation = slerp(theta, start, end) + print(theta, interpolation) \ No newline at end of file diff --git a/examples/downstream_Editing/utils_analysis.py b/examples/downstream_Editing/utils_analysis.py new file mode 100644 index 0000000..c8e3f91 --- /dev/null +++ b/examples/downstream_Editing/utils_analysis.py @@ -0,0 +1,59 @@ + +task_list = ["alpha", "beta", "Villin", "Pin1", "peptide_binding"] + + +text_prompt_dict = { + "alpha": [101, 201], + "beta": [101, 201], + # "Villin": [101, 102, 201, 202], + # "Pin1": [101, 102, 201, 202], + # "hYAP65": [101, 102, 201, 202], + "Villin": [101, 201], + "Pin1": [101, 201], + "hYAP65": [101, 201], + "peptide_binding": [101, 201], +} + + +def prase_hit_ratio(filename): + hit, total, hit_ratio = None, None, None + second_hit, second_total, second_hit_ratio = None, None, None + try: + f = open(filename, "r") + while True: + line = f.readline() + if not line: + break + + line = line.strip() + if line.startswith("hit:"): + hit = int(line.split(":")[1].strip()) + elif line.startswith("total:"): + total = int(line.split(":")[1].strip()) + elif line.startswith("hit ratio:"): + hit_ratio = float(line.split(":")[1].strip()) + + elif line.startswith("eval hit:"): + hit = int(line.split(":")[1].strip()) + elif line.startswith("eval total:"): + total = int(line.split(":")[1].strip()) + elif line.startswith("eval hit ratio:"): + hit_ratio = float(line.split(":")[1].strip()) + + elif line.startswith("DSSP hit:"): + second_hit = int(line.split(":")[1].strip()) + elif line.startswith("DSSP total:"): + second_total = int(line.split(":")[1].strip()) + elif line.startswith("DSSP hit ratio:"): + second_hit_ratio = float(line.split(":")[1].strip()) + + elif line.startswith("pLDDT hit:"): + second_hit = int(line.split(":")[1].strip()) + elif line.startswith("pLDDT total:"): + second_total = int(line.split(":")[1].strip()) + assert total == second_total + elif line.startswith("pLDDT hit ratio:"): + second_hit_ratio = float(line.split(":")[1].strip()) + except: + pass + return hit, total, hit_ratio, second_hit, second_total, second_hit_ratio diff --git a/examples/downstream_Editing/utils_peptide_editing.py b/examples/downstream_Editing/utils_peptide_editing.py new file mode 100644 index 0000000..38e9aad --- /dev/null +++ b/examples/downstream_Editing/utils_peptide_editing.py @@ -0,0 +1,214 @@ +from tqdm import tqdm +import numpy as np +import os +import json +from Bio.PDB.Polypeptide import three_to_one + +import torch +import torch.nn as nn +from torch.utils.data import Dataset, DataLoader +from torch_geometric.data import Data, Batch +from ProteinDT.models import FoldingBindingInferenceModel + + +class ProteinBindingDataset(Dataset): + def __init__( + self, data_folder, + protein_tokenizer, protein_max_sequence_len, + text_tokenizer=None, text_max_sequence_len=None, text_prompt=None, + dataset_size=None + ): + self.dataset_file_path = os.path.join(data_folder, "preprocessed_data.csv") + self.PDB_mapping_file_path = os.path.join(data_folder, "PDB_mapping_data.txt") + self.PDB_idx2text_file_path = os.path.join(data_folder, "PDB_idx2text.json") + f = open(self.PDB_idx2text_file_path, "r") + PDB_idx2text = json.load(f) + self.dataset_size = dataset_size + + self.PDB_id2peptide_seq, self.peptide_seq2PDB_id, self.PDB_id2protein_seq = {}, {}, {} + f = open(self.PDB_mapping_file_path, 'r') + for line in f.readlines(): + line = line.strip().split(',') + PDB_id, peptide_seq, protein_seq = line[0], line[1], line[2] + self.PDB_id2peptide_seq[PDB_id] = peptide_seq + self.peptide_seq2PDB_id[peptide_seq] = PDB_id + self.PDB_id2protein_seq[PDB_id] = protein_seq + + f = open(self.dataset_file_path, 'r') + peptide_sequence_list, protein_sequence_list, PDB_id_list, text_sequence_list = [], [], [], [] + for line in f.readlines(): + line = line.strip().split(',') + peptide_sequence = line[0] + peptide_sequence = peptide_sequence.replace(" ", "") + PDB_id = self.peptide_seq2PDB_id[peptide_sequence] + peptide_sequence = " ".join(peptide_sequence) + peptide_sequence_list.append(peptide_sequence) + PDB_id_list.append(PDB_id) + protein_sequence_list.append(self.PDB_id2protein_seq[PDB_id]) + text = PDB_idx2text[PDB_id] + text = text.split(".")[0]+"." + if text_prompt is not None: + text = text_prompt.format(text) + text_sequence_list.append(text) + self.peptide_sequence_list = peptide_sequence_list + self.protein_sequence_list = protein_sequence_list + self.PDB_id_list = PDB_id_list + self.text_sequence_list = text_sequence_list + + if self.dataset_size is not None: + self.peptide_sequence_list = self.peptide_sequence_list[:self.dataset_size] + self.PDB_id_list = self.PDB_id_list[:self.dataset_size] + + self.protein_tokenizer = protein_tokenizer + self.protein_max_sequence_len = protein_max_sequence_len + self.text_tokenizer = text_tokenizer + self.text_max_sequence_len = text_max_sequence_len + + return + + def __getitem__(self, index): + peptide_sequence = self.peptide_sequence_list[index] + protein_sequence = self.protein_sequence_list[index] + text_sequence = self.text_sequence_list[index] + PDB_id = self.PDB_id_list[index] + + peptide_sequence_encode = self.protein_tokenizer(peptide_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + peptide_sequence_input_ids = peptide_sequence_encode.input_ids.squeeze() + peptide_sequence_attention_mask = peptide_sequence_encode.attention_mask.squeeze() + + batch = { + "PDB_id": PDB_id, + "peptide_sequence": peptide_sequence, + "protein_sequence": protein_sequence, + "text_sequence": text_sequence, + "peptide_sequence_input_ids": peptide_sequence_input_ids, + "peptide_sequence_attention_mask": peptide_sequence_attention_mask, + } + + if self.text_tokenizer is not None: + text_sequence_encode = self.text_tokenizer(text_sequence, truncation=True, max_length=self.text_max_sequence_len, padding='max_length', return_tensors='pt') + text_sequence_input_ids = text_sequence_encode.input_ids + text_sequence_attention_mask = text_sequence_encode.attention_mask + batch["text_sequence_input_ids"] = text_sequence_input_ids + batch["text_sequence_attention_mask"] = text_sequence_attention_mask + + return batch + + def __len__(self): + return len(self.peptide_sequence_list) + + +def load_oracle_evaluator(device, input_model_path=None): + if input_model_path is None: + input_model_path = os.path.join("datasets_and_checkpoints/peptide_binding/MISATO/model_final.pth") + + eval_prediction_model = FoldingBindingInferenceModel(input_model_path=input_model_path) + eval_prediction_model = eval_prediction_model.to(device) + return eval_prediction_model + + +@torch.no_grad() +def evaluate_folding(protein_sequence_list, eval_prediction_model): + eval_prediction_model.eval() + + PDB_data_list = [] + for protein_sequence in protein_sequence_list: + print("protein_sequence", protein_sequence) + + PDB_data = eval_prediction_model.folding(protein_sequence) + + PDB_data_list.extend(PDB_data) + + return PDB_data_list + + +def get_aa_index(residue): + letter_to_num = {'C': 4, 'D': 3, 'S': 15, 'Q': 5, 'K': 11, 'I': 9, + 'P': 14, 'T': 16, 'F': 13, 'A': 0, 'G': 7, 'H': 8, + 'E': 6, 'L': 10, 'R': 1, 'W': 17, 'V': 19, + 'N': 2, 'Y': 18, 'M': 12, "X":20} + one_letter = three_to_one(residue) + return letter_to_num[one_letter] + + +def parse_PDB_data(PDB_data): + # https://www.biostat.jhsph.edu/~iruczins/teaching/260.655/links/pdbformat.pdf + + residue_type_list, ca_pos_list, c_pos_list, n_pos_list = [], [], [], [] + for line in PDB_data.split("\n"): + if line.startswith("ATOM"): + line = ' '.join(line.split()) + line = line.split(" ") + atom_type = line[2] + residue_type = line[3] + x = float(line[6]) + y = float(line[7]) + z = float(line[8]) + if atom_type == "CA": + residue_id = get_aa_index(residue_type) + residue_type_list.append(residue_id) + ca_pos_list.append([x, y, z]) + elif atom_type == "C": + c_pos_list.append([x, y, z]) + elif atom_type == "N": + n_pos_list.append([x, y, z]) + + residue_type_list = torch.tensor(residue_type_list, dtype=torch.int64) + ca_pos_list = torch.tensor(ca_pos_list, dtype=torch.float32) + c_pos_list = torch.tensor(c_pos_list, dtype=torch.float32) + n_pos_list = torch.tensor(n_pos_list, dtype=torch.float32) + + assert residue_type_list.shape[0] == ca_pos_list.shape[0] == c_pos_list.shape[0] == n_pos_list.shape[0] + + data = Data( + x=residue_type_list, + residue=residue_type_list, + pos_ca=ca_pos_list, + pos_c=c_pos_list, + pos_n=n_pos_list, + ) + return data + + +@torch.no_grad() +def evaluate_binding(peptide_PDB_id_list, PDB_id_list, peptide_idx2data, eval_prediction_model, device, args): + from ProteinDT.datasets.dataset_MISATO import BatchMISATO + + eval_prediction_model.eval() + + result_list = [] + for peptide_PDB, PDB_id in zip(peptide_PDB_id_list, PDB_id_list): + misato_data = peptide_idx2data[PDB_id] + protein_batch = BatchMISATO.from_data_list([misato_data]).to(device) + + protein_residue = protein_batch.protein_residue + protein_pos_N = protein_batch.protein_pos[protein_batch.protein_mask_n] + protein_pos_Ca = protein_batch.protein_pos[protein_batch.protein_mask_ca] + protein_pos_C = protein_batch.protein_pos[protein_batch.protein_mask_c] + + peptide_PDB_data = parse_PDB_data(peptide_PDB) + peptide_batch = Batch.from_data_list([peptide_PDB_data]).to(device) + + peptide_residue = peptide_batch.residue + peptide_pos_N = peptide_batch.pos_n + peptide_pos_Ca = peptide_batch.pos_ca + peptide_pos_C = peptide_batch.pos_c + + energy = eval_prediction_model.binding( + protein_residue, protein_pos_N, protein_pos_Ca, protein_pos_C, protein_batch.protein_batch, + peptide_residue, peptide_pos_N, peptide_pos_Ca, peptide_pos_C, peptide_batch.batch, + ) + + result_list.append(energy.detach().item()) + + result_list = np.array(result_list) + return result_list + + +@torch.no_grad() +def save_PDB_list(PDB_list, PDB_id_list, PDB_output_folder): + for i, (PDB, PDB_id) in enumerate(zip(PDB_list, PDB_id_list)): + file_name = os.path.join(PDB_output_folder, "{}_{}.txt".format(i, PDB_id)) + f = open(file_name, "w") + f.write("".join(PDB)) + return diff --git a/examples/downstream_TAPE.py b/examples/downstream_TAPE.py new file mode 100644 index 0000000..094cc4c --- /dev/null +++ b/examples/downstream_TAPE.py @@ -0,0 +1,199 @@ +import os + +import torch +from transformers import BertTokenizerFast, Trainer, set_seed, HfArgumentParser, TrainingArguments + +from ProteinDT.TAPE_benchmark import output_mode_mapping, dataset_processor_mapping +from ProteinDT.TAPE_benchmark import model_mapping +from ProteinDT.TAPE_benchmark import build_compute_metrics_fn +from ProteinDT.TAPE_benchmark import OntoProteinTrainer + +from dataclasses import dataclass, field + + +@dataclass +class GeneralArguments: + task_name: str = field( + default="ss3", + metadata={"help": "The name of the task to train on: " + ", ".join(dataset_processor_mapping.keys())} + ) + data_dir: str = field( + default="../data/downstream_datasets", + metadata={"help": "The input data dir. Should contain the .tsv files (or other data files) for the task."} + ) + mean_output: bool = field( + default=True, metadata={"help": "output of bert, use mean output or pool output"} + ) + optimizer: str = field( + default="AdamW", + metadata={"help": "use optimizer: AdamW(True) or Adam(False)."} + ) + overwrite_cache: bool = field( + default=False, metadata={"help": "Overwrite the cached training and evaluation sets"} + ) + frozen_bert: bool = field( + default=False, + metadata={"help": "frozen bert model."} + ) + pretrained_model: str = field(default="ProtBERT") # "ProtBERT", "ProtBERT_BFD", "OntoProtein", "ProteinDT" + pretrained_folder: str = field(default=None) + def __post_init__(self): + self.task_name = self.task_name.lower() + + +@dataclass +class DynamicTrainingArguments(TrainingArguments): + # For ensemble + save_strategy: str = field( + default='no', + metadata={"help": "The checkpoint save strategy to adopt during training."} + ) + evaluation_strategy: str = field( + default='steps', + metadata={"help": "The evaluation strategy to adopt during training."} + ) + eval_steps: int = field( + default=2000, + metadata={"help": "Number of update steps between two evaluations"} + ) + # Regularization + fix_layers: int = field( + default=0, + metadata={"help": "Fix bottom-n layers when optimizing"} + ) + evaluate_during_training: bool = field( + default=True, + metadata={"help": "evaluate during training."} + ) + fp16 = True + + +if __name__ == "__main__": + parser = HfArgumentParser((GeneralArguments, DynamicTrainingArguments)) + general_args, training_args = parser.parse_args_into_dataclasses() + print("general_args", general_args) + + set_seed(training_args.seed) + + model_name = "Rostlab/prot_bert" + chache_dir = "../data/temp_pretrained_ProtBert" + if general_args.pretrained_model == "ProtBERT_BFD": + model_name = "Rostlab/prot_bert_bfd" + chache_dir = "../data/temp_pretrained_ProtBert_BFD" + elif general_args.pretrained_model == "OntoProtein": + model_name = "zjukg/OntoProtein" + chache_dir = "../data/temp_pretrained_OntoProtein" + + tokenizer = BertTokenizerFast.from_pretrained(model_name, chache_dir=chache_dir, do_lower_case=False) + + output_mode = output_mode_mapping[general_args.task_name] + processor = dataset_processor_mapping[general_args.task_name](tokenizer) + num_labels = len(processor.get_labels()) + + train_dataset = (processor.get_train_examples(data_dir=general_args.data_dir)) + eval_dataset = (processor.get_dev_examples(data_dir=general_args.data_dir)) + + if general_args.task_name == 'remote_homology': + test_fold_dataset = ( + processor.get_test_examples(data_dir=general_args.data_dir, data_cat='test_fold_holdout') + ) + test_family_dataset = ( + processor.get_test_examples(data_dir=general_args.data_dir, data_cat='test_family_holdout') + ) + test_superfamily_dataset = ( + processor.get_test_examples(data_dir=general_args.data_dir, data_cat='test_superfamily_holdout') + ) + + elif general_args.task_name == 'ss3' or general_args.task_name == 'ss8': + cb513_dataset = ( + processor.get_test_examples(data_dir=general_args.data_dir, data_cat='cb513') + ) + ts115_dataset = ( + processor.get_test_examples(data_dir=general_args.data_dir, data_cat='ts115') + ) + casp12_dataset = ( + processor.get_test_examples(data_dir=general_args.data_dir, data_cat='casp12') + ) + + else: + test_dataset = ( + processor.get_test_examples(data_dir=general_args.data_dir, data_cat='test') + ) + + model = model_mapping[general_args.task_name].from_pretrained( + model_name, + cache_dir=chache_dir, + mean_output=general_args.mean_output, + num_labels=len(processor.get_labels()), + ) + if general_args.pretrained_model in ["ProteinDT"]: + assert general_args.pretrained_folder is not None + input_model_path = os.path.join(general_args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + missing_keys, unexpected_keys = model.bert.load_state_dict(state_dict, strict=False) + print("missing keys: {}".format(missing_keys)) + print("unexpected keys: {}".format(unexpected_keys)) + + if general_args.frozen_bert: + unfreeze_layers = ['layer.29', 'bert.pooler', 'classifier'] + for name, parameters in model.named_parameters(): + parameters.requires_grad = False + for tags in unfreeze_layers: + if tags in name: + parameters.requires_grad = True + break + + if general_args.task_name == 'stability' or general_args.task_name == 'fluorescence': + training_args.metric_for_best_model = "eval_spearmanr" + elif general_args.task_name == 'remote_homology': + training_args.metric_for_best_model = "eval_accuracy" + + if general_args.task_name == 'contact': + # training_args.do_predict=False + trainer = OntoProteinTrainer( + # model_init=init_model, + model=model, + args=training_args, + train_dataset=train_dataset, + eval_dataset=eval_dataset, + compute_metrics=build_compute_metrics_fn(general_args.task_name, output_type=output_mode), + data_collator=train_dataset.collate_fn, + optimizers=(None, None) + ) + else: + trainer = Trainer( + model=model, + args=training_args, + train_dataset=train_dataset, + eval_dataset=eval_dataset, + compute_metrics=build_compute_metrics_fn(general_args.task_name, output_type=output_mode), + data_collator=train_dataset.collate_fn, + optimizers=(None, None) + ) + + # Training + if training_args.do_train: + # pass + trainer.train() + trainer.save_model(training_args.output_dir) + tokenizer.save_pretrained(training_args.output_dir) + + # trainer.compute_metrics = metrics_mapping(args.task_name) + if general_args.task_name == 'remote_homology': + predictions_fold_family, input_ids_fold_family, metrics_fold_family = trainer.predict(test_fold_dataset) + predictions_family_family, input_ids_family_family, metrics_family_family = trainer.predict(test_family_dataset) + predictions_superfamily_family, input_ids_superfamily_family, metrics_superfamily_family = trainer.predict(test_superfamily_dataset) + print("metrics_fold: ", metrics_fold_family) + print("metrics_family: ", metrics_family_family) + print("metrics_superfamily: ", metrics_superfamily_family) + elif general_args.task_name == 'ss8' or general_args.task_name == 'ss3': + predictions_cb513, input_ids_cb513, metrics_cb513 = trainer.predict(cb513_dataset) + predictions_ts115, input_ids_ts115, metrics_ts115 = trainer.predict(ts115_dataset) + predictions_casp12, input_ids_casp12, metrics_casp12 = trainer.predict(casp12_dataset) + print("cb513: ", metrics_cb513) + print("ts115: ", metrics_ts115) + print("casp12: ", metrics_casp12) + else: + predictions_family, input_ids_family, metrics_family = trainer.predict(test_dataset) + print("metrics", metrics_family) \ No newline at end of file diff --git a/examples/downstream_TAPE_analysis.py b/examples/downstream_TAPE_analysis.py new file mode 100644 index 0000000..6bb9135 --- /dev/null +++ b/examples/downstream_TAPE_analysis.py @@ -0,0 +1,116 @@ +import os + + +def extract(file_path, task): + f_ = open(file_path, "r") + + if task in ["ss3", "ss8"]: + for line in f_.readlines(): + line = line.strip() + if line.startswith("cb513"): + line = line.replace("{", "").replace("}", "").replace(":", ",") + line = line.split(",") + value = float(line[4]) + value = "{:.5f}".format(value) + + elif task == "contact": + for line in f_.readlines(): + line = line.strip() + if line.startswith("metrics"): + line = line.replace("{", "").replace("}", "").replace(":", ",") + line = line.split(",") + value = float(line[3]) + value = "{:.5f}".format(value) + + elif task == "remote_homology": + for line in f_.readlines(): + line = line.strip() + if line.startswith("metrics_fold"): + line = line.replace("{", "").replace("}", "").replace(":", ",") + line = line.split(",") + value = float(line[4]) + value = "{:.5f}".format(value) + + elif task == "fluorescence": + for line in f_.readlines(): + line = line.strip() + if line.startswith("metrics"): + line = line.replace("{", "").replace("}", "").replace(":", ",") + line = line.split(",") + value = float(line[3]) + value = "{:.5f}".format(value) + + elif task == "stability": + for line in f_.readlines(): + line = line.strip() + if line.startswith("metrics"): + line = line.replace("{", "").replace("}", "").replace(":", ",") + line = line.split(",") + value = float(line[3]) + value = "{:.5f}".format(value) + + return value + + +task2hyper = { + "ss3": [ + "3-3e-5-5-2-8-0.08", + ], + "ss8": [ + "3-3e-5-5-2-8-0.08", + # "3-3e-5-5-2-16-0.08", + ], + "contact": [ + # "3-3e-5-10-1-1-0.08", + "3-3e-5-10-1-2-0.08", + ], + "remote_homology": [ + # "3-3e-5-10-1-64-0.08", + "3-3e-5-10-8-8-0.08", + ], + "fluorescence": [ + "3-3e-5-25-4-16-0.0-True", + ], + "stability": [ + # "3-3e-5-1-2-16-0.08", + # "3-3e-5-3-2-16-0.08", + "3-3e-5-5-2-16-0.08", + ], +} + +if __name__ == "__main__": + task_list = [ + "ss3", "ss8", "contact", "remote_homology", "fluorescence", "stability", + ] + pretrained_model_list=[ + "ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5", + "ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-InfoNCE-0.1-batch-9-gpu-8-epoch-5", + # "ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10", + ] + + for pretrained_mode in pretrained_model_list: + row = "ProteinCLAP" + + for task in task_list: + value_list = [] + for hyper in task2hyper[task]: + file_path = os.path.join("../output", pretrained_mode, "downstream_TAPE", task, hyper, "result.txt") + try: + value = extract(file_path, task) + value_list.append(value) + except: + print("% missing {}".format(file_path)) + + if len(value_list) > 0: + optimal_value = max(value_list) + print("task", task, value_list) + row = "{} & {}".format(row, optimal_value) + else: + row = "{} & {}".format(row, "--") + + print("%", pretrained_mode) + row += "\\\\" + print(row) + print() + print() + print() diff --git a/examples/downstream_Text2Protein/step_01_text_retrieval.py b/examples/downstream_Text2Protein/step_01_text_retrieval.py new file mode 100644 index 0000000..164acb9 --- /dev/null +++ b/examples/downstream_Text2Protein/step_01_text_retrieval.py @@ -0,0 +1,52 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import torch + + +def load_text_sequence_file(file_path): + text_sequence_list = [] + f = open(file_path, 'r') + for line_idx, line in enumerate(f.readlines()): + line = line.strip() + if line_idx % 2 == 0: + uniprot = line + else: + text_sequence = line.strip() + text_sequence_list.append(text_sequence) + return text_sequence_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + args = parser.parse_args() + print("arguments", args) + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + text_sequence_file = "../../data/SwissProtCLAP/text_sequence.txt" + text_sequence_list = load_text_sequence_file(text_sequence_file) + text_sequence_set = set(text_sequence_list) + print("len of text_sequence_list: {}".format(len(text_sequence_list))) + print("len of text_sequence_set: {}".format(len(text_sequence_set))) + # len of text_sequence_list: 541159 + # len of text_sequence_set: 146044 + text_sequence_list = list(text_sequence_list) + + output_file = "step_01_text_retrieval.txt" + f = open(output_file, 'w') + sampled_text_sequence_list = random.sample(text_sequence_list, 10000) + for text_sequence in sampled_text_sequence_list: + print(text_sequence, file=f) diff --git a/examples/downstream_Text2Protein/step_01_text_retrieval.txt b/examples/downstream_Text2Protein/step_01_text_retrieval.txt new file mode 100644 index 0000000..f5c3ffa --- /dev/null +++ b/examples/downstream_Text2Protein/step_01_text_retrieval.txt @@ -0,0 +1,10000 @@ +Promotes colloidosmotic lysis by binding to the midgut epithelial cells of Coleoptera. The crystal protein is produced during sporulation and is accumulated both as an inclusion and as part of the spore coat. Toxic segment of the protein is located in the N-terminus. Belongs to the delta endotoxin family. +Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication. Homooligomer. Both monomeric and oligomeric forms interact with RNA. Interacts with protein M. Interacts with NSP3; this interaction serves to tether the genome to the newly translated replicase-transcriptase complex at a very early stage of infection. Located inside the virion, complexed with the viral RNA. Probably associates with ER-derived membranes where it participates in viral RNA synthesis and virus budding. ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection. Phosphorylated on serine and threonine residues. Belongs to the betacoronavirus nucleocapsid protein family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Belongs to the Abd-B homeobox family. +Belongs to the bacterial ribosomal protein bL33 family. +Part of an ATP-driven transport system CPn0541/CPn0542/CPn0543 for a metal. Probably responsible for energy coupling to the transport system. Belongs to the ABC transporter superfamily. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Coactivator for the transcription factor DhaS. The heterotetramer formed by DhaQ and DhaS functions as transcriptional regulator. Activated by covalent binding of dihydroxyacetone to DhaQ. The complex activates the dhaKLM operon. Homodimer. Interacts with a homodimer of DhaS. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Allosterically activated by GTP. Probably inhibited by UTP. Positive cooperativity is observed with ATP as variable substrate, but it is strongly reduced in the presence of GTP. GTP enhances the affinity for ATP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Essential for the maintenance of cell size and integrity in response to osmotic stress. H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 manganese ions per subunit. Inhibited by the regulatory subunits VHS3 and SIS2. Interacts with SIS2 and VHS3, which regulate its activity. Present with 217 molecules/cell in log phase SD medium. Belongs to the PPP phosphatase family. PP-Z subfamily. Was originally thought to originate from a rabbit cDNA library and was known as protein phosphatase Z (PP-Z). +Involved in ethylene-dependent salt stress responses by reducing reactive oxygen species (ROS) accumulation. Triggered by EIN3. Increased sensitivity to salt. +Catalyzes the anaerobic reduction of fumarate to succinate (PubMed:24361839, PubMed:33107907). Uses NADH as the inherent electron donor in this process (PubMed:33107907). Is involved in anaerobic fumarate respiration in K.pneumoniae (PubMed:33107907). NAD(+) + succinate = fumarate + H(+) + NADH Binds 1 FAD per subunit. Binds 2 FMN prosthetic groups per subunit. 1 FMN is bound covalently, while the other is non-covalent. kcat is about 10 sec(-1). Optimum pH is 6.0-6.5. Monomer. Induced under anaerobic conditions in the presence of fumarate or malate, but not tartrate. Is repressed under aerobic conditions. Consists of three domains. The first domain of FRD (OYE-like, PF00724) is homologous to Old Yellow Enzyme (OYE). It carries a non-covalently bound FMN and is used for NADH oxidation. The second, FMN_bind domain (PF04205) contains a covalently bound FMN, that acts as an electron carrier between the two other domains of FRD. The C-terminal FAD_binding_2 domain contains a non-covalently bound FAD and forms a site for fumarate reduction. Is flavinylated on Thr-447 by ApbE2, encoded in a neighboring gene (PubMed:24361839). Flavinylation is essential for catalytic activity (PubMed:31834358). Cells lacking this gene lack cytoplasmic fumarate reductase activity, while retaining this activity in the membrane fraction. Belongs to the FAD-dependent oxidoreductase 2 family. FRD/SDH subfamily. +Potential odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Catalyzes the transfer of adenosine 5'-monophosphate (AMP) to Ser, Thr or Tyr residues of target proteins (AMPylation). ATP + L-tyrosyl-[protein] = diphosphate + O-(5'-adenylyl)-L-tyrosyl-[protein] ATP + L-threonyl-[protein] = 3-O-(5'-adenylyl)-L-threonyl-[protein] + diphosphate ATP + L-seryl-[protein] = 3-O-(5'-adenylyl)-L-seryl-[protein] + diphosphate Belongs to the SELO family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homodimer. Belongs to the ThiC family. +Transcriptional factor which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3'. Forms either a homodimer or a heterodimer with a related family member. Belongs to the COE family. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a lipid X + a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a lipid A disaccharide + H(+) + UDP Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Belongs to the LpxB family. +Potential calcium sensor. Although assigned as a calmodulin family member by Ref.4, it only contains EF-hand domains. +Involved in the biosynthesis of jasmonic acid, a growth regulator that is implicated also as a signaling molecule in plant defense. Converts 13-hydroperoxylinolenic acid to 12,13-epoxylinolenic acid (By similarity). (13S)-hydroperoxy-(9Z,11E,15Z)-octadecatrienoate = (9Z,13S,15Z)-12,13-epoxyoctadeca-9,11,15-trienoate + H2O Lipid metabolism; oxylipin biosynthesis. Not expressed in dark-grown seedlings. Not induced by red (R) light, or abrasion in dark-grown seedlings. Belongs to the cytochrome P450 family. +Multifunctional enzyme that converts the viral RNA genome into dsDNA in viral cytoplasmic capsids. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3'- to 5'-endonucleasic mode. Neo-synthesized pregenomic RNA (pgRNA) are encapsidated together with the P protein, and reverse-transcribed inside the nucleocapsid. Initiation of reverse-transcription occurs first by binding the epsilon loop on the pgRNA genome, and is initiated by protein priming, thereby the 5'-end of (-)DNA is covalently linked to P protein. Partial (+)DNA is synthesized from the (-)DNA template and generates the relaxed circular DNA (RC-DNA) genome. After budding and infection, the RC-DNA migrates in the nucleus, and is converted into a plasmid-like covalently closed circular DNA (cccDNA). The activity of P protein does not seem to be necessary for cccDNA generation, and is presumably released from (+)DNA by host nuclear DNA repair machinery (By similarity). a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Endonucleolytic cleavage to 5'-phosphomonoester. Terminal protein domain (TP) is hepadnavirus-specific. Spacer domain is highly variable and separates the TP and RT domains. Polymerase/reverse-transcriptase domain (RT) and ribonuclease H domain (RH) are similar to retrovirus reverse transcriptase/RNase H (By similarity). The polymerase/reverse transcriptase (RT) and ribonuclease H (RH) domains are structured in five subdomains: finger, palm, thumb, connection and RNase H. Within the palm subdomain, the 'primer grip' region is thought to be involved in the positioning of the primer terminus for accommodating the incoming nucleotide. The RH domain stabilizes the association of RT with primer-template (By similarity). Belongs to the hepadnaviridae P protein family. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. +Important for the metabolism of amino acids and Krebs-cycle related organic acids. In plants, it is involved in nitrogen metabolism and in aspects of carbon and energy metabolism (By similarity). 2-oxoglutarate + L-aspartate = L-glutamate + oxaloacetate Homodimer. In eukaryotes there are cytoplasmic, mitochondrial and chloroplastic isozymes. Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. +DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. Belongs to the NAD-dependent DNA ligase family. LigA subfamily. +Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS. aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-phosphate H2O + L-glutamine = L-glutamate + NH4(+) Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis. In the presence of PdxS, forms a dodecamer of heterodimers. Only shows activity in the heterodimer. Belongs to the glutaminase PdxT/SNO family. +3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs (By similarity). Exonucleolytic cleavage of poly(A) to 5'-AMP. Belongs to the CAF1 family. The predicted gene has been split into 2 genes: At3g25430 and At3g25440. +Putative solute transporter. Belongs to the SLC35F solute transporter family. +D-arabinose 5-phosphate + H2O + phosphoenolpyruvate = 3-deoxy-alpha-D-manno-2-octulosonate-8-phosphate + phosphate Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate: step 2/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsA family. +Tubulin is the major constituent of microtubules. The gamma chain is found at microtubule organizing centers (MTOC) such as the spindle poles or the centrosome. Pericentriolar matrix component that regulates alpha/beta chain minus-end nucleation, centrosome duplication and spindle formation (By similarity). Mainly localizes to the centrosome, but a fraction is found outside of the centrosome in the cytoplasm. Phosphorylation at Ser-131 by BRSK1 regulates centrosome duplication, possibly by mediating relocation of gamma-tubulin and its associated proteins from the cytoplasm to the centrosome. Belongs to the tubulin family. +Seems to be required for the assembly of the photosystem I complex. Belongs to the Ycf4 family. +Belongs to the bacterial ribosomal protein bL33 family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Interacts with PHB2; the interaction decreases in absence of SPHK2 (By similarity). Interacts with AFG1L (By similarity). Interacts with ABCB7; this interaction allows the regulation of cellular iron homeostasis and cellular reactive oxygen species (ROS) levels in cardiomyocytes (By similarity). Belongs to the cytochrome c oxidase IV family. +Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser) ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec) Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. Homodimer. The tRNA molecule binds across the dimer. Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily. +Has no ubiquitin ligase activity on its own. The UBE2V1-UBE2N heterodimer catalyzes the synthesis of non-canonical poly-ubiquitin chains that are linked through Lys-63. This type of poly-ubiquitination activates IKK and does not seem to involve protein degradation by the proteasome. Plays a role in the activation of NF-kappa-B mediated by IL1B, TNF, TRAF6 and TRAF2. Mediates transcriptional activation of target genes. Plays a role in the control of progress through the cell cycle and differentiation. Plays a role in the error-free DNA repair pathway and contributes to the survival of cells after DNA damage. Promotes TRIM5 capsid-specific restriction activity and the UBE2V1-UBE2N heterodimer acts in concert with TRIM5 to generate 'Lys-63'-linked polyubiquitin chains which activate the MAP3K7/TAK1 complex which in turn results in the induction and expression of NF-kappa-B and MAPK-responsive inflammatory genes. Together with RNF135 and UBE2N, catalyzes the viral RNA-dependent 'Lys-63'-linked polyubiquitination of RIG-I/DDX58 to activate the downstream signaling pathway that leads to interferon beta production (PubMed:31006531). UBE2V1-UBE2N together with TRAF3IP2 E3 ubiquitin ligase mediate 'Lys-63'-linked polyubiquitination of TRAF6, a component of IL17A-mediated signaling pathway. Heterodimer with UBE2N (PubMed:11057907, PubMed:16307917, PubMed:16893187). Interacts (UBE2V2-UBE2N heterodimer) with the E3 ligase STUB1 (via the U-box domain); the complex has a specific 'Lys-63'-linked polyubiquitination activity (PubMed:16307917). Interacts with TRAF6 (PubMed:11057907, PubMed:16307917). Excluded from the nucleolus. Additional isoforms seem to exist. Highly expressed in thyroid, pancreas, spinal cord, lymph node, trachea, adrenal gland, bone marrow and pancreas. Detected at low levels in heart, breast, placenta, brain, liver, kidney, stomach and lung. Down-regulated during differentiation of cultured colon adenocarcinoma cells. In human, PESD1/KUA and UBE2V1/UEV1 are adjacent genes which can produce independent proteins and can also be fused to form a PESD1-UBE2V1 hybrid protein. Belongs to the ubiquitin-conjugating enzyme family. +Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + H(+) + holo-[ACP] Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxD subfamily. +Type II interferon produced by immune cells such as T-cells and NK cells that plays crucial roles in antimicrobial, antiviral, and antitumor responses by activating effector immune cells and enhancing antigen presentation. Primarily signals through the JAK-STAT pathway after interaction with its receptor IFNGR1 to affect gene regulation. Upon IFNG binding, IFNGR1 intracellular domain opens out to allow association of downstream signaling components JAK2, JAK1 and STAT1, leading to STAT1 activation, nuclear translocation and transcription of IFNG-regulated genes. Many of the induced genes are transcription factors such as IRF1 that are able to further drive regulation of a next wave of transcription. Plays a role in class I antigen presentation pathway by inducing a replacement of catalytic proteasome subunits with immunoproteasome subunits. In turn, increases the quantity, quality, and repertoire of peptides for class I MHC loading. Increases the efficiency of peptide generation also by inducing the expression of activator PA28 that associates with the proteasome and alters its proteolytic cleavage preference. Up-regulates as well MHC II complexes on the cell surface by promoting expression of several key molecules such as cathepsins B/CTSB, H/CTSH, and L/CTSL (By similarity). Participates in the regulation of hematopoietic stem cells during development and under homeostatic conditions by affecting their development, quiescence, and differentiation (By similarity). Homodimer. Interacts with IFNGR1 (via extracellular domain); this interaction promotes IFNGR1 dimerization. Released primarily from activated T lymphocytes. Belongs to the type II (or gamma) interferon family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. It is uncertain whether Met-1 or Met-10 is the initiator. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Possesses antifungal activity and is also active on two tested Gram-positive bacteria but is non-toxic for Gram-negative bacteria and cultured human cells. Homodimer. Seed specific. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the AMP family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +May play a role in neurotransmitter secretion. Predominantly cytosolic. Also exists as a membrane-bound form which has been found associated with synaptic vesicles and also with the Golgi complex and immature secretory granules. Contaminating sequence. Potential poly-A sequence. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Secreted metalloproteinase that allows assimilation of proteinaceous substrates. Shows high activities on basic nuclear substrates such as histone and protamine. May be involved in virulence (By similarity). Preferential cleavage of bonds with hydrophobic residues in P1'. Also 3-Asn-|-Gln-4 and 8-Gly-|-Ser-9 bonds in insulin B chain. Binds 1 zinc ion per subunit. Belongs to the peptidase M35 family. Truncated N-terminus. +Integral membrane transporter that imports quinic acid to be catabolized as a carbon source. Interacts with creB. Ubiquitinated. Deubiquitinated by creB, probably to control its activity or amount. Belongs to the major facilitator superfamily. Sugar transporter (TC 2.A.1.1) family. +Belongs to the ParA family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Involved in aliphatic epoxide carboxylation (PubMed:10411892, PubMed:9150202). Catalyzes the reductive cleavage of the thioether bond of 2-oxopropyl-coenzyme M (2-KPC), and the subsequent carboxylation of the ketopropyl cleavage product, yielding the products acetoacetate and free coenzyme M (PubMed:10411892). acetoacetate + coenzyme M + NADP(+) = 2-oxopropyl-coenzyme M + CO2 + NADPH Binds 1 FAD per subunit. Inhibited (at 40%) by the coenzyme M analog 2-bromoethanesulfonate (BES). BES is a time-dependent inactivator of dithiothreitol-reduced 2-KPCC, where the redox active cysteines are in the free thiol forms. BES does not inactivate air-oxidized 2-KPCC, where the redox active cysteine pair is in the disulfide form. BES specifically alkylates the interchange thiol that facilitates thioether bond cleavage and enolacetone formation during catalysis. Alkene metabolism; propylene degradation. Homodimer (PubMed:9150202, PubMed:12390015). Component II of the aliphatic epoxide carboxylation complex together with components I, III and IV (PubMed:9150202, PubMed:10411892). Contains three domains, the FAD binding domain, the NADPH binding domain, and the dimerization domain (PubMed:12390015). The binding of the substrate induces a conformational change that results in the sequestration of the substrate at the dimer interface (PubMed:12390015, PubMed:16388586). The active site is a redox-active disulfide bond (PubMed:12390015, PubMed:16388586). 2-KPC reduction and carboxylation assumes the formation of a mixed disulfide between the interchange thiol (Cys-82) and coenzyme M (PubMed:16388586). Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. +Mediates visceral muscle contractile activity (myotropic activity). Belongs to the kinin family. +Probable lysosomal cobalamin transporter. Required to export cobalamin from lysosomes allowing its conversion to cofactors (By similarity). Belongs to the LIMR family. LMBRD1 subfamily. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. Monomer and homodimer (By similarity). Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved. A single SecA monomer interacts with SecY in the channel. Distribution is 50-50. Belongs to the SecA family. +Required for processing of 20S pre-rRNA precursor and biogenesis of 40S ribosomal subunits. May be required for trophinin-dependent regulation of cell adhesion during implantation of human embryos. Binds trophinin, tastin and cytokeratins. Associated with 40S ribosomal subunits. Found in the placenta from the sixth week of pregnancy. Was localized in the cytoplasm of the syncytiotrophoblast in the chorionic villi and in endometrial decidual cells at the uteroplacental interface. After week 10, the level decreased and then disappeared from placental villi. HeLa cells lacking BYSL show a delay in the processing of the 18S rRNA component of the 40S ribosomal subunit. HT-H cells lacking BYSL show trophinin-independent signaling through ERBB4. Belongs to the bystin family. Truncated N-terminus. +Cystine/H(+) symporter that mediates export of cystine, the oxidized dimer of cysteine, from lysosomes (PubMed:11689434, PubMed:18337546, PubMed:22232659, PubMed:29467429, PubMed:33208952, PubMed:15128704). Plays an important role in melanin synthesis by catalyzing cystine export from melanosomes, possibly by inhibiting pheomelanin synthesis (PubMed:22649030). In addition to cystine export, also acts as a positive regulator of mTORC1 signaling in kidney proximal tubular cells, via interactions with components of the v-ATPase and Ragulator complexes (By similarity). Also involved in small GTPase-regulated vesicle trafficking and lysosomal localization of LAMP2A, independently of cystine transporter activity (By similarity). H(+)(out) + L-cystine(out) = H(+)(in) + L-cystine(in) H(+)(out) + L-cystine(out) = H(+)(in) + L-cystine(in) H(+)(out) + L-cystine(out) = H(+)(in) + L-cystine(in) Interacts with components of the V-ATPase complex. Interacts with components of the Ragulator complex. Interacts with RRAGA/RagA and RRAGC/RagC (By similarity). Interacts with AP-3 complex subunit mu (AP3M1 or AP3M2) (PubMed:25753619). AP-3 complex is required for localization to the lysosome. Strongly expressed in pancreas, kidney (adult and fetal), skeletal muscle, melanocytes and keratinocytes (PubMed:22649030). Expressed at lower levels in placenta and heart. Weakly expressed in lung, liver and brain (adult and fetal) (PubMed:22649030). Represents 5-20 % of CTNS transcripts, with the exception of the testis that expresses both isoforms in equal proportions. The lysosomal targeting motif, together with the second PQ-loop mediate targeting to the lysosome. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the cystinosin family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Specifically deubiquitinates 'Lys-120' of histone H2A (H2AK119Ub), a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Deubiquitination of histone H2A is a prerequisite for subsequent phosphorylation at 'Ser-11' of histone H3 (H3S10ph), and is required for chromosome segregation when cells enter into mitosis. In resting B- and T-lymphocytes, phosphorylation by AURKB leads to enhance its activity, thereby maintaining transcription in resting lymphocytes. Regulates Hox gene expression via histone H2A deubiquitination. Prefers nucleosomal substrates. Does not deubiquitinate histone H2B. Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Homotetramer. The UBP-type zinc finger binds 3 zinc ions that form a pair of cross-braced ring fingers encapsulated within a third zinc finger in the primary structure. It recognizes the C-terminal tail of free ubiquitin. Phosphorylated at the onset of mitosis and dephosphorylated during the metaphase/anaphase transition. Phosphorylation by AURKB enhances the deubiquitinase activity. Belongs to the peptidase C19 family. USP16 subfamily. +Acyl-CoA thioesterases are a group of enzymes that catalyze the hydrolysis of acyl-CoAs to the free fatty acid and coenzyme A (CoASH), providing the potential to regulate intracellular levels of acyl-CoAs, free fatty acids and CoASH. H2O + hexadecanoyl-CoA = CoA + H(+) + hexadecanoate Homodimer. Expressed in all tissues examined. Up-regulated in nasopharyngeal carcinoma (at protein level). A functional variant in the transcriptional regulatory region of in ACOT7L cosegregates with disease phenotype in family affected by nasopharyngeal carcinoma. The variant creates an AP1-binding site that significantly enhances binding of AP1 to the promoter, resulting in up-regulation. Could be the product of a pseudogene. The peptide used to produce antibodies against ACOT7L matches at 85% with ACOT7 and the antibodies may not be specific to ACOT7L. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +Essential for recycling GMP and indirectly, cGMP. ATP + GMP = ADP + GDP Belongs to the guanylate kinase family. +Heavy-metal-binding protein (By similarity). Involved in disease resistance (PubMed:12684538). Up-regulated by cadmium. Efficiently farnesylated in vitro. Strongly increased bacterial disease susceptibility. Belongs to the HIPP family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Oxidative deamination of D-amino acids. A + a D-alpha-amino acid + H2O = a 2-oxocarboxylate + AH2 + NH4(+) Amino-acid degradation; D-alanine degradation; NH(3) and pyruvate from D-alanine: step 1/1. Belongs to the DadA oxidoreductase family. +Belongs to the UPF0234 family. +Extended N-terminus. +Has a post-transcriptional repressor function in flagellum biogenesis. Associates with the 5'-UTR of fljK mRNA and promotes its degradation. Belongs to the FlbT family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvP family. +Involved in oxygen transport from the lung to the various peripheral tissues. Heterotetramer of two alpha-D chains and two beta chains. Red blood cells. In birds, the alpha-D chain occurs in a minor hemoglobin component, called hemoglobin d, which is expressed in late embryonic and adult life. Belongs to the globin family. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate. L-leucyl-tRNA(Leu) + N-terminal L-glutamyl-[protein] = H(+) + N-terminal L-leucyl-L-glutamyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-aspartyl-[protein] = H(+) + N-terminal L-leucyl-L-aspartyl-[protein] + tRNA(Leu) Belongs to the R-transferase family. Bpt subfamily. +2-O-(alpha-D-mannosyl)-3-phosphoglycerate + H2O = (2R)-2-O-(alpha-D-mannosyl)-glycerate + phosphate Belongs to the HAD-like hydrolase superfamily. MPGP family. +Involved in local disassembly of cortical microtubules when associated with ICR5 and KIN13A. Component of the active ARAC10-IRC5-KIN13A complex (PubMed:24280391). Interacts with ICR5 (PubMed:22984069). Recruited along cortical microtubules upon interaction with ICR5. Belongs to the small GTPase superfamily. Rho family. +(2R)-O-phospho-3-sulfolactate + H2O = (2R)-3-sulfolactate + phosphate Belongs to the ComB family. +The C-terminal propeptide is autocleaved. Belongs to the peptidase S8 family. +Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. Homodimer. Belongs to the transketolase family. DXPS subfamily. +Involved in the biosynthesis of ADP-glucose, a building block required for the elongation reactions to produce glycogen. Catalyzes the reaction between ATP and alpha-D-glucose 1-phosphate (G1P) to produce pyrophosphate and ADP-Glc. alpha-D-glucose 1-phosphate + ATP + H(+) = ADP-alpha-D-glucose + diphosphate Glycan biosynthesis; glycogen biosynthesis. Homotetramer. Belongs to the bacterial/plant glucose-1-phosphate adenylyltransferase family. +Integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, functions primarily as a coreceptor for MHC class I molecule:peptide complex. The antigens presented by class I peptides are derived from cytosolic proteins while class II derived from extracellular proteins. Interacts simultaneously with the T-cell receptor (TCR) and the MHC class I proteins presented by antigen presenting cells (APCs). In turn, recruits the Src kinase LCK to the vicinity of the TCR-CD3 complex. A palmitoylation site in the cytoplasmic tail of CD8B chain contributes to partitioning of CD8 into the plasma membrane lipid rafts where signaling proteins are enriched. Once LCK recruited, it initiates different intracellular signaling pathways by phosphorylating various substrates ultimately leading to lymphokine production, motility, adhesion and activation of cytotoxic T-lymphocytes (CTLs). Additionally, plays a critical role in thymic selection of CD8+ T-cells. Forms disulfide-linked heterodimers with CD8A at the cell surface. Interacts with CD3D; this interaction couples TCR-CD3 with CD8. Interacts with LCK. Requires the partner CD8A for efficient cell surface expression (PubMed:3145196). The heterodimer CD8A/CD8B localizes to lipid rafts due to CD8B cytoplasmic tail palmitoylation. Isoform 1, isoform 3, isoform 5, isoform 6, isoform 7 and isoform 8 are expressed in both thymus and peripheral CD8+ T-cells. Expression of isoform 1 is higher in thymus CD8+ T-cells than in peripheral CD8+ T-cells. Expression of isoform 6 is higher in peripheral CD8+ T-cells than in thymus CD8+ T-cells. Phosphorylated as a consequence of T-cell activation. Palmitoylated at the cytoplasmic tail and thereby targets the heterodimer CD8A/CD8B to lipid rafts unlike CD8A homodimers. CD8 entry +Transcriptional repressor which forms a negative regulatory component of the circadian clock and acts independently of the circadian transcriptional repressors: CRY1, CRY2 and BHLHE41. In a histone deacetylase-dependent manner represses the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Abrogates the interaction of ARNTL/BMAL1 with the transcriptional coactivator CREBBP and can repress the histone acetyl-transferase activity of the CLOCK-ARNTL/BMAL1 heterodimer, reducing histone acetylation of its target genes. Rhythmically binds the E-box elements (5'-CACGTG-3') on circadian gene promoters and its occupancy shows circadian oscillation antiphasic to ARNTL/BMAL1. Interacts with the glucocorticoid receptor (NR3C1) and contributes to the repressive function in the glucocorticoid response. Interacts with ARNTL/BMAL1, PER2, CRY2, BHLHE41, HDAC1 NR3C1. Co-localizes with the CLOCK-ARNTL/BMAL1 heterodimer in the PML body. Expression in the liver oscillates in a circadian manner with highest levels at Zeitgeber time (ZT) 12 hours (at protein level). Expression in the heart, lung, stomach and kidney oscillate in a circadian manner with highest levels at approximately circadian time (CT) 12 hours. Its expression levels peak at circadian time 12 hours (CT12), 8 hours earlier than the peak of PER1/2 and CRY1/2 transcriptional repressors (peak CT20-CT24). Thus, it can repress the CLOCK-ARNTL/BMAL1 activity in a different time window compared to CRY and PER proteins. Mice exhibit a longer circadian period of locomotor activity, alteration in the expression of core clock genes and impairment of the response of the circadian clock to stress. The peaks of DBP, NR1D1 and PER1 gene expression persists longer in the liver between Zeitgeber times (ZT) 12-14 hours. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)). Belongs to the cytochrome c oxidase subunit 3 family. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Belongs to the bacterial ribosomal protein bL28 family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Belongs to the universal ribosomal protein uS2 family. +Blue light-dependent regulator that is the input of the circadian feedback loop. Has no photolyase activity for cyclobutane pyrimidine dimers or 6-4 photoproducts. Regulation of expression by light suggests a role in photoreception for locomotor activity rhythms. Light induces the degradation of cry, likely due to conformational change in the photoreceptor leading to targeting to the proteasome. Under circadian regulation, expression is influenced by the clock pacemaker genes period, timeless, Clock and cycle. Binding to tim irreversibly commits tim to proteasomal degradation. Functions, together with per, as a transcriptional repressor required for the oscillation of peripheral circadian clocks and for the correct specification of clock cells. Genes directly activated by the transcription factors Clock (Clk) and cycle (cyc) are repressed by cry. Necessary for light-dependent magnetosensitivity, an intact circadian system is not required for the magnetoreception mechanism to operate. Required for both the naive and trained responses to magnetic field, consistent with the notion that Cry is in the input pathway of magnetic sensing (By similarity). Binds 1 FAD per subunit. Interacts with tim and per; promoted by light conditions. Nuclear translocation initiates after the perception of a light signal. Accumulates in the perinuclear region about one hour before translocation into the nucleus. Translocation occurs through interaction with other Clock proteins such as tim and per (By similarity). FAD-binding region regulates cry stability, cry-tim interaction, and circadian photosensitivity. Photolyase/cryptochrome alpha/beta domain is sufficient for light detection and phototransduction. Belongs to the DNA photolyase class-1 family. +Belongs to the bacterial ribosomal protein bL34 family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Repressed under conditions of excess protein secretion capacity and derepressed when protein secretion becomes limiting. This is regulated by SecM. Belongs to the SecA family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. Was originally proposed to be fused with ccmD. +Involved in oxygen transport from the lung to the various peripheral tissues. Hemopressin acts as an antagonist peptide of the cannabinoid receptor CNR1. Hemopressin-binding efficiently blocks cannabinoid receptor CNR1 and subsequent signaling. Heterotetramer of two alpha chains and two beta chains. Red blood cells. Belongs to the globin family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +May play a role in postsynaptic function. The C-terminal gamma-secretase processed fragment, ALID1, activates transcription activation through APBB1 (Fe65) binding. Couples to JIP signal transduction through C-terminal binding. May interact with cellular G-protein signaling pathways. Can regulate neurite outgrowth through binding to components of the extracellular matrix such as heparin and collagen I. The gamma-CTF peptide, C30, is a potent enhancer of neuronal apoptosis. Monomer and homodimer. Heparin binding promotes homodimerization. Binds, via its C-terminus, to the PID domain of several cytoplasmic proteins, including APBB and APBA family members, MAPK8IP1 and DAB1 (By similarity). Binding to Dab1 inhibits its serine phosphorylation. Interacts with CPEB1. Interacts (via NPXY motif) with DAB2 (via PID domain); the interaction is impaired by tyrosine phosphorylation of the NPXY motif. Interacts (via NPXY motif) with DAB1. C-terminally processed in the Golgi complex. The NPXY sequence motif found in many tyrosine-phosphorylated proteins is required for the specific binding of the PID domain. However, additional amino acids either N- or C-terminal to the NPXY motif are often required for complete interaction. The NPXY site is also involved in clathrin-mediated endocytosis. Proteolytically cleaved by caspases during neuronal apoptosis. Cleaved, in vitro, at Asp-624 by caspase-3 (By similarity). N- and O-glycosylated. Binds zinc and copper in the extracellular domain. Zinc-binding increases heparin binding. No Cu(2+) reducing activity with copper-binding. Belongs to the APP family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in the mitochondria. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Subunit of the heterotrimeric GatCAB amidotransferase (AdT) complex, composed of A (qrsl1), B (gatb) and C (gatc) subunits. Belongs to the GatC family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Catalyzes the formation of N(4)-acetylcytidine (ac(4)C) at the wobble position of elongator tRNA(Met), using acetate and ATP as substrates. First activates an acetate ion to form acetyladenylate (Ac-AMP) and then transfers the acetyl group to tRNA to form ac(4)C34. acetate + ATP + cytidine(34) in elongator tRNA(Met) = AMP + diphosphate + N(4)-acetylcytidine(34) in elongator tRNA(Met) Belongs to the TmcAL family. +Lysophospholipase which preferentially deacylates unsaturated lysophosphatidylcholine (C18:1), generating glycerophosphocholine. Also can deacylate, to a lesser extent, lysophosphatidylethanolamine (C18:1), lysophosphatidyl-L-serine (C18:1) and lysophosphatidic acid (C16:0). a 1-acyl-sn-glycero-3-phosphocholine + H2O = a fatty acid + H(+) + sn-glycerol 3-phosphocholine 1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + H2O = (9Z)-octadecenoate + H(+) + sn-glycerol 3-phosphocholine 1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine + H2O = (9Z)-octadecenoate + H(+) + sn-glycero-3-phosphoethanolamine 1-(9Z-octadecenoyl)-sn-glycero-3-phospho-L-serine + H2O = (9Z)-octadecenoate + H(+) + sn-glycero-3-phospho-L-serine 1-hexadecanoyl-sn-glycero-3-phosphocholine + H2O = H(+) + hexadecanoate + sn-glycerol 3-phosphocholine 1-hexadecanoyl-sn-glycero-3-phosphate + H2O = H(+) + hexadecanoate + sn-glycerol 3-phosphate Expressed in the brain, liver, kidney, lung and testis. The 3 cNMP binding domains are required for localization to the endoplasmic reticulum. The cNMP binding domain 3 is involved in the binding to lipid droplets. Belongs to the NTE family. It is uncertain whether Met-1 or Met-27 is the initiator. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Involved in pyrimidine breakdown. H2O + uridine = D-ribose + uracil Belongs to the IUNH family. +May be involved in proton extrusion. Indirectly promotes efficient inorganic carbon uptake into chloroplasts. Belongs to the Cema family. +Belongs to the UPF0173 family. +Catalyzes the ATP- and NADPH-dependent reduction of carboxylic acids to the corresponding aldehydes (PubMed:28719588). Catalyzes the reduction of a very wide range of carboxylic acids, including benzoic acids, heterocyclic, phenylacetic, phenylpropanoic and fatty acid substrates (PubMed:28719588). a carboxylate + ATP + H(+) + NADPH = AMP + an aldehyde + diphosphate + NADP(+) Binds 1 phosphopantetheine covalently. The N-terminal domain likely catalyzes substrate activation by formation of an initial acyl-AMP intermediate, the central region contains the phosphopantetheine attachment site, and the C-terminal domain catalyzes the reduction by NADPH of the intermediate thioester formed from the attack of the phosphopantetheine thiol at the carbonyl carbon of acyl-AMP (By similarity). Large-scale domain motions occur between the adenylation and thiolation states. Phosphopantetheine binding alters the orientation of a key Asp, resulting in a productive orientation of the bound nicotinamide. This ensures that further reduction of the aldehyde product does not occur (PubMed:28719588). Belongs to the ATP-dependent AMP-binding enzyme family. Carboxylic acid reductase subfamily. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +Catalyzes the hydrolysis of UDP-3-O-myristoyl-N-acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate, the committed step in lipid A biosynthesis. a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 2/6. Belongs to the LpxC family. +Component of the spindle pole body (SPB) required for insertion of the nascent SPB into the nuclear envelope and for the proper execution of spindle pole body (SPB) duplication. Connects the central plaque of the SPB with the half-bridge. Required for proper localization of CDC5 at the SPB and for proper M-phase progression (By similarity). Homodimer. Interacts with KAR1, MPS2 and SPC29. Associates with the periphary of the central plaque. Belongs to the BBP1 family. +Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA). S-adenosyl-L-methionine + uridine(54) in tRNA = 5-methyluridine(54) in tRNA + H(+) + S-adenosyl-L-homocysteine S-adenosyl-L-methionine + uridine(341) in tmRNA = 5-methyluridine(341) in tmRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. TrmA subfamily. +Required for insertion of 4Fe-4S clusters for at least IspG. Binds 1 iron-sulfur cluster per subunit. Homodimer. Belongs to the HesB/IscA family. +Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily. +Catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH, to form 3-keto-L-gulonate. 3-dehydro-L-gulonate + NAD(+) = 2,3-dioxo-L-gulonate + H(+) + NADH 3-dehydro-L-gulonate + NADP(+) = 2,3-dioxo-L-gulonate + H(+) + NADPH Homodimer. Belongs to the LDH2/MDH2 oxidoreductase family. DlgD subfamily. +Regulates the transcription of the pyrimidine nucleotide (pyr) operon in response to exogenous pyrimidines. Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrR subfamily. +Homodimer and heterodimers. Belongs to the Casparian strip membrane proteins (CASP) family. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +This regulatory protein, when combined with SAM (S-adenosylmethionine) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. Homodimer. Does not bind DNA by a helix-turn-helix motif. Belongs to the MetJ family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the proton channel; it may play a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Component of an ATP synthase complex composed of ATP5PB, ATP5MC1, ATP5F1E, ATP5PD, ATP5ME, ATP5PF, ATP5MF, MT-ATP6, MT-ATP8, ATP5F1A, ATP5F1B, ATP5F1D, ATP5F1C, ATP5PO, ATP5MG, ATP5MK and ATP5MJ (By similarity). Interacts with DNAJC30; interaction is direct (By similarity). Belongs to the ATPase A chain family. +Binds to DNA non-specifically. Could be a regulatory factor involved in maltose metabolism. Belongs to the SfsA family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +The primary product of this enzyme is 4,2',4',6'-tetrahydroxychalcone (also termed naringenin-chalcone or chalcone) which can under specific conditions spontaneously isomerize into naringenin. 4-coumaroyl-CoA + 2 H(+) + 3 malonyl-CoA = 2',4,4',6'-tetrahydroxychalcone + 3 CO2 + 4 CoA Secondary metabolite biosynthesis; flavonoid biosynthesis. Expressed at low level in seedlings after illumination with UV light. No expression in flowers or tissue culture. Belongs to the thiolase-like superfamily. Chalcone/stilbene synthases family. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +Endothelial sialomucin, also called endomucin or mucin-like sialoglycoprotein, which interferes with the assembly of focal adhesion complexes and inhibits interaction between cells and the extracellular matrix. Highly expressed in heart and kidney, followed by brain, spleen, thymus, liver and lung. Exclusively expressed in endothelial cells. Highly O-glycosylated. Sialic acid-rich glycoprotein. +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 2 subfamily. +Bifunctional enzyme that catalyzes the oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcUA) to UDP-4-keto-arabinose (UDP-Ara4O) and the addition of a formyl group to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N) to form UDP-L-4-formamido-arabinose (UDP-L-Ara4FN). The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. NAD(+) + UDP-alpha-D-glucuronate = CO2 + NADH + UDP-beta-L-threo-pentopyranos-4-ulose (6S)-10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinose = (6S)-5,6,7,8-tetrahydrofolate + H(+) + UDP-4-deoxy-4-formamido-beta-L-arabinose Nucleotide-sugar biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose from UDP-alpha-D-glucuronate: step 1/3. Nucleotide-sugar biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose from UDP-alpha-D-glucuronate: step 3/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Homohexamer, formed by a dimer of trimers. In the N-terminal section; belongs to the Fmt family. UDP-L-Ara4N formyltransferase subfamily. In the C-terminal section; belongs to the NAD(P)-dependent epimerase/dehydratase family. UDP-glucuronic acid decarboxylase subfamily. +Putative adhesion molecule that mediates sialic-acid dependent binding to cells. Preferentially binds to alpha-2,3- or alpha-2,6-linked sialic acid. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface. Expressed by peripheral blood leukocytes (neutrophils and monocytes but not eosinophils). Found in liver, fetal liver, bone marrow, placenta, spleen and in lower levels in skeletal muscle, fetal brain, stomach, lung, thymus, prostate, brain, mammary, adrenal gland, colon, trachea, cerebellum, testis, small intestine and spinal cordon. Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases. Belongs to the immunoglobulin superfamily. SIGLEC (sialic acid binding Ig-like lectin) family. Siglec-9 +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Binds 1 zinc ion per subunit. Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily. +Catalyzes the rearrangement of 1-deoxy-D-xylulose 5-phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S. 1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + [sulfur-carrier protein ThiS]-C-terminal Gly-Gly + 2 H(+) + 2 H2O Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homotetramer. Forms heterodimers with either ThiH or ThiS. Belongs to the ThiG family. +Belongs to the TACO1 family. +Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity). Homodimer. Belongs to the inovirus G5P protein family. +Serine hydrolase; part of the gene cluster that mediates the biosynthesis of communesins, a prominent class of indole alkaloids with great potential as pharmaceuticals (PubMed:25571861). Communesins are biosynthesized by the coupling of tryptamine and aurantioclavine, two building blocks derived from L-tryptophan (PubMed:25571861). The L-tryptophan decarboxylase cnsB converts L-tryptophan to tryptamine, whereas the tryptophan dimethylallyltransferase cnsF converts L-tryptophan to 4-dimethylallyl tryptophan which is further transformed to aurantioclavine by the aurantioclavine synthase cnsA, probably aided by the catalase cnsD (PubMed:25571861). The cytochrome P450 monooxygenase cnsC catalyzes the heterodimeric coupling between the two different indole moieties, tryptamine and aurantioclavine, to construct vicinal quaternary stereocenters and yield the heptacyclic communesin scaffold (PubMed:26963294). The O-methyltransferase cnsE then methylates the communesin scaffold to produce communesin K, the simplest characterized communesin that contains the heptacyclic core (PubMed:25571861). The dioxygenase cnsJ converts communesin K into communesin I (PubMed:25571861). Acylation to introduce the hexadienyl group at position N16 of communesin I by the acyltransferase cnsK leads to the production of communesin B. The hexadienyl group is produced by the highly reducing polyketide synthase cnsI, before being hydrolytically removed from cnsI by the serine hydrolase cnsH, converted into hexadienyl-CoA by the CoA ligase cnsG, and then transferred to communesin I by cnsK (PubMed:25571861). Surprisingly, cnsK may also be a promiscuous acyltransferase that can tolerate a range of acyl groups, including acetyl-, propionyl-, and butyryl-CoA, which lead to communesins A, G and H respectively (PubMed:25571861). The roles of the alpha-ketoglutarate-dependent dioxygenases cnsM and cnsP have still to be determined (PubMed:25571861). Alkaloid biosynthesis. Belongs to the AB hydrolase 3 family. +After binding acetylcholine, the AChR responds by an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. Neuronal AChR seems to be composed of two different types of subunits: alpha and non-alpha (beta). Alpha-2 subunit can be combined to beta-2 or beta-4 to give rise to functional receptors. The alpha-2:beta-2 nAChR complex is proposed to be a heteropentamer with two subtypes: LS (low agonist sensitivity) with a (alpha-2)3:(beta-2)2 and HS (high agonist sensitivity) with a (alpha-2)2:(beta-2)3 stoichiometry; the subtypes differ in their subunit binding interfaces which are involved in ligand binding. Belongs to the ligand-gated ion channel (TC 1.A.9) family. Acetylcholine receptor (TC 1.A.9.1) subfamily. Alpha-2/CHRNA2 sub-subfamily. +Core component of nucleosome which plays a central role in DNA double strand break (DSB) repair. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family. Phosphorylated to form H2AS128ph (gamma-H2A) in response to DNA double-strand breaks (DSBs) generated by exogenous genotoxic agents and by stalled replication forks. Phosphorylation is dependent on the DNA damage checkpoint kinases MEC1/ATR and TEL1/ATM, spreads on either side of a detected DSB site and may mark the surrounding chromatin for recruitment of proteins required for DNA damage signaling and repair. Gamma-H2A is removed from the DNA prior to the strand invasion-primer extension step of the repair process and subsequently dephosphorylated. Dephosphorylation is necessary for efficient recovery from the DNA damage checkpoint (By similarity). Acetylated by ESA1 to form H2AK4ac and H2AK7ac. In contrast to vertebrates and insects, its C-terminus is not monoubiquitinated. Belongs to the histone H2A family. To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-6; H2AK7ac = acetylated Lys-10; H2AS128ph = phosphorylated Ser-131. +Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6-phosphate and D-lactate. H2O + N-acetyl-D-muramate 6-phosphate = (R)-lactate + N-acetyl-D-glucosamine 6-phosphate Amino-sugar metabolism; N-acetylmuramate degradation. Homodimer. A lyase-type mechanism (elimination/hydration) is suggested for the cleavage of the lactyl ether bond of MurNAc 6-phosphate, with the formation of an alpha,beta-unsaturated aldehyde intermediate with (E)-stereochemistry, followed by the syn addition of water to give product. Belongs to the GCKR-like family. MurNAc-6-P etherase subfamily. +Phosphorylates thymidine and thymidine analogs, such as azidothymidine (AZT). Part of the salvage pathway for pyrimidine deoxyribonucleotide synthesis (By similarity). ATP + thymidine = ADP + dTMP + H(+) Homotetramer. Two molecules of substrate bind to each enzyme tetramer. Belongs to the thymidine kinase family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. Binds 2 heme groups. One heme group is bound covalently by a single cysteine link, the other one non-covalently. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Heme 1 (or BH or b566) is high-potential and absorbs at about 566 nm, and heme 2 (or BL or b562) is low-potential and absorbs at about 562 nm. Belongs to the cytochrome b family. PetB subfamily. +Belongs to the aspartyl/asparaginyl beta-hydroxylase family. +Binds 3 Zn(2+) ions per subunit. Homotrimer. Belongs to the PHP family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. Binds to the N-terminal domain of the chaperone ClpA. Belongs to the ClpS family. +Belongs to the universal ribosomal protein uL29 family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Involved in methylamine metabolism. Essential for the maturation of the beta subunit of MADH, presumably via a step in the biosynthesis of tryptophan tryptophylquinone (TTQ), the cofactor of MADH. One-carbon metabolism; methylamine degradation. Binds 2 heme c groups covalently per subunit. +Binds 1 zinc ion per subunit. Belongs to the histidinol dehydrogenase family. +Belongs to the major facilitator superfamily. TCR/Tet family. +Binds specifically to voltage-gated sodium channels (Nav) (site 3), thereby delaying their inactivation. This toxin retains the greatest capacity to discriminate between the cardiac (Nav1.5/SCN5A) and neuronal sodium channels (2.5 nM versus 120 nM, when electrophysiologically tested and 14 nM versus 400 nM, when tested by ion flux), whereas its paralog Anthopleurin-B has the highest affinity of all anemone toxins for the mammalian sodium channel (PubMed:13806, PubMed:7612595, PubMed:17092528). Its ability to differentiate between cardiac and skeletal channels appears to be associated with domain 4 of the channel (PubMed:9306007). This toxin does not slow or inhibit closed-state inactivation of cardiac sodium channels, but selectively modifies inactivation from the open-state (PubMed:8576699). It does not display phospholipid-binding activities, suggesting that the domain IV S3-S4 linker is located at the extracellular surface and not buried in the phospholipid bilayer (By similarity). Belongs to the sea anemone sodium channel inhibitory toxin family. Type I subfamily. +mRNA cap-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. In the eIF-3 complex, eif3d specifically recognizes and binds the 7-methylguanosine cap of a subset of mRNAs. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The eIF-3 complex appears to include tif32/eif3a, SPAC25G10.08/eif3b, tif33/eif3c, SPBC4C3.07/eif3f, tif35/eif3g and sum1/eif3i. This set of common subunits may also associate exclusively with either moe1/eif3d and int6/eif3e, or with SPAC821.05/eif3h and SPAC1751.03/eif3m. The eIF-3 complex may also include SPAC3A12.13c/eif3j. The RNA gate region regulates mRNA cap recognition to prevent promiscuous mRNA-binding before assembly of eif3d into the full eukaryotic translation initiation factor 3 (eIF-3) complex. Reduced rate of protein synthesis, although the polyribosome content is not affected. Enhanced sensitivity to caffeine and defective spore formation. Belongs to the eIF-3 subunit D family. +Bifunctional enzyme. Involved in de novo dTMP biosynthesis. Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, DNA precursor synthesis, and for the conversion of dUMP to dTMP. (6S)-5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + H(+) + NADPH (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP = 7,8-dihydrofolate + dTMP Cofactor biosynthesis; tetrahydrofolate biosynthesis; 5,6,7,8-tetrahydrofolate from 7,8-dihydrofolate: step 1/1. Homodimer. In the N-terminal section; belongs to the dihydrofolate reductase family. In the C-terminal section; belongs to the thymidylate synthase family. +Corepressor targeting diverse transcription regulators. Isoform 2 probably acts as a scaffold for specialized synapses (By similarity). Functions in brown adipose tissue (BAT) differentiation. Interacts with HIPK2 and PNN (By similarity). Interacts with the transcription factors ZNF217, BKLF, delta EF1/AREB6/ZEB, EVI-1 and Friend of GATA (FOG) via the consensus motif P-X-[DNS]-L-[STVA]. Interacts also with the C-terminus of adenovirus E1A protein. Can form a complex with BKLF on a CACCC-box oligonucleotide. Can form homodimers or heterodimers of CTBP1 and CTBP2. Interacts with NRIP1 and WIZ. Interacts with PRDM16; represses white adipose tissue (WAT)-specific genes expression. Interacts with MCRIP1 (By similarity). Found in all tissues except spleen and liver. Strong expression confined to the embryonic stages. Phosphorylation by HIPK2 on Ser-428 induces proteasomal degradation. Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. +This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to an endomembrane compartment. ATP + Ca(2+)(in) + H2O = ADP + Ca(2+)(out) + H(+) + phosphate Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIA subfamily. +Functions during spermatogenesis as a chaperone for a range of client proteins that are important for sperm adhesion onto the egg zona pellucida and for subsequent penetration of the zona pellucida. Required for normal sperm migration from the uterus into the oviduct. Required for normal male fertility. Binds calcium ions (By similarity). Interacts with PPIB and PDILT. Interacts with ADAM2 (By similarity). Belongs to the calreticulin family. +On the 2D-gel the determined pI of this unknown protein is: 8.3, its MW is: 28 kDa. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Transcription factor that binds and activates the promoter of thyroid specific genes such as thyroglobulin, thyroperoxidase, and thyrotropin receptor. Crucial in the maintenance of the thyroid differentiation phenotype. May play a role in lung development and surfactant homeostasis. Forms a regulatory loop with GRHL2 that coordinates lung epithelial cell morphogenesis and differentiation. Activates the transcription of GNRHR and plays a role in enhancing the circadian oscillation of its gene expression. Represses the transcription of the circadian transcriptional repressor NR1D1 (By similarity). Interacts with WWTR1. Thyroid and lung. Phosphorylated on serine residues by STK3/MST2. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Disease susceptibility is associated with variants affecting the gene represented in this entry. Belongs to the NK-2 homeobox family. Truncated N-terminus. +Belongs to the universal ribosomal protein uS2 family. +Binds 1 zinc ion per subunit. Belongs to the peptidase M48B family. +Expressed only in the forespore compartment of sporulating cells. Belongs to the SspK family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Monomer. Belongs to the adenylate kinase family. +Nuclease required for the repair of DNA interstrand cross-links (ICL). Acts as a 5'-3' exonuclease that anchors at a cut end of DNA and cleaves DNA successively at every third nucleotide, allowing to excise an ICL from one strand through flanking incisions. Hydrolytically removes 5'-nucleotides successively from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides. Binds 2 magnesium or manganese ions per subunit. Belongs to the FAN1 family. +Required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis. PQQ is probably formed by cross-linking a specific glutamate to a specific tyrosine residue and excising these residues from the peptide. Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. Belongs to the PqqA family. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +Sequence-specific endonuclease that cleaves unmethylated GATC sequences. It is involved in DNA mismatch repair. Belongs to the MutH family. +Thiolesterase that catalyzes the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid. an S-(2-hydroxyacyl)glutathione + H2O = a 2-hydroxy carboxylate + glutathione + H(+) Binds 2 Zn(2+) ions per subunit. Secondary metabolite metabolism; methylglyoxal degradation; (R)-lactate from methylglyoxal: step 2/2. Monomer. Belongs to the metallo-beta-lactamase superfamily. Glyoxalase II family. +Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. an organic molecule + O2 + reduced [NADPH--hemoprotein reductase] = an alcohol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Liver. Not found in the lung, kidney and prostate. Constitutively expressed. Belongs to the cytochrome P450 family. +Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. AH2 + H2O2 = A + 2 H2O 2 H2O2 = 2 H2O + O2 Binds 1 heme b (iron(II)-protoporphyrin IX) group per dimer. Homodimer or homotetramer. Formation of the three residue Trp-Tyr-Met cross-link is important for the catalase, but not the peroxidase activity of the enzyme. Belongs to the peroxidase family. Peroxidase/catalase subfamily. +Promotes colloidosmotic lysis by binding to the midgut epithelial cells of Coleoptera. This protein is not toxic in its natural form. It is highly toxic to Colorado potato beetle larvae after an in vitro solubilization and trypsin activation step. The crystal protein is produced during sporulation and is accumulated both as an inclusion and as part of the spore coat. Toxic segment of the protein is located in the N-terminus. Belongs to the delta endotoxin family. +Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo-MPT) cofactor (Moco or molybdenum cofactor) to form Mo-molybdopterin guanine dinucleotide (Mo-MGD) cofactor. GTP + H(+) + Mo-molybdopterin = diphosphate + Mo-molybdopterin guanine dinucleotide Monomer. The N-terminal domain determines nucleotide recognition and specific binding, while the C-terminal domain determines the specific binding to the target protein. Belongs to the MobA family. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +Catalyzes the cleavage of 5-oxoproline to form L-glutamate coupled to the hydrolysis of ATP to ADP and inorganic phosphate. 5-oxo-L-proline + ATP + 2 H2O = ADP + H(+) + L-glutamate + phosphate Forms a complex composed of PxpA, PxpB and PxpC. Belongs to the LamB/PxpA family. +Belongs to the major facilitator superfamily. DHA1 family. MdtH (TC 2.A.1.2.21) subfamily. +Heterodimer of a type I and a type II keratin. KRT6 isomers associate with KRT16 and/or KRT17. Expressed in adult epithelia including the tongue, esophagus/trachea, eye and skin. Localized preferentially to the suprabasal layers of thickened epidermis in injured and chemically treated skin. By injury, and treatment of the skin with the phorbol ester PMA. There are two types of cytoskeletal and microfibrillar keratin, I (acidic) and II (neutral to basic) (40-55 and 56-70 kDa, respectively). Belongs to the intermediate filament family. +Belongs to the UPF0311 family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Lipid transfer protein involved in seed and ovule maturation and development, probably by regulating the fatty acids homeostasis during suberin and sporopollenin biosynthesis or deposition. Restricted to stamen, pollen and sporophytic tissues (PubMed:14671020, PubMed:24460633). Also detected, at low levels, in stems and leaves (PubMed:14671020). Inability to limit tetrazolium salt uptake in seeds, development of hair-like structures on seeds, altered pollen morphologies, deformed or collapsed, and decreased levels of omega-hydroxy fatty acids in seed coats. Belongs to the plant LTP family. Extended C-terminus. +Required for normal synaptic spine architecture and function. Necessary for DISC1 and GRM5 localization to postsynaptic density complexes and for both N-methyl D-aspartate receptor-dependent and metabotropic glutamate receptor-dependent long term depression (By similarity). Interacts with CNKSR2 and DLG4 (PubMed:12390249). Interacts with CTNND2/Catenin delta-2. Forms a complex with N-cadherin through CTNND2 (By similarity). Interacts with CAMK2A (PubMed:10827168). Brain-specific. Highly concentrated at synapses. Expression of isoform 2 is predominant at E18, but decreased during postnatal development paralleling increased expression of isoform 4 and isoform 5. O-glycosylated and phosphorylated. This is the only isoform to have a potential transmembrane domain. Belongs to the LAP (LRR and PDZ) protein family. +Bifunctional enzyme that catalyzes both the deamination of dCTP to dUTP and the hydrolysis of dUTP to dUMP without releasing the toxic dUTP intermediate. dCTP + 2 H2O = diphosphate + dUMP + NH4(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP: step 1/1. Homotrimer. Belongs to the dCTP deaminase family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. PetL is important for photoautotrophic growth as well as for electron transfer efficiency and stability of the cytochrome b6-f complex. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the PetL family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Part of the RNA polymerase complex. Belongs to the archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit family. +Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine. Is not active against the DD- or LL-isomers of diaminopimelate. H(+) + meso-2,6-diaminoheptanedioate = CO2 + L-lysine Is activated by 2,3-dimercaptopropan-1-ol. Optimum pH is 6.7-6.8. Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1. Up-regulated by LysR. Repressed in the presence of lysine. Belongs to the Orn/Lys/Arg decarboxylase class-II family. LysA subfamily. +Responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs. uridine(13) in tRNA = pseudouridine(13) in tRNA Belongs to the pseudouridine synthase TruD family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +Belongs to the plant self-incompatibility (S1) protein family. +Stabilizes TBP binding to an archaeal box-A promoter. Also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). Belongs to the TFIIB family. +Cell wall-anchored surface receptor that participates in the extraction of heme from oxidized methemoglobin/metHb to enable growth on hemoglobin as a sole iron source (By similarity). Receives heme from IsdB and transfers it to IsdC (By similarity). Also plays a role in the inhibition of host immune response. Protects S.aureus against the bactericidal protease activity of apolactoferrin. Decreases bacterial cellular hydrophobicity, which renders S.aureus resistant to bactericidal human skin fatty acids as well as to beta-defensins and cathelicidin. Also binds fibronectin and chains B-beta and gamma of fibrinogen, promoting clumping of S.aureus with fibrinogen. Involved in adherence of S.aureus to human desquamated nasal epithelial cells and is required for nasal colonization (By similarity). Monomer. Interacts with IsdC (By similarity). Interacts with IsdB (By similarity). Encodes an LPXTG motif-containing sorting signal that targets to the cell wall, which is catalyzed by sortase A. Repressed by fur in the presence of iron. The NEAT domain is responsible for binding Fe(3+) and Fe(2+) heme and fibrinogen. The NEAT domain is an inhibitor of apolactoferrin activity, while the C-domain confers resistance to bovine lactoferricin (By similarity). Belongs to the IsdA family. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +Counteracts the host humoral immune response by inhibiting the processing and the amidolytic activity of host PAP1 and PAP3. Thereby, melanization of host hemolymph, normally producing several reactive intermediates toxic for viruses, is deregulated and proper immune response cannot occur (By similarity). Interacts with host PAP1, PAP3 and SPH2. Belongs to the polydnaviridae EGF-like motif protein family. +Displays ATPase and GTPase activities. Belongs to the RapZ-like family. +Plays an essential role in autophagy: interacts with ATG12-ATG5 to mediate the conjugation of phosphatidylethanolamine (PE) to LC3 (MAP1LC3A, MAP1LC3B or MAP1LC3C), to produce a membrane-bound activated form of LC3 named LC3-II. Thereby, controls the elongation of the nascent autophagosomal membrane. Homooligomer. Part of either the minor and major complexes respectively composed of 4 sets of ATG12-ATG5 and ATG16L1 (400 kDa) or 8 sets of ATG12-ATG5 and ATG16L1 (800 kDa). Recruited to omegasomes membranes by WIPI2. Omegasomes are endoplasmic reticulum connected strutures at the origin of preautophagosomal structures. Localized to preautophagosomal structure (PAS) where it is involved in the membrane targeting of ATG5. Belongs to the WD repeat ATG16 family. Extended N-terminus. +ATP + L-aspartate + NH4(+) = AMP + diphosphate + H(+) + L-asparagine Amino-acid biosynthesis; L-asparagine biosynthesis; L-asparagine from L-aspartate (ammonia route): step 1/1. Belongs to the class-II aminoacyl-tRNA synthetase family. AsnA subfamily. +The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpA family. +Substrate adapter for ufmylation, the covalent attachment of the ubiquitin-like modifier UFM1 to substrate proteins. Belongs to the DDRGK1 family. +Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine. H(+) + S-adenosyl-L-methionine = CO2 + S-adenosyl 3-(methylsulfanyl)propylamine Binds 1 pyruvoyl group covalently per subunit. Amine and polyamine biosynthesis; S-adenosylmethioninamine biosynthesis; S-adenosylmethioninamine from S-adenosyl-L-methionine: step 1/1. Heterooctamer of four alpha and four beta chains arranged as a tetramer of alpha/beta heterodimers. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl group blocking the N-terminus of the alpha chain. Belongs to the prokaryotic AdoMetDC family. Type 2 subfamily. +Involved in inducible protoporphyrin IX influx and heme efflux. By oxygen and heme deficiency. N-glycosylated. Belongs to the lipid-translocating exporter (LTE) (TC 9.A.26.1) family. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Homodimer. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 3 subfamily. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Methylated by PrmB. Belongs to the universal ribosomal protein uL3 family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy-D-galactonate. D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O Binds 1 Mg(2+) ion per subunit. Carbohydrate acid metabolism; D-galactonate degradation; D-glyceraldehyde 3-phosphate and pyruvate from D-galactonate: step 1/3. Reaction proceeds via an anti dehydration. Belongs to the mandelate racemase/muconate lactonizing enzyme family. GalD subfamily. +Specifically inhibits an endogenous intracellular serine proteinase (proteinase A). Belongs to the protease inhibitor I9 family. +V region of the variable domain of immunoglobulin light chains that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268). Immunoglobulins are composed of two identical heavy chains and two identical light chains; disulfide-linked. There are several alleles. The sequence shown is that of IMGT allele IGLV9-49*01. For an example of a full-length immunoglobulin lambda light chain see AC P0DOX8. +Displays ATPase and GTPase activities. Belongs to the RapZ-like family. +Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway. D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = beta-D-fructose 6-phosphate + D-erythrose 4-phosphate Carbohydrate degradation; pentose phosphate pathway; D-glyceraldehyde 3-phosphate and beta-D-fructose 6-phosphate from D-ribose 5-phosphate and D-xylulose 5-phosphate (non-oxidative stage): step 2/3. Belongs to the transaldolase family. Type 2 subfamily. +Negatively regulates its own expression and that of the subsequent genes in the proximal part of the division and cell wall (dcw) gene cluster. Acts by binding directly to DNA. May also regulate the expression of genes outside the dcw cluster. Forms oligomers. Belongs to the MraZ family. +Oxidoreductase; part of the gene cluster that mediates the biosynthesis of pestheic acid, a diphenyl ether which is a biosynthetic precursor of the unique chloropupukeananes (PubMed:24302702). The biosynthesis initiates from condensation of acetate and malonate units catalyzed by the non-reducing PKS ptaA (PubMed:24302702). As the ptaA protein is TE/CLC domain-deficient, hydrolysis and Claisen cyclization of the polyketide could be catalyzed by ptaB containing a beta-lactamase domain (PubMed:24302702). The ptaB protein might hydrolyze the thioester bond between the ACP of ptaA and the intermediate to release atrochrysone carboxylic acid, which is spontaneously dehydrated to form endocrocin anthrone (PubMed:24302702). Endocrocin anthrone is then converted to endocrocin, catalyzed by the anthrone oxygenase ptaC (PubMed:24302702). Spontaneous decarboxylation of endocrocin occurs to generate emodin (PubMed:24302702). An O-methyltransferase (ptaH or ptaI) could methylate emodin to form physcion (PubMed:24302702). PtaJ could then catalyze the oxidative cleavage of physcion, and rotation of the intermediate could then afford desmethylisosulochrin (PubMed:24302702). PtaF, a putative NADH-dependent oxidoreductase, might also participate in the oxidative cleavage step (PubMed:24302702). Desmethylisosulochrin is then transformed by another O-methyltransferase (ptaH or ptaI) to form isosulochrin (PubMed:24302702). Chlorination of isosulochrin by ptaM in the cyclohexadienone B ring then produces chloroisosulochrin (PubMed:24302702). PtaE is responsible for the oxidative coupling reactions of both benzophenones isosulouchrin and chloroisosulochrin to RES-1214-1 and pestheic acid respectively, regardless of chlorination. Secondary metabolite biosynthesis. The cluster is expressed in rice fermentation medium (PubMed:25623211). Expression is correlated with the production of pestheic acid (PubMed:24302702). Three regulators are located in the cluster (ptaR1, ptaR2 and ptaR3), suggesting that the production of pestheic acid is controlled by a complex regulatory mechanism (PubMed:24302702). Abolishes the production of pestheic acid and RES-1214-1, but accumulates isosulochrin and chloroisosulochrin (PubMed:24302702). Belongs to the multicopper oxidase family. +Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P). D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate from glycerone phosphate: step 1/1. Homodimer. Belongs to the triosephosphate isomerase family. +Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins. Interacts with the Sec translocase complex via SecD. Specifically interacts with transmembrane segments of nascent integral membrane proteins during membrane integration. Belongs to the OXA1/ALB3/YidC family. Type 1 subfamily. +Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate intermediate into D-glycero-beta-D-manno-heptose 1-phosphate by removing the phosphate group at the C-7 position. D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O = D-glycero-beta-D-manno-heptose 1-phosphate + phosphate Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate: step 2/4. Bacterial outer membrane biogenesis; LPS core biosynthesis. Monomer. Belongs to the GmhB family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved. Distribution is 50-50. Belongs to the SecA family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase. Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Prokaryotic type I sub-subfamily. +May be involved in a cell-to cell programmed cell death (PCD) signaling mechanism. Up-regulated by fungal elicitor (PubMed:12833529). Up-regulated in both heat- and senescence-induced programmed cell death (PCD) (PubMed:15276441). Phosphorylated on tyrosine. Identified as a cargo protein of vacuolar sorting receptors (PubMed:23738689). This was based on interactions with truncated vacuolar sorting receptors and their co-secretion in the culture medium (PubMed:23738689). This function is however not supported by recent evidences. +Catalyzes oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs. AH2 + O2 + uridine(34) in tRNA = 5-hydroxyuridine(34) in tRNA + A + H2O Belongs to the TrhO family. +Probably involved in peptidoglycan hydrolysis. +Has apparently no steroid dehydrogenase activity. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD-dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme. 2 S-adenosyl-L-methionine + uroporphyrinogen III = H(+) + precorrin-2 + 2 S-adenosyl-L-homocysteine NAD(+) + precorrin-2 = 2 H(+) + NADH + sirohydrochlorin 2 H(+) + siroheme = Fe(2+) + sirohydrochlorin Cofactor biosynthesis; adenosylcobalamin biosynthesis; precorrin-2 from uroporphyrinogen III: step 1/1. Cofactor biosynthesis; adenosylcobalamin biosynthesis; sirohydrochlorin from precorrin-2: step 1/1. Porphyrin-containing compound metabolism; siroheme biosynthesis; precorrin-2 from uroporphyrinogen III: step 1/1. Porphyrin-containing compound metabolism; siroheme biosynthesis; siroheme from sirohydrochlorin: step 1/1. Porphyrin-containing compound metabolism; siroheme biosynthesis; sirohydrochlorin from precorrin-2: step 1/1. In the N-terminal section; belongs to the precorrin-2 dehydrogenase / sirohydrochlorin ferrochelatase family. In the C-terminal section; belongs to the precorrin methyltransferase family. +As a likely component of a histone deacetylase complex, together with saeg-2 and hda-2, functions downstream of the cAMP-dependent kinase egl-4 to regulate the expression of genes required for egg-laying and foraging. May be a component of a histone deacetylase complex containing saeg-2, saeg-1 and hda-2. May interact with egl-4. Ubiquitously expressed. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds a dinuclear copper A center per subunit. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Found in a complex with TMEM177, COA6, COX18, COX20, SCO1 and SCO2. Interacts with TMEM177 in a COX20-dependent manner. Interacts with COX20. Interacts with COX16 (By similarity). Belongs to the cytochrome c oxidase subunit 2 family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Assists the correct folding of nascent IpaB. Once it is bound to IpaB, it binds to IpaC and impedes their premature association that would lead to their degradation in the absence of IpcG. Belongs to the LcrH/SycD chaperone family. +Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis: the synthesis of acetylglutamate from glutamate and acetyl-CoA, and of ornithine by transacetylation between acetylornithine and glutamate. L-glutamate + N(2)-acetyl-L-ornithine = L-ornithine + N-acetyl-L-glutamate acetyl-CoA + L-glutamate = CoA + H(+) + N-acetyl-L-glutamate Amino-acid biosynthesis; L-arginine biosynthesis; L-ornithine and N-acetyl-L-glutamate from L-glutamate and N(2)-acetyl-L-ornithine (cyclic): step 1/1. Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 1/4. Heterodimer of an alpha and a beta chain. The alpha and beta chains are autoproteolytically processed from a single precursor protein within the mitochondrion. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the ArgJ family. +Binds single-stranded DNA at the primosome assembly site (PAS). Component of the preprimosomal complex composed of PriA, PriB, PriC, DnaB and DnaT. Upon transient interaction with DnaG it forms the primosome. Belongs to the PriB family. +To E.coli CvpA. +Microtubule binding protein that promotes the stabilization of dynamic microtubules. Required for mitotic spindle formation (By similarity). Interacts with microtubules. Belongs to the CLASP family. +Intracellular mono-ADP-ribosyltransferase that may play a role in different processes through the mono-ADP-ribosylation of proteins involved in those processes (PubMed:23103912, PubMed:22701565, PubMed:25043379). May play a role in the unfolded protein response (UPR), by ADP-ribosylating and activating EIF2AK3 and ERN1, two important UPR effectors (PubMed:23103912). May also mediate mono-ADP-ribosylation of karyopherin KPNB1 a nuclear import factor (PubMed:22701565). May not modify proteins on arginine or cysteine residues compared to other mono-ADP-ribosyltransferases (PubMed:22701565). L-aspartyl-[protein] + NAD(+) = 4-O-(ADP-D-ribosyl)-L-aspartyl-[protein] + nicotinamide L-lysyl-[protein] + NAD(+) = H(+) + N(6)-(ADP-D-ribosyl)-L-lysyl-[protein] + nicotinamide L-glutamyl-[protein] + NAD(+) = 5-O-(ADP-D-ribosyl)-L-glutamyl-[protein] + nicotinamide Interacts with KPNB1. The N-terminal PARP alpha-helical domain is regulatory, it packs against the catalytic domain, and may relay effector-binding event to the NAD-binding site. Auto-mono-ADP-ribosylated. Belongs to the ARTD/PARP family. +Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. Homodimer. Belongs to the transketolase family. DXPS subfamily. +Catalyzes the decarboxylation of L-tyrosine to produce tyramine for methanofuran biosynthesis. Can also catalyze the decarboxylation of L-aspartate to produce beta-alanine for coenzyme A (CoA) biosynthesis. H(+) + L-tyrosine = CO2 + tyramine H(+) + L-aspartate = beta-alanine + CO2 Cofactor biosynthesis; methanofuran biosynthesis. Cofactor biosynthesis; coenzyme A biosynthesis. Belongs to the group II decarboxylase family. MfnA subfamily. +Reversible hydration of carbon dioxide. H(+) + hydrogencarbonate = CO2 + H2O Binds 1 zinc ion per subunit. Belongs to the beta-class carbonic anhydrase family. +Belongs to the bacterial ribosomal protein bL33 family. +Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel (PubMed:22096102). uS4 is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly (PubMed:15590835). Component of the small ribosomal subunit (SSU). Mature yeast ribosomes consist of a small (40S) and a large (60S) subunit. The 40S small subunit contains 1 molecule of ribosomal RNA (18S rRNA) and 33 different proteins (encoded by 57 genes). The large 60S subunit contains 3 rRNA molecules (25S, 5.8S and 5S rRNA) and 46 different proteins (encoded by 81 genes) (PubMed:9559554, PubMed:22096102). Interacts with snoRNA U3. uS11 interacts with MPP10. Component of the ribosomal small subunit (SSU) processome composed of at least 40 protein subunits and snoRNA U3 (PubMed:15590835). Present with 63300 molecules/cell in log phase SD medium. There are 2 genes for uS4 in yeast. Belongs to the universal ribosomal protein uS4 family. +Catalyzes the final step of fatty acid oxidation in which acetyl-CoA is released and the CoA ester of a fatty acid two carbons shorter is formed. acetyl-CoA + an acyl-CoA = a 3-oxoacyl-CoA + CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadJ) and two beta chains (FadI). Belongs to the thiolase-like superfamily. Thiolase family. +Targets vasopressin-oxytocin related receptors (By similarity). Binds calcium (PubMed:17331075). Expressed by the venom duct. The cysteine framework is C-C. Belongs to the vasopressin/oxytocin family. +Belongs to the DEFL family. Lacks 1 of the 4 disulfide bonds, which are conserved features of the family. +Regulates membrane-cell wall junctions and localized cell wall deposition. Required for establishment of the Casparian strip membrane domain (CSD) and the subsequent formation of Casparian strips, a cell wall modification of the root endodermis that determines an apoplastic barrier between the intraorganismal apoplasm and the extraorganismal apoplasm and prevents lateral diffusion (By similarity). Homodimer and heterodimers. Very restricted localization following a belt shape within the plasma membrane which coincides with the position of the Casparian strip membrane domain in the root endodermis. Belongs to the Casparian strip membrane proteins (CASP) family. +May be involved in induction of apoptosis in CD4(+) T-cells, but not CD8(+) T-cells or hepatocytes. Secreted by hepatocytes. Belongs to the UPF0669 family. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. Belongs to the FlgI family. +Belongs to the bacterial ribosomal protein bS16 family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 1 subfamily. +a 2-oxocarboxylate + H(+) = an aldehyde + CO2 H(+) + pyruvate = acetaldehyde + CO2 Binds 1 Mg(2+) per subunit. Binds 1 thiamine pyrophosphate per subunit. Homotetramer. Belongs to the TPP enzyme family. +Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate. ATP + formate + N(1)-(5-phospho-beta-D-ribosyl)glycinamide = ADP + H(+) + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (formate route): step 1/1. Homodimer. Belongs to the PurK/PurT family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Catalyzes the ferrous insertion into protoporphyrin IX. 2 H(+) + heme b = Fe(2+) + protoporphyrin IX Porphyrin-containing compound metabolism; protoheme biosynthesis; protoheme from protoporphyrin-IX: step 1/1. Belongs to the ferrochelatase family. +Negative regulator of store-operated Ca(2+) entry (SOCE) involved in protecting cells from Ca(2+) overfilling. In response to cytosolic Ca(2+) elevation after endoplasmic reticulum Ca(2+) refilling, promotes a slow inactivation of STIM (STIM1 or STIM2)-dependent SOCE activity: possibly act by facilitating the deoligomerization of STIM to efficiently turn off ORAI when the endoplasmic reticulum lumen is filled with the appropriate Ca(2+) levels, and thus preventing the overload of the cell with excessive Ca(2+) ions. Interacts with STIM1; the interaction is inhibit by th interaction of STIM1 with EFHB. Translocates to the endoplasmic reticulum-plasma membrane (ER-PM) region in a STIM1-dependent manner following cytosolic Ca(2+) elevation. Highly expressed in macrophages. The cytoplasmic C-terminal region mediates interaction with STIM1, while the N-terminal lumenal region mediates regulation of SOCE activity. Belongs to the SARAF family. +Belongs to the universal ribosomal protein uS3 family. +Protamines substitute for histones in the chromatin of sperm during the haploid phase of spermatogenesis. They compact sperm DNA into a highly condensed, stable and inactive complex. Interacts with TDRP. Testis. Proteolytic processing into mature chains is required for histone eviction during spermatogenesis. Transition proteins (TNP1 and TNP2) are required for processing. Belongs to the protamine P2 family. +Positive regulator of neurite outgrowth by stabilizing myosin regulatory light chain (MRLC). It prevents MIR-mediated MRLC ubiquitination and its subsequent proteasomal degradation (By similarity). Interacts with MYLIP/MIR. Belongs to the canopy family. +Involved in iron-sulfur (Fe-S) cluster assembly. May act as a regulator of Fe-S biogenesis. Belongs to the frataxin family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Belongs to the UPF0178 family. +Binds 2 Zn(2+) ions per subunit. Belongs to the Gfa family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Catalyzes the synthesis of activated sulfate. adenosine 5'-phosphosulfate + ATP = 3'-phosphoadenylyl sulfate + ADP + H(+) Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 2/3. Belongs to the APS kinase family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). Together with AhpC, AhpD and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system. Appears to be essential for Mtb pathogenesis. (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + acetyl-CoA = (R)-N(6)-(S(8)-acetyldihydrolipoyl)-L-lysyl-[protein] + CoA Binds 2 lipoyl cofactors covalently. Inhibited by rhodanine compounds. Some of them almost exclusively kill non-replicating mycobacteria in synergy with products of host immunity, such as nitric oxide and hypoxia, and are effective on bacteria within macrophages. Optimum pH is 8.0 for PDH complex activity. Half-maximal activity is observed at pH 7.0 and pH 9.0. Activity is abolished at pH < 5. Forms a 24-polypeptide structural core with octahedral symmetry (By similarity). Identified in a complex with AhpC, AhpD and Lpd. Part of the PDH complex, consisting of multiple copies of AceE (E1), DlaT (E2) and Lpd (E3). Cells lacking this gene show severely retarded growth in vitro, and display no PDH activity. They are also more sensitive to nitrosative stress caused by NaNO(2), and to macrophage-induced killing in vitro. They also show at least 20-fold reduction in survival in a mouse tuberculosis model, and are unable to cause disease in a guinea pig model of tuberculosis infection. Disruption of dlaT leads to high up-regulation of the expression of the bkdABC operon. Is the only lipoylated protein in strain H37Rv grown on a standard rich medium. However, in a DlaT-deficient strain, another protein, BkdC, becomes lipoylated. Belongs to the 2-oxoacid dehydrogenase family. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Involved in biosynthesis of the thiamine precursor thiazole. Catalyzes the conversion of NAD and glycine to adenosine diphosphate 5-(2-hydroxyethyl)-4-methylthiazole-2-carboxylic acid (ADT), an adenylated thiazole intermediate. The reaction includes an iron-dependent sulfide transfer from a conserved cysteine residue of the protein to a thiazole intermediate. The enzyme can only undergo a single turnover, which suggests it is a suicide enzyme. May have additional roles in adaptation to various stress conditions and in DNA damage tolerance. [ADP-thiazole synthase]-L-cysteine + glycine + NAD(+) = [ADP-thiazole synthase]-dehydroalanine + ADP-5-ethyl-4-methylthiazole-2-carboxylate + 2 H(+) + 3 H2O + nicotinamide Binds 1 Fe cation per subunit. Homooctamer. During the catalytic reaction, a sulfide is transferred from Cys-220 to a reaction intermediate, generating a dehydroalanine residue. Belongs to the THI4 family. +Hydroxylase/desaturase; part of the gene cluster that mediates the biosynthesis of cercosporin, a light-activated, non-host-selective toxin (PubMed:29844193). The perylenequinone chromophore of cercosporin absorbs light energy to attain an electronically-activated triplet state and produces active oxygen species such as the hydroxyl radical, superoxide, hydrogen peroxide or singlet oxygen upon reaction with oxygen molecules (PubMed:11701851). These reactive oxygen species cause damage to various cellular components including lipids, proteins and nucleic acids (PubMed:11701851). The first step of cercosporin biosynthesis is performed by the polyketide synthase CTB1 which catalyzes the formation of nor-toralactone (Probable). The starter unit acyltransferase (SAT) domain of CTB1 initiates polyketide extension by the selective utilization of acetyl-CoA, which is elongated to the heptaketide in the beta-ketoacyl synthase (KS) domain by successive condensations with six malonyl units introduced by the malonyl acyltransferase (MAT) domain. The product template (PT) domain catalyzes C4-C9 and C2-C11 aldol cyclizations and dehydrations to a trihydroxynaphthalene, which is thought to be delivered to the thioesterase (TE) domain for product release (Probable). The bifunctional enzyme CTB3 then methylates nor-toralactone to toralactone before conducting an unusual oxidative aromatic ring opening (Probable). The O-methyltransferase CTB2 further methylates the nascent OH-6 of the CBT3 product, blocking further oxidation at this site before the reductase CTB6 reduces the 2-oxopropyl ketone at position C7, giving naphthalene (Probable). The FAD-dependent monooxygenase CTB5 in concert with the multicopper oxidase CTB12 are responsible for homodimerization of naphthalene with CTB7 installing the dioxepine moiety, finally producing cercosporin (Probable). The fasciclin domain-containing protein CTB11 might act with CTB5 and CTB12 whereas the roles of CTB9 and CTB10 have still to be elucidated (By similarity). Mycotoxin biosynthesis. Abolishes the production of cercosporin but accumulates a red, cercosporin-like metabolite called precercosporin. Belongs to the asaB hydroxylase/desaturase family. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. Belongs to the radical SAM superfamily. Lipoyl synthase family. +Belongs to the plant dehydrin family. +Specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of cytidine at position 56 in tRNAs. cytidine(56) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(56) in tRNA + H(+) + S-adenosyl-L-homocysteine Homodimer. Belongs to the aTrm56 family. +Belongs to the universal stress protein B family. +Lysozymes have primarily a bacteriolytic function (Probable). Shows antibacterial activity against Gram-positive bacterium M.luteus but shows no activity against Gram-negative bacterium E.coli (PubMed:25098233). Likely to play a role in the eradication of ingested pathogens during their passage through the intestine (Probable). Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins. Expressed only in the midgut where it localizes to a few cells in the posterior region in all larval stages. Belongs to the glycosyl hydrolase 22 family. +Catalyzes the conversion of heme O to heme A by two successive hydroxylations of the methyl group at C8. The first hydroxylation forms heme I, the second hydroxylation results in an unstable dihydroxymethyl group, which spontaneously dehydrates, resulting in the formyl group of heme A. 2 A + Fe(II)-heme o + H2O = 2 AH2 + Fe(II)-heme a Porphyrin-containing compound metabolism; heme A biosynthesis; heme A from heme O: step 1/1. Interacts with CtaB. Belongs to the COX15/CtaA family. Type 1 subfamily. +Central component of cohesin, a complex required for chromosome cohesion during the cell cycle. The cohesin complex may form a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. Cohesion is coupled to DNA replication and is involved in DNA repair. The cohesin complex also plays an important role in spindle pole assembly during mitosis and in chromosomes movement. Forms a heterodimer with SMC1A or SMC1B in cohesin complexes (PubMed:10072753). Cohesin complexes are composed of the SMC1 (SMC1A or meiosis-specific SMC1B) and SMC3 heterodimer attached via their SMC hinge domain, RAD21 which link them, and one STAG protein (STAG1, STAG2 or STAG3), which interacts with RAD21. Also found in meiosis-specific cohesin complexes. Found in a complex with SMC1A, CDCA5 and RAD21, PDS5A/SCC-112 and PDS5B/APRIN. Interacts with MXI1, MXD3 and MXD4. Interacts with NUMA1, and forms a ternary complex with KIF3B and KIFAP3, suggesting a function in tethering the chromosomes to the spindle pole and a function in chromosome movement. Interacts with PDS5A and WAPL; regulated by SMC3 acetylation. Interacts (via SMC hinge domain) with KIAA1328 (via N- and C-terminal domains). Interacts with DDX11, SYCP2 and STAG3. Found in a cohesin complex with SMC1A, RAD21 and STAG1. The SMC1A-SMC3 heterodimer interacts with the NIPBL-MAU2 heterodimer (By similarity). Interacts with RPGR (PubMed:16043481). Interacts with the NuRD complex component HDAC2; the interaction is direct (By similarity). Associates with chromatin. Before prophase it is scattered along chromosome arms. During prophase, most of cohesin complexes dissociate from chromatin probably because of phosphorylation by PLK, except at centromeres, where cohesin complexes remain. At anaphase, the RAD21 subunit of the cohesin complex is cleaved, leading to the dissociation of the complex from chromosomes, allowing chromosome separation. The phosphorylated form at Ser-1082 is preferentially associated with unsynapsed chromosomal regions (By similarity). The flexible SMC hinge domain, which separates the large intramolecular coiled coil regions, allows the heterotypic interaction with the corresponding domain of SMC1A or SMC1B, forming a V-shaped heterodimer. The two heads of the heterodimer are then connected by different ends of the cleavable RAD21 protein, forming a ring structure (By similarity). Phosphorylated at Ser-1082 in a SPO11-dependent manner. Acetylation at Lys-105 and Lys-106 by ESCO1 is important for genome stability and S phase sister chromatid cohesion. Regulated by DSCC1, it is required for processive DNA synthesis, coupling sister chromatid cohesion establishment during S phase to DNA replication (By similarity). Deacetylation by HDAC8, regulates release of the cohesin complex from chromatin (By similarity). Ubiquitinated by the DCX(DCAF15) complex, leading to its degradation. Belongs to the SMC family. SMC3 subfamily. Was originally isolated as a proteoglycan protein (explaining its name). Although not excluded, such secreted function is not clear. +Catalyzes the hydrolysis of complex carboxylic polyesters found in the cell wall of plants (By similarity). Degrades cutin, a macromolecule that forms the structure of the plant cuticle (By similarity). Allows pathogenic fungi to penetrate through the cuticular barrier into the host plant during the initial stage of fungal infection (By similarity). cutin + H2O = cutin monomers. The 2 disulfide bonds play a critical role in holding the catalytic residues in juxta-position; reduction of the disulfide bridges results in the complete inactivation of the enzyme. Belongs to the cutinase family. +Transposase that mediates sequence-specific genomic rearrangements (PubMed:26406119, PubMed:28504702). Can induce genomic rearrangements that inactivate the HPRT1 gene (PubMed:27491780). Induces site-specific DNA rearrangements, including intrachromosomal deletions, as well as inversions, duplications and translocations, in rhabdoid tumors that share developmental origin with cells that normally express PGBD5, even though these tumors may not exhibit apparent widespread genomic instability. This activity recurrently targets regulatory elements and tumor suppressor genes and promotes cell transformation. Has been domesticated very early in vertebrate evolution, approximately 500 million years ago, in the common ancestor of cephalochordates and vertebrates. Truncated N-terminus. Truncated N-terminus. +Mediates chemotaxis towards D-galactose, L-arabinose and D-fucose but not towards D-fructose. Probably part of a binding-protein high affinity uptake system. Induced by D-galactose, L-arabinose and D-fucose. Not induced by stress conditions such as nitrogen limitation, osmotic stress, salt stress or temperature stress. SbpA from A.brasilense cannot complement an Agrobacterium chvE mutant with regard to vir gene expression. Belongs to the bacterial solute-binding protein 2 family. +Heterogeneous nuclear ribonucleoprotein (hnRNP) implicated in mRNA processing mechanisms. Component of the CRD-mediated complex that promotes MYC mRNA stability. Isoform 1 and isoform 2 are associated in vitro with pre-mRNA, splicing intermediates and mature mRNA protein complexes. Isoform 1 binds to apoB mRNA AU-rich sequences (By similarity). Isoform 1 is part of the APOB mRNA editosome complex and may modulate the postranscriptional C to U RNA-editing of the APOB mRNA through either by binding to A1CF (APOBEC1 complementation factor), to APOBEC1 or to RNA itself (By similarity). May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain (By similarity). Interacts in vitro preferentially with poly(A) and poly(U) RNA sequences. Isoform 2 may be involved in cytoplasmic vesicle-based mRNA transport through interaction with synaptotagmins. Identified in the spliceosome C complex. Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1. Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Identified in a mRNP granule complex, at least composed of ACTB, ACTN4, DHX9, ERG, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPD, HNRNPL, HNRNPR, HNRNPU, HSPA1, HSPA8, IGF2BP1, ILF2, ILF3, NCBP1, NCL, PABPC1, PABPC4, PABPN1, RPLP0, RPS3, RPS3A, RPS4X, RPS8, RPS9, SYNCRIP, YBX1 and untranslated mRNAs. Interacts with GTPBP1 (By similarity). Isoform 1 is a component of the APOB mRNA editosome complex. Isoform 1 interacts with APOBEC1 and A1CF. Part of a complex associated with the FOS mCRD domain and consisting of PABPC1, PAIP1, CSDE1/UNR, HNRPD and SYNCRIP. Isoform 2 interacts with HNRPR. Interacts with POLR2A hyperphosphorylated C-terminal domain. Interacts with HABP4 (By similarity). Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1. Isoform 1 and isoform 2 interact with SMN. Isoform 2 interacts through its C-terminal domain with SYT7, SYT8 and SYT9. The non-phosphorylated and phosphorylated forms are colocalized with PAIP1 in polysomes. Localized in cytoplasmic mRNP granules containing untranslated mRNAs (By similarity). Isoforms 1 and 2 are expressed predominantly in the nucleoplasm. According to PubMed:10734137, isoform 2 is predominantly found in cytoplasm. The tyrosine phosphorylated form bound to RNA is found in microsomes. Ubiquitous. Detected in heart, brain, spleen, lung, liver, skeletal muscle, adipocytes, kidney and testis. Expressed in spinal cord at 14 dpc and onwards. The domain containing eight Arg-Gly-Gly repeats (RGG/RXR-box) may be involved in RNA-binding and protein-protein interactions. It is methylated by PRMT1, and essential for nuclear localization (By similarity). Phosphorylated on tyrosine. The membrane-bound form found in microsomes is phosphorylated in vitro by insulin receptor tyrosine kinase (INSR). Phosphorylation is inhibited upon binding to RNA, whereas the cytoplasmic form is poorly phosphorylated. May be due to a competing donor splice site and to an exon inclusion. +One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS17 family. +ATP + H2O = ADP + H(+) + phosphate Belongs to the helicase family. Truncated N-terminus. +Probably participates in a plant defense mechanism. Reduces growth of and increases mortality in larvae of D.saccharalis. Kills cultured SF-9 cells of S.frugiperda probably by disrupting plasma membranes. Has hemolytic activity against human erythrocytes. Has no antibacterial activity against E.coli strain ATCC 8739 and S.aureus strain ATCC 25923. Expressed in leaves, flowers, peduncles and seeds (at protein level). The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. This is a cyclic peptide. Belongs to the cyclotide family. Bracelet subfamily. This peptide is cyclic. The start position was chosen by similarity to OAK1 (kalata-B1) for which the DNA sequence is known. +Part of the gene cluster that mediates the biosynthesis of the selective antifungal agent ascochitine, an o-quinone methide that plays a possible protective role against other microbial competitors in nature and is considered to be important for pathogenicity of legume-associated Didymella species (PubMed:31554725). The pathway probably begins with the synthesis of a keto-aldehyde intermediate by the ascochitine non-reducing polyketide synthase pksAC from successive condensations of 4 malonyl-CoA units, presumably with a simple acetyl-CoA starter unit (Probable). Release of the keto-aldehyde intermediate is consistent with the presence of the C-terminal reductive release domain (Probable). The HR-PKS (orf7) probably makes a diketide starter unit which is passed to the non-reducing polyketide synthase pksAC for further extension, producing ascochital and ascochitine (Probable). The aldehyde dehydrogenase (orf1), the 2-oxoglutarate-dependent dioxygenase (orf3) and the dehydrogenase (orf9) are probably involved in subsequent oxidations of methyl groups to the carboxylic acid of the heterocyclic ring (Probable). The ascochitine gene cluster also includes a gene encoding a short peptide with a cupin domain (orf2) that is often found in secondary metabolite gene clusters and which function has still to be determined (Probable). Mycotoxin biosynthesis. Belongs to the oryJ family. +Modulates the action of auxin, and may function as plant growth regulator that alters phytohormone responses. Expressed during rhizobium-induced nodule formation. In 4-day old nodules it is found in all the cells of the center of the nodule primordium and also occurs in the region of the root pericycle facing the nodule primordium. At day 5, expression is seen in the complete central tissue. At day 20 expressed in the complete prefixation zone II, and in the proximal part of this zone it is found only in the infected cells but not in the uninfected cells. At the transition of prefixation zone II into interzone II-III expression decreases in the infected cells. In the fixation zone III, expression is induced in the uninfected cells and in the proximal part of this zone it is undetectable. Present at high levels in the pericycle of the nodule vascular bundle. +Expressed in pancreas, esophagus, bone marrow and keratinocytes. Product of a dubious CDS prediction. +Homodimer. CutC-nlpE double mutants show increased copper sensitivity (PubMed:7635807). However, the copper sensitivity phenotype of the mutant was later shown to be due to the loss of MicL sRNA and elevated Lpp levels (PubMed:25030700). Belongs to the CutC family. Was originally thought to be involved in copper homeostasis (PubMed:7635807), however, the copper sensitivity phenotype of the mutant was later shown to be due to the loss of MicL sRNA which leads to elevated Lpp levels (PubMed:25030700). Silent mutations in this protein that disrupt the promoter of micL are copper sensitive. +Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of a wide variety of acceptor molecules bearing a hydroxyl or an amine groupe. Sulfonation increases the water solubility of most compounds, and therefore their renal excretion, but it can also result in bioactivation to form active metabolites. Displays broad substrate specificity for small phenolic compounds. Plays an important role in the sulfonation of endogenous molecules such as steroid hormones and 3,3'-diiodothyronin (By similarity). Mediates the sulfate conjugation of a variety of xenobiotics, including the drugs acetaminophen and minoxidil. Mediates also the metabolic activation of carcinogenic N-hydroxyarylamines leading to highly reactive intermediates capable of forming DNA adducts, potentially resulting in mutagenesis (By similarity). May play a role in gut microbiota-host metabolic interaction. O-sulfonates 4-ethylphenol (4-EP), a dietary tyrosine-derived metabolite produced by gut bacteria. The product 4-EPS crosses the blood-brain barrier and may negatively regulate oligodendrocyte maturation and myelination, affecting the functional connectivity of different brain regions associated with the limbic system. 3'-phosphoadenylyl sulfate + a phenol = adenosine 3',5'-bisphosphate + an aryl sulfate + H(+) 17beta-estradiol + 3'-phosphoadenylyl sulfate = 17beta-estradiol 3-sulfate + adenosine 3',5'-bisphosphate + H(+) 3'-phosphoadenylyl sulfate + 4-ethylphenol = 4-ethylphenyl sulfate + adenosine 3',5'-bisphosphate + H(+) Homodimer. Distal lung parenchyma. Belongs to the sulfotransferase 1 family. +Present with 704 molecules/cell in log phase SD medium. Belongs to the UPF0659 family. +Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. D2 is needed for assembly of a stable PSII complex. 2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2 The D1/D2 heterodimer binds P680, chlorophylls that are the primary electron donor of PSII, and subsequent electron acceptors. It shares a non-heme iron and each subunit binds pheophytin, quinone, additional chlorophylls, carotenoids and lipids. There is also a Cl(-1) ion associated with D1 and D2, which is required for oxygen evolution. The PSII complex binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Phosphorylated in vitro (PubMed:1885590). 2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water. Belongs to the reaction center PufL/M/PsbA/D family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds 2 heme A groups non-covalently per subunit. Binds a copper B center. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of a catalytic core of 3 subunits and several supernumerary subunits. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII). Belongs to the heme-copper respiratory oxidase family. +Involved in the detoxification of xenobiotics and in the activation of ester and amide prodrugs. Hydrolyzes aromatic and aliphatic esters, but has no catalytic activity toward amides or a fatty acyl-CoA ester. Displays fatty acid ethyl ester synthase activity, catalyzing the ethyl esterification of oleic acid to ethyloleate. Converts monoacylglycerides to free fatty acids and glycerol. Hydrolyzes of 2-arachidonoylglycerol and prostaglandins. Hydrolyzes cellular cholesteryl esters to free cholesterols and promotes reverse cholesterol transport (RCT) by facilitating both the initial and final steps in the process. First of all, allows free cholesterol efflux from macrophages to extracellular cholesterol acceptors and secondly, releases free cholesterol from lipoprotein-delivered cholesteryl esters in the liver for bile acid synthesis or direct secretion into the bile. a carboxylic ester + H2O = a carboxylate + an alcohol + H(+) cholesteryl (9Z-octadecenoate) + H2O = (9Z)-octadecenoate + cholesterol + H(+) 2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + glycerol + H(+) H2O + prostaglandin E2 1-glyceryl ester = glycerol + H(+) + prostaglandin E2 a cholesterol ester + H2O = a fatty acid + cholesterol + H(+) H2O + prostaglandin F2alpha 1-glyceryl ester = glycerol + H(+) + prostaglandin F2alpha Homotrimer and homohexamer. Binds to beta-glucuronidase (By similarity). Moves from cytoplasm to lipid droplets upon lipid loading. Associates with lipid droplets independently of triglycerides (TG) content of the droplets and hydrolyzes cholesteryl esters more efficiently from mixed droplets. Belongs to the type-B carboxylesterase/lipase family. +This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium (By similarity). Transports calcium to the vacuole and participates in the control of cytosolic free calcium (PubMed:23895559). ATP + Ca(2+)(in) + H2O = ADP + Ca(2+)(out) + H(+) + phosphate Increases cytosolic free calcium level (PubMed:23895559). Resistance to cadmium (PubMed:23895559). Decreases cell population growth in serum (PubMed:29113016). Sensitive to calcium (PubMed:23895559). Abnormal level of calcineurin-mediated signaling pathway gene RNA, transepithelial migration gene RNA, and antioxidant gene RNA (PubMed:29113016). Decreases VCX1 RNA level and increases ECA1 RNA level during cellular response to calcium (PubMed:23895559). Decreases urease activity (PubMed:29113016). Avirulence in a mouse systemic model of infection; decreases lung fungal burden and abolishes brain fungal burden (PubMed:29113016). Decreases virulence in a mouse intranasal inhalation infection model; decreases lung fungal burden and abolishes brain fungal burden (PubMed:23895559). Severely decreases transepithelial migration through the host blood-brain barrier (PubMed:29113016). Increases susceptibility to phagocytosis by macrophages (PubMed:29113016). Phenotypes enhanced in a double knockout with VCX1 (PubMed:23895559). Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. +Forms an efflux pump with AaeA. Could function as a metabolic relief valve, allowing to eliminate certain compounds when they accumulate to high levels in the cell. Positively coregulated with aaeA and aaeX by AaeR. Belongs to the aromatic acid exporter ArAE (TC 2.A.85) family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Binds 2 manganese ions per subunit. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Monomer. Belongs to the BPG-independent phosphoglycerate mutase family. +Endonuclease that is involved in the suppression of homologous recombination and may therefore have a key role in the control of bacterial genetic diversity. Homodimer. Belongs to the DNA mismatch repair MutS family. MutS2 subfamily. +The light-harvesting complex (LHC) functions as a light receptor, it captures and delivers excitation energy to photosystems with which it is closely associated. Binds at least 14 chlorophylls (8 Chl-a and 6 Chl-b) and carotenoids such as lutein and neoxanthin. The LHC complex consists of chlorophyll a-b binding proteins. The N-terminus of the protein extends into the stroma where it is involved with adhesion of granal membranes and post-translational modifications; both are believed to mediate the distribution of excitation energy between photosystems I and II. Photoregulated by reversible phosphorylation of its threonine residues. Belongs to the light-harvesting chlorophyll a/b-binding (LHC) protein family. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Belongs to the UPF0370 family. +Cytochrome P450 monooxygenase; part of the gene cluster that mediates the biosynthesis of communesins, a prominent class of indole alkaloids with great potential as pharmaceuticals (PubMed:25571861). Communesins are biosynthesized by the coupling of tryptamine and aurantioclavine, two building blocks derived from L-tryptophan (PubMed:25571861). The L-tryptophan decarboxylase cnsB converts L-tryptophan to tryptamine, whereas the tryptophan dimethylallyltransferase cnsF converts L-tryptophan to 4-dimethylallyl tryptophan which is further transformed to aurantioclavine by the aurantioclavine synthase cnsA, probably aided by the catalase cnsD (PubMed:25571861). The cytochrome P450 monooxygenase cnsC catalyzes the heterodimeric coupling between the two different indole moieties, tryptamine and aurantioclavine, to construct vicinal quaternary stereocenters and yield the heptacyclic communesin scaffold (PubMed:26963294). The O-methyltransferase cnsE then methylates the communesin scaffold to produce communesin K, the simplest characterized communesin that contains the heptacyclic core (PubMed:25571861). The dioxygenase cnsJ converts communesin K into communesin I (PubMed:25571861). Acylation to introduce the hexadienyl group at position N16 of communesin I by the acyltransferase cnsK leads to the production of communesin B. The hexadienyl group is produced by the highly reducing polyketide synthase cnsI, before being hydrolytically removed from cnsI by the serine hydrolase cnsH, converted into hexadienyl-CoA by the CoA ligase cnsG, and then transferred to communesin I by cnsK (PubMed:25571861). Surprisingly, cnsK may also be a promiscuous acyltransferase that can tolerate a range of acyl groups, including acetyl-, propionyl-, and butyryl-CoA, which lead to communesins A, G and H respectively (PubMed:25571861). The roles of the alpha-ketoglutarate-dependent dioxygenases cnsM and cnsP have still to be determined (PubMed:25571861). Alkaloid biosynthesis. Abolishes the biosynthesis of communesins A and B and leads to the accumulation of aurantioclavine. Belongs to the cytochrome P450 family. +Filament-forming cytoskeletal GTPase. Required for normal organization of the actin cytoskeleton. Plays a role in the biogenesis of polarized columnar-shaped epithelium. Required for the progression through mitosis through regulation of chromosome congression. During anaphase, may be required for chromosome segregation and spindle elongation. Plays a role in ciliogenesis and collective cell movements including convergent extension during gastrulation. In cilia, required for the integrity of the diffusion barrier at the base of the primary cilium that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Controls cell shape and not polarization of cells during convergent extension (By similarity). Septins polymerize into heterooligomeric protein complexes that form filaments, and associate with cellular membranes, actin filaments and microtubules. GTPase activity is required for filament formation. Can form heterooligomers with other family members and form filaments. Interacts with wdpcp (By similarity). Localizes at the base of the cilia near the morphological distinction between the cilia and plasma membranes. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Septin GTPase family. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +May play a role in vesicular transport during the biogenesis of melanosomes. Part of the multisubunit transport protein particle (TRAPP) complex. Heterodimer with TRAPPC3 (By similarity). The heterodimer TRAPPC3-TRAPPC6A interacts with TRAPPC2L. Interacts with TRAPPC2L (By similarity). Belongs to the TRAPP small subunits family. BET3 subfamily. +Belongs to the HAD-like hydrolase superfamily. +Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits. Component of the small ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains about 33 different proteins and 1 molecule of RNA (18S). The 60S subunit contains about 49 different proteins and 3 molecules of RNA (25S, 5.8S and 5S). Interacts with rps21. Deficiency of 40S ribosomal subunit formation, this is likely to be caused by insufficient 18S rRNA stability. There are two genes for S0 in S.pombe. Belongs to the universal ribosomal protein uS2 family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Essential for recycling GMP and indirectly, cGMP. ATP + GMP = ADP + GDP Belongs to the guanylate kinase family. +Catalyzes the NAD(+)-dependent oxidation of L-threonine to 2-amino-3-ketobutyrate. L-threonine + NAD(+) = (2S)-2-amino-3-oxobutanoate + H(+) + NADH Binds 2 Zn(2+) ions per subunit. Amino-acid degradation; L-threonine degradation via oxydo-reductase pathway; glycine from L-threonine: step 1/2. Homotetramer. Belongs to the zinc-containing alcohol dehydrogenase family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Beta-glucosidases are one of a number of cellulolytic enzymes involved in the degradation of cellulosic biomass. Catalyzes the last step releasing glucose from the inhibitory cellobiose (By similarity). Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose. Glycan metabolism; cellulose degradation. Covalently-linked to the cell wall. Belongs to the glycosyl hydrolase 17 family. +Type I collagen is a member of group I collagen (fibrillar forming collagen). Trimers of one alpha 2(I) and two alpha 1(I) chains. Expressed in bones. Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains. These protein fragments were extracted from an ancient phalanx bone collected at Arroyo Del Moro in Argentina. Belongs to the fibrillar collagen family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Catalyzes the conversion of pppGpp to ppGpp. Guanosine pentaphosphate (pppGpp) is a cytoplasmic signaling molecule which together with ppGpp controls the 'stringent response', an adaptive process that allows bacteria to respond to amino acid starvation, resulting in the coordinated regulation of numerous cellular activities. guanosine 3'-diphosphate 5'-triphosphate + H2O = guanosine 3',5'-bis(diphosphate) + H(+) + phosphate Purine metabolism; ppGpp biosynthesis; ppGpp from GTP: step 2/2. Belongs to the GppA/Ppx family. GppA subfamily. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. Binds 2 heme groups. One heme group is bound covalently by a single cysteine link, the other one non-covalently. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Heme 1 (or BH or b566) is high-potential and absorbs at about 566 nm, and heme 2 (or BL or b562) is low-potential and absorbs at about 562 nm. Belongs to the cytochrome b family. PetB subfamily. +Converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate, the first intermediate in the biosynthesis of coenzyme methanopterin. GTP + H2O = 7,8-dihydroneopterin 2',3'-cyclic phosphate + diphosphate + formate + H(+) Binds 1 Fe(2+) ion per subunit. Cofactor biosynthesis; 5,6,7,8-tetrahydromethanopterin biosynthesis. Homodimer. Belongs to the GTP cyclohydrolase IV family. +Catalyzes the S-methylation of thiopurine drugs such as 6-mercaptopurine (also called mercaptopurine, 6-MP or its brand name Purinethol) using S-adenosyl-L-methionine as the methyl donor (PubMed:18484748). TPMT activity modulates the cytotoxic effects of thiopurine prodrugs. A natural substrate for this enzyme has yet to be identified. S-adenosyl-L-methionine + a thiopurine = S-adenosyl-L-homocysteine + a thiopurine S-methylether. mercaptopurine + S-adenosyl-L-methionine = 6-methylthiopurine + H(+) + S-adenosyl-L-homocysteine Monomer. Belongs to the class I-like SAM-binding methyltransferase superfamily. TPMT family. +Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs. Part of the 50S ribosomal subunit. Probably part of the RNase P complex. Belongs to the eukaryotic ribosomal protein eL8 family. Extended N-terminus. +Sodium-dependent dopamine transporter which terminates the action of dopamine by its high affinity sodium-dependent reuptake into presynaptic terminals (PubMed:11125028, PubMed:12606774, PubMed:24037379, PubMed:25970245). Also transports tyramine and norepinephrine, shows less efficient transport of octopamine and does not transport serotonin (PubMed:11125028, PubMed:12606774). Plays a role in the regulation of the rest/activity cycle (PubMed:16093388, PubMed:25232310). Expression is restricted to dopaminergic neurons in the central nervous system. Low levels in 0-4 hour embryos with strong expression in late embryos at 12-24 hours and during larval development. Expression decreases during pupal development and increases again in adult flies with heads showing higher levels than bodies. No effect on fertility or longevity but mutants display longer periods of daily activity than controls, reduced rest, enhanced sensitivity to mechanical stimuli when inactive and decreased rest rebound in response to rest deprivation (PubMed:16093388). Impaired aversive olfactory memory due to excessive dopaminergic signaling (PubMed:25232310). RNAi-mediated knockdown in neurons causes significant reduction in the sleep-like rest state with total daily resting periods decreased to about half of that of control flies (PubMed:25232310). 10-fold less sensitive to cocaine than mammalian dopamine transporter SLC6A3. Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. +Involved in calcium binding and microtubule stabilization. Belongs to the TCTP family. +Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery. ATP-dependent cleavage of peptide bonds with broad specificity. Allosterically activated by HslU binding. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the peptidase T1B family. HslV subfamily. +Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation, including the primary periplasmic chaperone SurA and the lipoprotein Pal. The catalytic subunit MsrP is non-stereospecific, being able to reduce both (R-) and (S-) diastereoisomers of methionine sulfoxide. a quinone + H2O + L-methionyl-[protein] = a quinol + L-methionyl-(S)-S-oxide-[protein] a quinone + H2O + L-methionyl-[protein] = a quinol + L-methionyl-(R)-S-oxide-[protein] Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit. Heterodimer of a catalytic subunit (MsrP) and a heme-binding subunit (MsrQ). Is attached to the inner membrane when interacting with the MsrQ subunit. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the MsrP family. +Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds directly to 7S RNA and mediates binding of the 54 kDa subunit of the SRP. Part of the signal recognition particle protein translocation system, which is composed of SRP and FtsY. Archaeal SRP consists of a 7S RNA molecule of 300 nucleotides and two protein subunits: SRP54 and SRP19. No effect on cell growth, membrane protein insertion, protein secretion, or ribosome levels. Belongs to the SRP19 family. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Protein modification; protein ubiquitination. Homodimer or heterodimer with BPM3 and BPM5. Interacts with CUL3A and CUL3B. Interacts with RAP2-4 and RAP2-13. Binds to MYB56 at the promoter of FLOWERING LOCUS T (FT) (PubMed:25343985). Ubiquitous. The BTB/POZ domain mediates the interaction with some component of ubiquitin ligase complexes. May be due to intron retention. Belongs to the Tdpoz family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Belongs to the UPF0262 family. +Required for biogenesis of the 60S ribosomal subunit. Belongs to the BRX1 family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +The complex LTO1:YAE1 may function as a target specific adapter that probably recruits apo-RPLI1 to the cytosolic iron-sulfur protein assembly (CIA) complex machinery. May be required for biogenesis of the large ribosomal subunit and initiation of translation. May form a complex with LTO1. Belongs to the YAE1 family. +Tethering factor involved in autophagy. Involved in autophagosome maturation by promoting the autophagosome fusion with lysosomes: acts by associating with both the ATG5-ATG12 conjugate and phosphatidylinositol-3-phosphate (PtdIns(3)P) present at the surface of autophagosomes. Also involved in selective autophagy against bacterial pathogens, by being required for phagophore/preautophagosomal structure biogenesis and maturation (By similarity). Interacts with ATG5; the interaction is direct. Interacts with WIPI2. Interacts with the ATG5-ATG12 conjugate, the interaction is however mutually exclusive with ATG16, since it does not interact with ATG12-ATG5-ATG16 complex. Localizes to Lysosome membranes, and binds PtdIns(3)P at the surface of autophagosome. Localizes to autolysosomes, a vesicle formed by the fusion between autophagosomes and lysosomes (By similarity). The PH domain mediates the binding to phosphatidylinositol-3-phosphate (PtdIns(3)P). Belongs to the TECPR1 family. +Probable thiol-disulfide oxidoreductase that may be involved in the redox regulation of a number of cytosolic enzymes. Belongs to the thioredoxin family. The active site contains a CVPC motif wich differs from the conserved CGPC motif. +The mitochondria from the S male-sterile cytoplasm of maize contain unique DNA-protein complexes, designated S-1 and S-2. These complexes consist of double-stranded linear DNAs with proteins covalently attached to the 5'-termini. +Protein modifier that is covalently attached to lysine residues of substrate proteins, thereby targeting them for proteasomal degradation. The tagging system is termed pupylation. Protein degradation; proteasomal Pup-dependent pathway. Strongly interacts with the proteasome-associated ATPase ARC through a hydrophobic interface; the interacting region of Pup lies in its C-terminal half. There is one Pup binding site per ARC hexamer ring. The N-terminal unstructured half of Pup provides a signal required to initiate unfolding and degradation by the proteasome but is not needed for pupylation, while the C-terminal helical half of Pup interacts with ARC to target proteins to the proteasome. Belongs to the prokaryotic ubiquitin-like protein family. +Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. It is involved in repression of photomorphogenesis in darkness by regulating the activity of COP1-containing Ubl ligase complexes (By similarity). Component of the CSN complex, probably composed of CSN1, CSN2, CSN3, CSN4, CSN5 (CSN5A or CSN5B), CSN6 (CSN6A or CSN6B), CSN7 and CSN8. Phosphorylated. Belongs to the CSN7/EIF3M family. CSN7 subfamily. +Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Binds 2 divalent ions per subunit. Binds 1 potassium ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Homotetramer; dimer of dimers. Belongs to the AdoMet synthase family. +Belongs to the UPF0750 family. +Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. ATP + NAD(+) = ADP + H(+) + NADP(+) Belongs to the NAD kinase family. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +D-mannitol 1-phosphate + NAD(+) = beta-D-fructose 6-phosphate + H(+) + NADH Belongs to the mannitol dehydrogenase family. +Belongs to the sodium:solute symporter (SSF) (TC 2.A.21) family. +Secreted subtilisin-like serine protease with keratinolytic activity that contributes to pathogenicity. Belongs to the peptidase S8 family. +Endoplasmic reticulum disulfide reductase involved both in the correct folding of proteins and degradation of misfolded proteins. Required for efficient folding of proteins in the endoplasmic reticulum by catalyzing the removal of non-native disulfide bonds formed during the folding of proteins, such as LDLR. Also involved in endoplasmic reticulum-associated degradation (ERAD) by reducing incorrect disulfide bonds in misfolded glycoproteins recognized by EDEM1. Interaction with HSPA5 is required its activity, not for the disulfide reductase activity, but to facilitate the release of DNAJC10 from its substrate. Promotes apoptotic signaling pathway in response to endoplasmic reticulum stress (By similarity). Interacts with HSPA5 (via its J domain). Interacts with EDEM1 (By similarity). Thioredoxin domains 3 and 4 are the primary reductase domains. The thioredoxin-like regions Trxb 1 and 2 lack a redox-active CXXC motif. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Repressor involved in the biosynthesis of the osmoprotectant glycine betaine. It represses transcription of the choline transporter BetT and the genes of BetAB involved in the synthesis of glycine betaine (By similarity). Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway [regulation]. +Belongs to the major facilitator superfamily. DHA1 family. MdtH (TC 2.A.1.2.21) subfamily. +Belongs to the universal ribosomal protein uS2 family. +Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol. 2 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) = a cardiolipin + glycerol Belongs to the phospholipase D family. Cardiolipin synthase subfamily. ClsA sub-subfamily. +Catalyzes the sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine. H2O + L-histidinol + 2 NAD(+) = 3 H(+) + L-histidine + 2 NADH Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 9/9. Belongs to the histidinol dehydrogenase family. +Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P). D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate from glycerone phosphate: step 1/1. Homodimer. Belongs to the triosephosphate isomerase family. +Possibly the antitoxin component of a type II toxin-antitoxin (TA) system. Its cognate toxin is VapC3 (Potential). Belongs to the UPF0330 family. +Belongs to the SfsA family. +Toxic component of a type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB18 (By similarity). Belongs to the PINc/VapC protein family. +Interacts with DDX6. Interacts with MCRIP1. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the MCRIP family. +Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery. ATP-dependent cleavage of peptide bonds with broad specificity. Allosterically activated by HslU binding. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the peptidase T1B family. HslV subfamily. +Catalyzes the deamination of 5-methylthioadenosine and S-adenosyl-L-homocysteine into 5-methylthioinosine and S-inosyl-L-homocysteine, respectively. Is also able to deaminate adenosine. H(+) + H2O + S-adenosyl-L-homocysteine = NH4(+) + S-inosyl-L-homocysteine H(+) + H2O + S-methyl-5'-thioadenosine = NH4(+) + S-methyl-5'-thioinosine Binds 1 zinc ion per subunit. Belongs to the metallo-dependent hydrolases superfamily. MTA/SAH deaminase family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Catalyzes the production of L-lysyl-tRNA(Lys)transfer and the transfer of a lysyl group from L-lysyl-tRNA(Lys) to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG), one of the components of the bacterial membrane with a positive net charge. LPG synthesis contributes to the resistance to cationic antimicrobial peptides (CAMPs) and likely protects M.tuberculosis against the CAMPs produced by competiting microorganisms (bacteriocins). In fact, the modification of anionic phosphatidylglycerol with positively charged L-lysine results in repulsion of the peptides. ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys) 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-lysyl-tRNA(Lys) = 1,2-diacyl-sn-glycero-3-phospho-1'-(3'-O-L-lysyl)-sn-glycerol + tRNA(Lys) Binds 3 Mg(2+) ions per subunit. There are two lysyl-tRNA ligases in M.tuberculosis. In the N-terminal section; belongs to the LPG synthetase family. In the C-terminal section; belongs to the class-II aminoacyl-tRNA synthetase family. +Facilitates sperm penetration into the layer of cumulus cells surrounding the egg by digesting hyaluronic acid. Involved in induction of the acrosome reaction in the sperm. Involved in follicular atresia, the breakdown of immature ovarian follicles that are not selected to ovulate. Induces ovarian granulosa cell apoptosis, possibly via apoptotic signaling pathway involving CASP8 and CASP3 activation, and poly(ADP-ribose) polymerase (PARP) cleavage. Has no hyaluronidase activity in embryonic fibroblasts in vitro. Has no hyaluronidase activity in granulosa cells in vitro. Random hydrolysis of (1->4)-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate. Mostly present in low-density vesicles. Low levels in higher density vesicles of late endosomes and lysosomes. Localized in punctate cytoplasmic vesicles and in perinuclear structures, but does not colocalize with LAMP1. Localized on the plasma membrane over the acrosome and on the surface of the midpiece of the sperm tail. N-glycosylated. Belongs to the glycosyl hydrolase 56 family. +Involved in concentration and sorting of cargo proteins of the multivesicular body (MVB) for incorporation into intralumenal vesicles. Belongs to the BRO1 family. The predicted gene AN6194 has been split into 2 genes: AN10778 and AN10788. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Mitochondrial intermembrane chaperone that participates in the import and insertion of some multi-pass transmembrane proteins into the mitochondrial inner membrane. Also required for the transfer of beta-barrel precursors from the TOM complex to the sorting and assembly machinery (SAM complex) of the outer membrane. Acts as a chaperone-like protein that protects the hydrophobic precursors from aggregation and guide them through the mitochondrial intermembrane space. The TIM8-TIM13 complex is non essential and only mediates the import of few proteins, while the predominant TIM9-TIM10 70 kDa complex is crucial and mediates the import of much more proteins (By similarity). Heterohexamer; composed of 3 copies of TIM8 and 3 copies of TIM13, named soluble 70 kDa complex. Associates with the TIM22 complex, whose core is composed of TIM22 and TIM54. Interacts with the transmembrane regions of multi-pass transmembrane proteins in transit (By similarity). The twin CX3C motif contains 4 conserved Cys residues that form 2 disulfide bonds in the mitochondrial intermembrane space. However, during the transit of TIM8 from cytoplasm into mitochondrion, the Cys residues probably coordinate zinc, thereby preventing folding and allowing its transfer across mitochondrial outer membrane (By similarity). Belongs to the small Tim family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell. Belongs to the MinE family. +This is a receptor for PACAP-27 and PACAP-38. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase. May regulate the release of adrenocorticotropin, luteinizing hormone, growth hormone, prolactin, epinephrine, and catecholamine. May play a role in spermatogenesis and sperm motility. Causes smooth muscle relaxation and secretion in the gastrointestinal tract. Interacts (via N-terminal extracellular domain) with ADCYAP1. Most abundant in the brain, low expression in the lung, liver, thymus, spleen, pancreas and placenta. Belongs to the G-protein coupled receptor 2 family. +3-keto-steroid reductase; part of the third module of ergosterol biosynthesis pathway that includes the late steps of the pathway (PubMed:15552648). ERG27 is a catalytic component of the C-4 demethylation complex that catalyzes the reduction of the keto group on the C-3 (PubMed:15552648). The third module or late pathway involves the ergosterol synthesis itself through consecutive reactions that mainly occur in the endoplasmic reticulum (ER) membrane. Firstly, the squalene synthase ERG9 catalyzes the condensation of 2 farnesyl pyrophosphate moieties to form squalene, which is the precursor of all steroids. Squalene synthase is crucial for balancing the incorporation of farnesyl diphosphate (FPP) into sterol and nonsterol isoprene synthesis. Secondly, the squalene epoxidase ERG1 catalyzes the stereospecific oxidation of squalene to (S)-2,3-epoxysqualene, which is considered to be a rate-limiting enzyme in steroid biosynthesis. Then, the lanosterol synthase ERG7 catalyzes the cyclization of (S)-2,3 oxidosqualene to lanosterol, a reaction that forms the sterol core. In the next steps, lanosterol is transformed to zymosterol through a complex process involving various demethylation, reduction and desaturation reactions. The lanosterol 14-alpha-demethylase ERG11 (also known as CYP51) catalyzes C14-demethylation of lanosterol to produce 4,4'-dimethyl cholesta-8,14,24-triene-3-beta-ol, which is critical for ergosterol biosynthesis. The C-14 reductase ERG24 reduces the C14=C15 double bond of 4,4-dimethyl-cholesta-8,14,24-trienol to produce 4,4-dimethyl-cholesta-8,24-dienol. 4,4-dimethyl-cholesta-8,24-dienol is substrate of the C-4 demethylation complex ERG25-ERG26-ERG27 in which ERG25 catalyzes the three-step monooxygenation required for the demethylation of 4,4-dimethyl and 4alpha-methylsterols, ERG26 catalyzes the oxidative decarboxylation that results in a reduction of the 3-beta-hydroxy group at the C-3 carbon to an oxo group, and ERG27 is responsible for the reduction of the keto group on the C-3. ERG28 has a role as a scaffold to help anchor ERG25, ERG26 and ERG27 to the endoplasmic reticulum and ERG29 regulates the activity of the iron-containing C4-methylsterol oxidase ERG25. Then, the sterol 24-C-methyltransferase ERG6 catalyzes the methyl transfer from S-adenosyl-methionine to the C-24 of zymosterol to form fecosterol. The C-8 sterol isomerase ERG2 catalyzes the reaction which results in unsaturation at C-7 in the B ring of sterols and thus converts fecosterol to episterol. The sterol-C5-desaturase ERG3 then catalyzes the introduction of a C-5 double bond in the B ring to produce 5-dehydroepisterol. The C-22 sterol desaturase ERG5 further converts 5-dehydroepisterol into ergosta-5,7,22,24(28)-tetraen-3beta-ol by forming the C-22(23) double bond in the sterol side chain. Finally, ergosta-5,7,22,24(28)-tetraen-3beta-ol is substrate of the C-24(28) sterol reductase ERG4 to produce ergosterol (Probable). Facilitates the association of ERG7 with lipid particles preventing its digestion in the endoplasmic reticulum and the lipid particles. 3-dehydro-4alpha-methylzymosterol + H(+) + NADPH = 4alpha-methylzymosterol + NADP(+) Steroid biosynthesis; zymosterol biosynthesis; zymosterol from lanosterol: step 5/6. Heterotetramer of ERG25, ERG26, ERG27 and ERG28 (By similarity). ERG28 acts as a scaffold to tether ERG27 and other 4,4-demethylation-related enzymes, forming a demethylation enzyme complex, in the endoplasmic reticulum. Interacts with ERG25 and ERG28. Also interacts with ERG7, but only in lipid particles (By similarity). Expression is increased by itraconazole (which targets the lanosterol demethylase CYP51/ERG11) and by zaragozic acid A (which targets the squalene synthase ERG9). Leads to complete loss of both 3-keto reductase and oxidosqualene cyclase (performed by ERG7) activities, compromising all sterol synthesis. Belongs to the short-chain dehydrogenases/reductases (SDR) family. ERG27 subfamily. +Acts as component of the STAGA transcription coactivator-HAT complex. Mediates the interaction of STAGA complex with the CRX and is involved in CRX-dependent gene activation. Necessary for microtubule cytoskeleton stabilization. Component of the STAGA transcription coactivator-HAT complex, at least composed of SUPT3H, GCN5L2, TAF5L, TAF6L, SUPT7L, TADA3L, TAD1L, TAF10, TAF12, TRRAP, TAF9 and ATXN7. The STAGA core complex is associated with a subcomplex required for histone deubiquitination composed of ATXN7L3, ENY2 and USP22. Interacts with SORBS1, PSMC1 and CRX. Interacts with TRRAP, GCN5L2 and TAF10. Interacts with alpha tubulin. In addition to a diffuse distribution throughout the nucleus, it is associated with the nuclear matrix and the nucleolus. It is able to shuttle between the nucleus and cytoplasm. Isoform a and isoform b are expressed in CNS, but isoform a is expressed predominantly in the peripherical tissues. Isoform b is also highly expressed in the frontal lobe, skeletal muscle and spinal cord and is expressed at a lower level in the lung, lymphoblast and intestine. Proteolytically cleaved. The cleavage may be involved in SCA7 degeneration: the isoform fragments may exert distinct toxic influences that could contribute to selective neurodegeneration. Sumoylation decreases the aggregation propensity and cellular toxicity of forms with an expanded poly-Gln region but has no effect on subcellular location or interaction with components of the STAGA complex. The poly-Gln region of ATXN7 is highly polymorphic (4 to 18 repeats) in the normal population and is expanded to about 38-130 repeats in SCA7 patients. Intermediate alleles with 28 to 35 repeats are prone to further expansion. The disease is caused by variants affecting the gene represented in this entry. Belongs to the ataxin-7 family. +Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene). 5-methylsulfanyl-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate Binds 1 Mg(2+) ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 3/6. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 4/6. Monomer. Belongs to the HAD-like hydrolase superfamily. MasA/MtnC family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Belongs to the bacterial ribosomal protein bS16 family. +Involved in the regulation of the iron regulon in response to decreased mitochondrial iron-sulfur cluster synthesis. May be involved in mitochondrial organization and biogenesis. Interacts with FRA1, GRX3 and GRX4. Present with 2050 molecules/cell in log phase SD medium. Belongs to the BolA/IbaG family. +Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). Component of the Mediator complex. Belongs to the Mediator complex subunit 20 family. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +The light-harvesting complex (LHC) functions as a light receptor, it captures and delivers excitation energy to photosystems with which it is closely associated. Binds at least 14 chlorophylls (8 Chl-a and 6 Chl-b) and carotenoids such as lutein and neoxanthin. The LHC complex consists of chlorophyll a-b binding proteins. The N-terminus of the protein extends into the stroma where it is involved with adhesion of granal membranes and post-translational modifications; both are believed to mediate the distribution of excitation energy between photosystems I and II. Photoregulated by reversible phosphorylation of its threonine residues. Belongs to the light-harvesting chlorophyll a/b-binding (LHC) protein family. +Catalyzes the oxidative demethylation of N-methyl-L-tryptophan. H2O + N(alpha)-methyl-L-tryptophan + O2 = formaldehyde + H2O2 + L-tryptophan Binds 1 FAD per subunit. Monomer. Belongs to the MSOX/MTOX family. MTOX subfamily. +Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Present with 125 molecules/cell in log phase SD medium. Belongs to the peptidase C19 family. +Belongs to the FAM110 family. +Component of the nascent polypeptide-associated complex (NAC), a dynamic component of the ribosomal exit tunnel, protecting the emerging polypeptides from interaction with other cytoplasmic proteins to ensure appropriate nascent protein targeting. The NAC complex also promotes mitochondrial protein import by enhancing productive ribosome interactions with the outer mitochondrial membrane and blocks the inappropriate interaction of ribosomes translating non-secretory nascent polypeptides with translocation sites in the membrane of the endoplasmic reticulum. EGD2 may also be involved in transcription regulation (By similarity). Part of the nascent polypeptide-associated complex (NAC), consisting of EGD2 and EGD1. NAC associates with ribosomes via EGD1 (By similarity). Predominantly cytoplasmic, may also transiently localize to the nucleus. Belongs to the NAC-alpha family. +Belongs to the bacterial ribosomal protein bL36 family. +Belongs to the HesB/IscA family. +Catalyzes the rearrangement of 1-deoxy-D-xylulose 5-phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S. 1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + [sulfur-carrier protein ThiS]-C-terminal Gly-Gly + 2 H(+) + 2 H2O Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homotetramer. Forms heterodimers with either ThiH or ThiS. Belongs to the ThiG family. +Catalyzes the transfer of a N-acetyl-glucosamine moiety to 1D-myo-inositol 3-phosphate to produce 1D-myo-inositol 2-acetamido-2-deoxy-glucopyranoside 3-phosphate in the mycothiol biosynthesis pathway. 1D-myo-inositol 3-phosphate + UDP-N-acetyl-alpha-D-glucosamine = 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside 3-phosphate + H(+) + UDP Homodimer. Belongs to the glycosyltransferase group 1 family. MshA subfamily. +Expressed mainly in roots and flowers. Lower in stems and leaves. Up-regulated by cold and dehydration stresses. Down-regulated by heat shock stress. A pair of annexin repeats may form one binding site for calcium and phospholipid. Belongs to the annexin (TC 1.A.31.1) family. +Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) Binds 1 zinc ion per subunit. Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. Belongs to the class-II aminoacyl-tRNA synthetase family. +May have a major role in the perfection of crystallization, involved either in the pore structure itself or in the organization of the pores within the linear array of terminal synthesizing complexes (TCs). Glycan metabolism; bacterial cellulose biosynthesis. +Energy-transducing component of the chromatin-remodeling complexes NURF (nucleosome-remodeling factor), ACF (ATP-utilizing chromatin assembly and remodeling factor), and CHRAC (chromatin accessibility complex) (PubMed:10856248, PubMed:11447119). NURF catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. It is required for homeotic gene expression, proper larval blood cell development, normal male X chromosome morphology, ecdysteroid signaling and metamorphosis (PubMed:12502740, PubMed:16264191, PubMed:8521501, PubMed:8521502). Component of the NURF complex composed of Caf1-55, E(bx), Nurf-38 and Iswi (PubMed:8521502). Component of the chromatin accessibility complex (CHRAC), composed of Chrac-14, Chrac-16, Acf and Iswi (PubMed:10856248, PubMed:11447119). Interacts directly with Chrac-14 and this interaction is further stabilized by associated Chrac-16 (PubMed:10856248). Present throughout embryonic, larval and pupal development and in female adults. Present at low levels in adult males (at protein level). Belongs to the SNF2/RAD54 helicase family. ISWI subfamily. +Cytokine that stimulates the proliferation of T-lymphocytes. Stimulation by IL15 requires interaction of IL15 with components of the IL2 receptor, including IL2RB and probably IL2RG but not IL2RA (By similarity). In neutrophils, stimulates phagocytosis probably by signaling through the IL15 receptor, which results in kinase SYK activation (By similarity). Expressed in many tissues including heart, spleen, lung, liver, muscle and kidney (at mRNA level). Expressed in many tissues including heart, spleen, lung, liver, muscle and kidney (at protein level). Belongs to the IL-15/IL-21 family. +Acyltransferase which mediates the conversion of lysophosphatidylinositol (1-acylglycerophosphatidylinositol or LPI) into phosphatidylinositol (1,2-diacyl-sn-glycero-3-phosphoinositol or PI) (LPIAT activity). Prefers arachidonoyl-CoA or eicosapentaenoic acid (EPA) as the acyl donor. Prefers sn-2-LPI rather than sn-1-LPI as the acyl acceptor. Lysophospholipid acyltransferases (LPLATs) catalyze the reacylation step of the phospholipid remodeling pathway also known as the Lands cycle (By similarity). a 1-acyl-sn-glycero-3-phospho-(1D-myo-inositol) + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + CoA a 1-acyl-sn-glycero-3-phosphate + a fatty acyl-[ACP] = a 1,2-diacyl-sn-glycero-3-phosphate + holo-[ACP] Lipid metabolism; phospholipid metabolism. Belongs to the membrane-bound acyltransferase family. +Immediate-early protein playing a role in various cellular processes including proliferation, adhesion, migration, differentiation and survival (PubMed:15181016, PubMed:15611078, PubMed:12695522, PubMed:21344378, PubMed:12050162). Acts by binding to integrins or membrane receptors such as NOTCH1 (PubMed:12695522, PubMed:21344378, PubMed:15611078). Essential regulator of hematopoietic stem and progenitor cell function (PubMed:17463287). Inhibits myogenic differentiation through the activation of Notch-signaling pathway (PubMed:12050162). Inhibits vascular smooth muscle cells proliferation by increasing expression of cell-cycle regulators such as CDKN2B or CDKN1A independently of TGFB1 signaling (PubMed:20139355). Ligand of integrins ITGAV:ITGB3 and ITGA5:ITGB1, acts directly upon endothelial cells to stimulate pro-angiogenic activities and induces angiogenesis. In endothelial cells, supports cell adhesion, induces directed cell migration (chemotaxis) and promotes cell survival (PubMed:12695522). Also plays a role in cutaneous wound healing acting as integrin receptor ligand. Supports skin fibroblast adhesion through ITGA5:ITGB1 and ITGA6:ITGB1 and induces fibroblast chemotaxis through ITGAV:ITGB5. Seems to enhance bFGF-induced DNA synthesis in fibroblasts (PubMed:15611078). Involved in bone regeneration as a negative regulator (By similarity). Enhances the articular chondrocytic phenotype, whereas it repressed the one representing endochondral ossification (PubMed:21871891). Impairs pancreatic beta-cell function, inhibits beta-cell proliferation and insulin secretion (By similarity). Plays a role as negative regulator of endothelial pro-inflammatory activation reducing monocyte adhesion, its anti-inflammatory effects occur secondary to the inhibition of NF-kappaB signaling pathway (PubMed:21063504). Contributes to the control and coordination of inflammatory processes in atherosclerosis (By similarity). Attenuates inflammatory pain through regulation of IL1B- and TNF-induced MMP9, MMP2 and CCL2 expression. Inhibits MMP9 expression through ITGB1 engagement (PubMed:21871891). Interacts with FBLN1. Interacts (via CTCK domain) with NOTCH1 (via the EGF-like repeat region) (PubMed:12050162). Interacts with GJA1/CX43 (PubMed:15181016, PubMed:15213231). Interacts with ITGA5:ITGB1, ITGAV:ITGB3 and ITGAV:ITGB5 (PubMed:12695522, PubMed:15611078). Interacts with ZDHHC22; the interaction may lead to CCN3 palmitoylation (By similarity). Localizes at the gap junction in presence of GJA1. Expressed in endiothelial cells (at protein level) (PubMed:21063504). Expressed in bone marrow, thymic cells and nephroblastoma. Increased expression in Wilms tumor of the stromal type. Expressed in primitive compartments of umbilical vein cord. Expression is down-regulated by WT1. Expression is down-regulated by pro-inflammatory stimuli such as TNF or IL1B (PubMed:24722330, PubMed:21063504). Expression is induced by laminar shear stress and statins (PubMed:21063504). May be palmitoylated on Cys-244, which is important for extracellular secretion. Belongs to the CCN family. +Part of the ABC transporter complex LolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone, LolA. Responsible for the formation of the LolA-lipoprotein complex in an ATP-dependent manner. The complex is composed of two ATP-binding proteins (LolD) and two transmembrane proteins (LolC and LolE). Belongs to the ABC transporter superfamily. Lipoprotein translocase (TC 3.A.1.125) family. +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Binds 1 zinc ion per subunit. Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily. +Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) Binds 1 zinc ion per subunit. Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. Belongs to the class-II aminoacyl-tRNA synthetase family. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Involved in repair of UV radiation-induced DNA damage. Catalyzes the photoreactivation of pyrimidine [6-4] pyrimidone photoproduct (6-4 products). Binds specifically to DNA containing 6-4 products and repairs these lesions in a visible light-dependent manner. Not required for repair of cyclobutane pyrimidine dimer (CPD). (6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA). Binds 1 FAD per subunit. Expressed in siliques, flowers and leaves. Not detected in roots. Expressed at all developmental stages. Not induced by white or UV-B light. Belongs to the DNA photolyase class-1 family. Truncated N-terminus. Truncated N-terminus. +Plays an essential role in the regulation of viral gene expression by both activating and repressing host RNA polymerase II-mediated transcription. Binds with high affinity to the sequence 5'-ATCGTC-3'. Activates transcription by recruiting a form of the host TFIID to promoters and stabilizing the pre-initiation complex formation. Negatively regulates its own transcription. This immediate early (IE) protein is absolutely necessary for the transition from IE transcription to later viral gene transcription. Forms homodimers (PubMed:2991559, PubMed:28505309). Interacts with transcriptional regulator ICP27; this interaction is required for proper incorporation of ICP4 into virions (PubMed:8995681). Interacts with host TBP and host TAF1; these interactions help the stabilization of the pre-nitiation complex on specific promoters (PubMed:8649420). Interacts with host GTF2B (PubMed:8392607). Localizes to the cytoplasm when phosphorylated. The N-terminal and C-terminal domains are required for the transcriptional activation function of ICP4. ADP-ribosylated. The long stretch of Ser is a major site of phosphorylation. Only the phosphorylated forms are capable of interacting with beta or gamma genes. Belongs to the herpesviridae ICP4 family. +Plays a role in intracellular vesicle trafficking and exocytosis (PubMed:24843546). May play a role in maintaining insulin-containing dense core vesicles in pancreatic beta-cells and in preventing their degradation. May play a role in insulin secretion (PubMed:24843546). Interacts with membranes containing phosphatidylinositol 3-phosphate (PtdIns(3P)) (By similarity). Interacts with PTPRN. The PX domain mediates specific binding to membranes enriched in phosphatidylinositol 3-phosphate (PtdIns(P3)). Belongs to the sorting nexin family. Extended N-terminus. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Component of MIOREX complexes, large expressome-like assemblies of ribosomes with factors involved in all the steps of post-transcriptional gene expression. Associates with the mitochondrial ribosome. Present with 3280 molecules/cell in log phase SD medium. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Cytochrome P450 monooxygenase that is able to use 7-ethoxycoumarin, anthracene, phenanthrene and trans-stilbene as substrates for oxidation. Secondary metabolite biosynthesis. Belongs to the cytochrome P450 family. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit binds the periplasmic potassium ions and delivers the ions to the membrane domain of KdpB through an intramembrane tunnel. The system is composed of three essential subunits: KdpA, KdpB and KdpC. Belongs to the KdpA family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. +Part of the Tol-Pal system, which plays a role in outer membrane invagination during cell division and is important for maintaining outer membrane integrity. The Tol-Pal system is composed of five core proteins: the inner membrane proteins TolA, TolQ and TolR, the periplasmic protein TolB and the outer membrane protein Pal. They form a network linking the inner and outer membranes and the peptidoglycan layer. Belongs to the TolB family. +GTPase-activating protein (GAP) for ADP ribosylation factor 6 (ARF6). GAP activity stimulated by phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidic acid. Interacts with RAB35 (GTP-bound form); the interaction is direct and probably recruits ACAP2 to membranes. Interacts with MICALL1; the interaction is indirect through RAB35 (By similarity). Widely expressed. Highest level in lung. +Catalyzes the covalent attachment of ubiquitin to other proteins. S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine. Protein modification; protein ubiquitination. Mutants in this gene exhibit several, largely neuronal defects including lesions affecting the neuronal connectivity of the giant fiber with the 'jumping muscle', and the axons of photoreceptor cells R7 and R8 fail to make the proper right-angle turn into the medulla (hence the term 'bendless'). Belongs to the ubiquitin-conjugating enzyme family. +Transcription factor that binds to the octamer motif (5'-ATTTGCAT-3') (By similarity). Acts as a transcriptional activator when binding cooperatively with SOX4, SOX11, or SOX12 to gene promoters (By similarity). Acts as a transcriptional repressor of myelin-specific genes (PubMed:1975954). Neural tissues and testis. Transiently increased in rapidly dividing Schwann cells in response to sciatic nerve transection 2 days post-injury. Belongs to the POU transcription factor family. Class-3 subfamily. +Catalyzes the 13-hydroxylation of gibberellins (GAs). Determines the ratio of GA4 and GA1. Converts GA12 into GA53. Highly expressed in shoot, spikelet and uppermost internode. Detected in roots, leaves and anthers. Up-regulated by bioactive gibberellins. No visible phenotype and no change in the levels of 13-OH GAs; due to the redundancy with CYP714B1. Cyp714b1 and cyp714b2 double mutants have decreased levels of 13-OH GAs, increased levels of 13-H GAs, including GA4, and longer uppermost internode. Overexpression of CYP714B2 in a heterologous system causes semi-dwarfism and increased 13-OH GAs content. Belongs to the cytochrome P450 family. +Metalloprotease with anticoagulant activity. Cleaves fibrinogen Aalpha (FGA), gamma (FGG) and Bbeta (FGB) chains after positions 'Asn-121', 'Lys-160' and 'Pro-102', respectively. Breaks down cross-linked and non-cross-linked fibrin clots. Prevents and reverts platelet aggregation induced by ADP and collagen. Prevents thrombin-induced platelet clotting. Does not affect plasma levels of coagulation factors prothrombin (F2), V (F5), VII (F7), VIII (F8), IX (F9), X (F10), XI (F11), XII (F12), plasma kallikrein (KLKB1) and kininogen-1 (KNG1). Inhibited by EDTA, cysteine, DTT and sodium phosphate. Partially inhibited by EGTA, citrate, Tris and glycine. Not inhibited by DFP, PMSF, iodacetic acid and leupeptin. Requires sodium chloride concentrations higher than 0.15 M for activity. Optimum pH is 7.5. Active from pH 5.5 to 11. Active at 37 degrees Celsius. Activity reversibly reduced to 26% and 0% at 25 degrees Celsius and 4 degrees Celsius, respectively. Complete and irreversible loss of activity after 15 min at 60 degrees Celsius. Expressed mainly in the posterior salivary glands and, to a lesser extent, in the anterior salivary glands and secreted into the proboscis (at protein level). Presumably not injected into the host's bloodstream, as feeding by H.ghilianii does not cause prolonged bleeding of resulting wounds. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate. ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterodimer of GatD and GatE. Belongs to the asparaginase 1 family. GatD subfamily. +Actins are highly conserved proteins that are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells. Belongs to the actin family. +Catalyzes the synthesis of beta-nicotinate D-ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP. 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H2O + nicotinate = ADP + diphosphate + nicotinate beta-D-ribonucleotide + phosphate Cofactor biosynthesis; NAD(+) biosynthesis; nicotinate D-ribonucleotide from nicotinate: step 1/1. Transiently phosphorylated on a His residue during the reaction cycle. Phosphorylation strongly increases the affinity for substrates and increases the rate of nicotinate D-ribonucleotide production. Dephosphorylation regenerates the low-affinity form of the enzyme, leading to product release. Belongs to the NAPRTase family. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the cyclophilin-type PPIase family. PPIase H subfamily. +Catalyzes the synthesis of activated sulfate. adenosine 5'-phosphosulfate + ATP = 3'-phosphoadenylyl sulfate + ADP + H(+) Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 2/3. Belongs to the APS kinase family. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP = 7,8-dihydrofolate + dTMP Pyrimidine metabolism; dTTP biosynthesis. Homodimer. Belongs to the thymidylate synthase family. Bacterial-type ThyA subfamily. +Cell wall formation. ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) + phosphate Binds 2 magnesium or manganese ions per subunit. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the D-alanine--D-alanine ligase family. +Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems. This G protein is involved in 1-methyladenine-induced oocyte maturation. G proteins are composed of 3 units; alpha, beta and gamma. The alpha chain contains the guanine nucleotide binding site. Belongs to the G-alpha family. G(i/o/t/z) subfamily. +The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. Belongs to the RecF family. +Component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery. Required for maturation of extramitochondrial Fe-S proteins. The NUBP1-NUBP2 heterotetramer forms a Fe-S scaffold complex, mediating the de novo assembly of an Fe-S cluster and its transfer to target apoproteins. Implicated in the regulation of centrosome duplication. Negatively regulates cilium formation and structure. Binds 4 [4Fe-4S] clusters per heterotetramer. Contains two stable clusters in the N-termini of NUBP1 and two labile, bridging clusters between subunits of the NUBP1-NUBP2 heterotetramer. Heterotetramer of 2 NUBP1 and 2 NUBP2 chains. Interacts with KIFC1. Interacts with the BBS/CCT complex subunit CCT1. Enriched in centrioles of microtubule asters during prophase, prometaphase and telophase stages of mitosis. Localized at centrioles and in the nucleus at interphase. Colocalizes with nubp-2 at prometaphase. Specifically localizes to the axenome of motile cilia as opposed to primary non-motile cilia. Localization is independent of NUBP2 and KIFC1. Belongs to the Mrp/NBP35 ATP-binding proteins family. NUBP1/NBP35 subfamily. +Belongs to the FMN-dependent alpha-hydroxy acid dehydrogenase family. +Involved in the nuclear export of mRNA species bearing retroviral constitutive transport elements (CTE) and in the export of mRNA from the nucleus to the cytoplasm (TAP/NFX1 pathway). The NXF1-NXT1 heterodimer is involved in the export of HSP70 mRNA in conjunction with ALYREF/THOC4 and THOC5 components of the TREX complex. ALYREF/THOC4-bound mRNA is thought to be transferred to the NXF1-NXT1 heterodimer for export. Also involved in nuclear export of m6A-containing mRNAs: interaction between SRSF3 and YTHDC1 facilitates m6A-containing mRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export. Heterodimer (via NTF2 domain) with NXT1 (By similarity). The formation of NXF1-NXT1 heterodimers is required for the NXF1-mediated nuclear mRNA export (By similarity). Forms a complex with RANBP2/NUP358, NXT1 and RANGAP1 (By similarity). Associates with the exon junction complex (EJC) (PubMed:12093754). Associates with the transcription/export (TREX) complex (By similarity). Found in a mRNA complex with UPF3A and UPF3B (By similarity). Found in a post-splicing complex with RBM8A, UPF1, UPF2, UPF3A, UPF3B and RNPS1 (By similarity). Interacts (via N-terminus) with DHX9 (via N-terminus); this interaction is direct and negatively regulates NXF1-mediated nuclear export of constitutive transport element (CTE)-containing cellular mRNAs (By similarity). Interacts with FYTTD1/UIF (By similarity). Interacts with EIF4A3 (By similarity). Interacts with NUP42 (By similarity). Interacts with ALYREF/THOC4 (PubMed:10786854). Interacts with CHTOP (By similarity). Interacts with FRG1 (via N-terminus) (By similarity). Interacts with LUZP4 (By similarity). Interacts with FMR1; the interaction occurs in a mRNA-dependent and polyribosomes-independent manner in the nucleus (By similarity). Interacts with CPSF6 (via N-terminus); this interaction is direct (By similarity). Interacts with RBM15 (By similarity). Interacts with RBM15B (By similarity). Interacts with MCM3AP; this interaction is not mediated by RNA (By similarity). Interacts with DDX3X (via C-terminus); this interaction may be partly involved in DDX3X nuclear export and in NXF1 localization to stress granules. Interacts with PABPC1/PABP1 (By similarity). Localized predominantly in the nucleoplasm and at both the nucleoplasmic and cytoplasmic faces of the nuclear pore complex. Shuttles between the nucleus and the cytoplasm. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRNA. The association with the TREX complex seems to occur in regions surrounding nuclear speckles known as perispeckles. Nucleus; nuclear rim. Expressed ubiquitously. The minimal CTE binding domain consists of an RNP-type RNA binding domain (RBD) and leucine-rich repeats. The nucleoporin binding domain consists of a NTF2 domain (also called NTF2-like domain) and a TAP-C domain (also called UBA-like domain). It has 2 nucleoporin-FG-repeats binding sites (one in the NTF2 and the other in the TAP-C domain) which contribute to nucleoporin association and act synergistically to export cellular mRNAs. The NTF2 domain is functional only in the presence of NXT1 and is essential for the export of mRNA from the nucleus. It inhibits RNA binding activity through an intramolecular interaction with the N-terminal RNA binding domain (RBD); the inhibition is removed by an association with the TREX complex, specifically involving ALYREF/THOC4 and THOC5. The TAP-C domain mediates direct interactions with nucleoporin-FG-repeats and is necessary and sufficient for localization of NXF1 to the nuclear rim. The conserved loop 594-NWD-596 of the TAP-C domain has a critical role in the interaction with nucleoporins. The leucine-rich repeats are essential for the export of mRNA from the nucleus. The RNA-binding domain is a non-canonical RNP-type domain. Belongs to the NXF family. +Catalyzes the transfer of adenosine 5'-monophosphate (AMP) to Ser, Thr or Tyr residues of target proteins (AMPylation). ATP + L-tyrosyl-[protein] = diphosphate + O-(5'-adenylyl)-L-tyrosyl-[protein] ATP + L-threonyl-[protein] = 3-O-(5'-adenylyl)-L-threonyl-[protein] + diphosphate ATP + L-seryl-[protein] = 3-O-(5'-adenylyl)-L-seryl-[protein] + diphosphate Belongs to the SELO family. +Together with the serine/threonine kinase PknD, may play a role in the specific interactions with host proteins during intracellular growth. Phosphorylates IncG, an inclusion-membrane protein required for the modification of the nascent chlamydial inclusion. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts with PknD, interacts with and phosphorylates IncG. Autophosphorylates on serine and threonine residues. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. Gln-136 is present instead of the conserved Asp which is expected to be a proton acceptor in the active site. +Hydrolyzes fatty acids from S-acylated cysteine residues in proteins with a strong preference for palmitoylated G-alpha proteins over other acyl substrates. Mediates the deacylation of G-alpha proteins such as GPA1 in vivo, but has weak or no activity toward palmitoylated Ras proteins. Has weak lysophospholipase activity in vitro; however such activity may not exist in vivo. H2O + S-hexadecanoyl-L-cysteinyl-[protein] = H(+) + hexadecanoate + L-cysteinyl-[protein] Belongs to the AB hydrolase superfamily. AB hydrolase 2 family. +Transcriptional repressor (PubMed:25578968). Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a higher activity for H3K4me3 and H3K4me2 than H3K4me1 (PubMed:29233856). No activity on H3K9me3/2, H3K36me3/2 and H3K27me3/2 (PubMed:29233856). Function as a nocturne 'eraser' to counteract the diurnal 'writer' methylase activity of ATXR3/SDG2 thus orchestrating the circadian rythm of histone modifications (e.g. H3K4me3) and modulating the rythmic expression of diurnal target genes; this mechanism relies also on the circadian clock oscillators CCA1 and LHY (PubMed:31429787). Involved in a negative regulation of root meristem growth upon suboptimal root growth conditions (PubMed:31826870). Represses FT and TSF expression to inhibit the floral transition. Binds around the transcription start site of the FT locus. Involved in the DRM2-mediated maintenance of DNA methylation, but not required for the de novo DNA methylation. Required for demethylating histone H3K4me3 at the target of RNA silencing. Counteracts the DNA methylation of expressed transgenes; specific attenuation of transgene DNA methylation enhances the production of aberrant RNAs (e.g. uncapped and antisense) that readily induce systemic RDR6-dependent post-transcriptional transgene silencing (PTGS) spreading (PubMed:33986281). Together with NAC051/NAC052 and NAC050, regulates gene expression and flowering time, probably by the promotion of RNA-mediated gene silencing (PubMed:25578968). Together with JMJ16 and JMJ17, required for plant growth and development (PubMed:31038749). Promotes local and systemic immunity (especially toward the bacterial pathogen Pseudomonas syringae Pst DC3000 avrRpt2) by regulating positively pathogen-induced H3K4me3 enrichment and expression of defense genes involved in salicylic acid (SA)- and pipecolic acid (Pip)-mediated defense pathways (e.g. PR1, FMO1, ALD1 and SARD4) (PubMed:31622519). 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + O2 = CO2 + formaldehyde + N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + succinate 2-oxoglutarate + N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + O2 = CO2 + formaldehyde + N(6)-methyl-L-lysyl(4)-[histone H3] + succinate 2-oxoglutarate + N(6)-methyl-L-lysyl(4)-[histone H3] + O2 = CO2 + formaldehyde + L-lysyl(4)-[histone H3] + succinate 3 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl(4)-[histone H3] + 3 succinate Binds 1 Fe(2+) ion per subunit. Interacts with NAC050 and NAC051/NAC052 (PubMed:25578968, PubMed:26617990). Interacts with THAL in the nucleus (PubMed:27792779). Not detected in the nucleolus and the chromocenters. Expressed in shoot apex, primary root tip, trichomes of young leaves, leaf vascular tissues, anther filaments and styles. Detected in inflorescences, leaves, stems, roots and siliques. Mostly expressed in floral organs, and, at low levels, in other organs (PubMed:25578968). Expressed in mature root vasculature and throughout root meristem. Circadian-regulation with peak levels occurring at night and lower levels after dawn under both diurnal and constant light conditions in a CCA1- and LHY-dependent manner. Early flowering (especially in long day conditions), but normal development of all organs (PubMed:31038749). Partially redundant with ELF6. Increased H3K4 methylation on specific genes, thus leading to their derepression (PubMed:25578968, PubMed:31826870). Slightly increased levels of CCA1 and LHY circadian oscillators transcription factors as well as of other clock genes such as TOC1, PRR5, PRR7, PRR9, GI, ELF3, ELF4, and LUX associated with higher H3K4me3 levels near their promoters (PubMed:31429787). Impaired systemic RDR6-dependent post-transcriptional transgene silencing (PTGS) associated with reduced production of aberrant RNAs (e.g. uncapped and antisense) (PubMed:33986281). Abnormal root meristem size as well as partial suppression of reduced root meristem size and growth vigor observed in brx mutants (PubMed:31826870). Compromised in both local and systemic defense responses to the bacterial pathogen Pseudomonas syringae Pst DC3000 avrRpt2 due to abnormal H3K4me3 enrichment and reduced expression of defense genes involved in salicylic acid (SA)- and pipecolic acid (Pip)-mediated defense pathways (e.g. PR1, FMO1, ALD1 and SARD4) (PubMed:31622519). The double mutant jmj17-1 jmj14-1 has an early flowering phenotype (especially in long day conditions) (PubMed:31038749). The triple mutant jmj17-1 jmj14-1 jmj16-1 flowers even earlier (PubMed:31038749). Belongs to the JARID1 histone demethylase family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +V region of the variable domain of T cell receptor (TR) beta chain that participates in the antigen recognition (PubMed:24600447). Alpha-beta T cell receptors are antigen specific receptors which are essential to the immune response and are present on the cell surface of T lymphocytes. Recognize peptide-major histocompatibility (MH) (pMH) complexes that are displayed by antigen presenting cells (APC), a prerequisite for efficient T cell adaptive immunity against pathogens (PubMed:25493333). Binding of alpha-beta TR to pMH complex initiates TR-CD3 clustering on the cell surface and intracellular activation of LCK that phosphorylates the ITAM motifs of CD3G, CD3D, CD3E and CD247 enabling the recruitment of ZAP70. In turn ZAP70 phosphorylates LAT, which recruits numerous signaling molecules to form the LAT signalosome. The LAT signalosome propagates signal branching to three major signaling pathways, the calcium, the mitogen-activated protein kinase (MAPK) kinase and the nuclear factor NF-kappa-B (NF-kB) pathways, leading to the mobilization of transcription factors that are critical for gene expression and essential for T cell growth and differentiation (PubMed:23524462). The T cell repertoire is generated in the thymus, by V-(D)-J rearrangement. This repertoire is then shaped by intrathymic selection events to generate a peripheral T cell pool of self-MH restricted, non-autoaggressive T cells. Post-thymic interaction of alpha-beta TR with the pMH complexes shapes TR structural and functional avidity (PubMed:15040585). Alpha-beta TR is a heterodimer composed of an alpha and beta chain; disulfide-linked. The alpha-beta TR is associated with the transmembrane signaling CD3 coreceptor proteins to form the TR-CD3 (TcR or TCR). The assembly of alpha-beta TR heterodimers with CD3 occurs in the endoplasmic reticulum where a single alpha-beta TR heterodimer associates with one CD3D-CD3E heterodimer, one CD3G-CD3E heterodimer and one CD247 homodimer forming a stable octomeric structure. CD3D-CD3E and CD3G-CD3E heterodimers preferentially associate with TR alpha and TR beta chains, respectively. The association of the CD247 homodimer is the last step of TcR assembly in the endoplasmic reticulum and is required for transport to the cell surface. There are several alleles. The sequence shown is that of IMGT allele TRBV10-2*01. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +Part of the ABC transporter complex LptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane. Component of the lipopolysaccharide transport and assembly complex. The LptBFG transporter is composed of two ATP-binding proteins (LptB) and two transmembrane proteins (LptF and LptG) (By similarity). Belongs to the LptF/LptG family. +Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-aspartyl-tRNA(Asx) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +This protein is postulated to act both as terminal energy acceptor (by its phycobilin-like domains) and as a linker polypeptide (by its repeats and arms) that stabilizes the phycobilisome core architecture. Has intrinsic bilin lyase activity (By similarity). Heterodimer of ApcF (a variant beta-allophycocyanin). Phycobilisomes of this organism are composed of a two cylinder core, from which six rods radiate. The core is mainly composed of allophycocyanin alpha and beta chains and of minor components (By similarity). Anchors the phycobilisome perpendicularly to the cytoplasmic surface of the thylakoid membrane. Contains one covalently linked bilin chromophore. This protein autochromophorylates (By similarity). Belongs to the phycobilisome linker protein family. +Catalyzes the reduction of FMN to FMNH2 which is used to reduce pyrimidine by RutA via the Rut pathway. FMNH2 + NAD(+) = FMN + 2 H(+) + NADH Belongs to the non-flavoprotein flavin reductase family. RutF subfamily. +Part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair. The complex may facilitate opening of the processed DNA ends to aid in the recruitment of HerA and NurA. Mre11 binds to DSB ends and has both double-stranded 3'-5' exonuclease activity and single-stranded endonuclease activity. Binds 2 manganese ions per subunit. Nuclease activity is regulated by Rad50. Homodimer. Forms a heterotetramer composed of two Mre11 subunits and two Rad50 subunits. Belongs to the MRE11/RAD32 family. +Methylates ribosomal protein L11. L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. PrmA family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Phospholipid scramblase that acts downstream of ced-9 and caspase ced-3 to promote phosphatidylserine exposure on apoptotic cell surface (PubMed:24225442, PubMed:23845944). Phosphatidylserine is a specific marker only present at the surface of apoptotic cells and acts as a specific signal for engulfment (PubMed:24225442, PubMed:23845944). Regulates apoptosis kinetics during embryonic development (PubMed:10882128, PubMed:1936965, PubMed:24225442, PubMed:23845944). Not required for engulfment of germ cell corpses (PubMed:9927601). a 1,2-diacyl-sn-glycero-3-phospho-L-serine(in) = a 1,2-diacyl-sn-glycero-3-phospho-L-serine(out) Cleavage by ced-3 activates ced-8 function in promoting phosphatidylserine exposure at the surface of apoptotic cells. Delayed cell death process. Belongs to the XK family. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +The basal body constitutes a major portion of the flagellar organelle and consists of five rings (E,L,P,S, and M) mounted on a central rod. The rod consists of about 26 subunits of FlgG in the distal portion, and FlgB, FlgC and FlgF are thought to build up the proximal portion of the rod with about 6 subunits each. Belongs to the flagella basal body rod proteins family. +Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription (By similarity). Found in a complex with PUF60 and far upstream element (FUSE) DNA segment. Interacts with PUF60 and JTV1 (By similarity). Ubiquitinated. This targets the protein for proteasome-mediated degradation (By similarity). +Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA (By similarity). Component of the heptameric LSM1-LSM7 complex, which consists of LSM1, LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. Component of the heptameric LSM2-LSM8 complex, which consists of LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. The LSm subunits form a seven-membered ring structure with a doughnut shape (By similarity). Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily. +Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (accB), biotin carboxylase (accC) and two subunits each of ACCase subunit alpha (accA) and ACCase subunit beta (accD). Belongs to the AccA family. +Probable ATPase of unknown function. Its presence in a non-photosynthetic plant (Epifagus virginiana) and experiments in tobacco indicate that it has an essential function which is probably not related to photosynthesis. Belongs to the Ycf2 family. +Catalyzes the attachment of asparagine to tRNA(Asn) in the mitochondrion. ATP + L-asparagine + tRNA(Asn) = AMP + diphosphate + H(+) + L-asparaginyl-tRNA(Asn) Present with 784 molecules/cell in log phase SD medium. Belongs to the class-II aminoacyl-tRNA synthetase family. +Represses transcription of the icaADBC operon necessary for biofilm production. Homodimer. Cells display an increase of ica transcription of about 100-fold, and poly-N-acetylglucosamine polysaccharide (PNAG) synthesis about 10-fold. Adherence to polystyrene microtiter wells also increases. Double deletion of icaR and tcaR increases ica transcription about 500-fold, and poly-N-acetylglucosamine polysaccharide (PNAG) synthesis about 100-fold. Adherence is significantly greater than that of the single icaR mutant. Binding to the ica operator DNA involves two IcaR dimers and is highly cooperative. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Probably essential, it was not disrupted in a global transposon mutagenesis study. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. +Nucleoporin essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity. Forms dimers and possibly higher-order oligomers. N-glycosylated, but not all potential glycosylation sites may be used. Contains high-mannose type oligosaccharides. Phosphorylated at Ser-1880 in mitosis specifically; not phosphorylated in interphase. Belongs to the NUP210 family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +Catalyzes the deamination of dCTP to dUTP. dCTP + H(+) + H2O = dUTP + NH4(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 1/2. Homotrimer. Belongs to the dCTP deaminase family. +Cleaves viral precursor proteins (pTP, pIIIa, pVI, pVII, pVIII, and pX) inside newly assembled particles giving rise to mature virions. Protease complexed to its cofactor slides along the viral DNA to specifically locate and cleave the viral precursors. Mature virions have a weakened organization compared to the unmature virions, thereby facilitating subsequent uncoating. Without maturation, the particle lacks infectivity and is unable to uncoat. Late in adenovirus infection, in the cytoplasm, may participate in the cytoskeleton destruction. Cleaves host cell cytoskeletal keratins K7 and K18. Cleaves proteins of the adenovirus and its host cell at two consensus sites: -Yaa-Xaa-Gly-Gly-|-Xaa- and -Yaa-Xaa-Gly-Xaa-|-Gly- (in which Yaa is Met, Ile or Leu, and Xaa is any amino acid). Requires DNA and protease cofactor for maximal activation. Inside nascent virions, becomes partially activated by binding to the viral DNA, allowing it to cleave the cofactor that binds to the protease and fully activates it. Actin, like the viral protease cofactor, seems to act as a cofactor in the cleavage of cytokeratin 18 and of actin itself. Interacts with protease cofactor pVI-C; this interaction is necessary for protease activation. Present in about 10 copies per virion. Expressed in the late phase of the viral replicative cycle. All late proteins expressed from the major late promoter are produced by alternative splicing and alternative polyadenylation of the same gene giving rise to non-overlapping ORFs. A leader sequence is present in the N-terminus of all these mRNAs and is recognized by the viral shutoff protein to provide expression although conventional translation via ribosome scanning from the cap has been shut off in the host cell. Belongs to the peptidase C5 family. +May play a role in intracellular calcium sensing and homeostasis. May act as a negative regulator of plasma membrane calcium-transporting ATPases preventing calcium efflux from the cell (By similarity). Interacts with STIM1; stimulated by depletion of intracellular calcium. Interacts with ORAI1. Interacts with the plasma membrane calcium-transporting ATPases ATP2B1 and ATP2B4. Interacts with ATP1A1, ATP2A2, KPNB1 and XPO1 (By similarity). Translocates from the endoplasmic reticulum to the cell membrane in response to a depletion of intracellular calcium and is detected at punctae corresponding to junctions between the endoplasmic reticulum and the cell membrane. Belongs to the TMEM20 family. +Catalyzes the ATP-dependent phosphorylation of D-glucosamine (GlcN) to D-glucosamine 6-phosphate. May be involved in the phosphorylation of acquired extracellular GlcN derived from the hydrolysis of chitosan, i.e., in the incorporation of exogenous GlcN into the bacterial GlcNAc metabolism. To a lesser extent, is also active on glucose, but is unable to phosphorylate maltose, 18 other sugars and several aminoglycoside antibiotics. ATP + D-glucosamine = ADP + D-glucosamine 6-phosphate + H(+) Binds 2 Mg(2+) ions per subunit. Monomer. Belongs to the actinobacterial glucosamine kinase family. +Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Is involved in the demethylation of trimethylated 'Lys-9' on histone H3 (H3K9me3), leading to an increase in ribosomal RNA expression. Also catalyzes the hydroxylation of 60S ribosomal protein L27a on 'His-39' (By similarity). May play an important role in cell growth and survival. May be involved in ribosome biogenesis, most likely during the assembly process of pre-ribosomal particles. 2-oxoglutarate + L-histidyl-[ribosomal protein uL15] + O2 = (3S)-3-hydroxy-L-histidyl-[ribosomal protein uL15] + CO2 + succinate Binds 1 Fe(2+) ion per subunit. Predominantly expressed in testis. Expressed at high levels in spleen, thymus, and colon, but barely detectable in brain, skeletal muscle, and seminal vesicle (at protein level). In testis, expressed in the nuclei of spermatogonia at all stages of the seminiferous epithelial cycle, and in meiotic prophase cells such as preleptotene, leptotene and zygotene, and weakly in early pachytene spermatocytes, but is absent in late pachytene spermatocytes, spermatids and mature sperm (at protein level). Up-regulated in experimentally-induced cryptorchid testis. Belongs to the ROX family. MINA53 subfamily. +A number of isoforms are produced. According to EST sequences. Belongs to the bHLH protein family. +Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. Homodimer. Belongs to the transketolase family. DXPS subfamily. +A non-essential component of RNA polymerase (RNAP). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) RNAP is composed of a core of 2 alpha, a beta and a beta' subunit. The core is associated with a delta subunit, and at least one of epsilon or omega. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit epsilon family. +Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals (By similarity). Adaptor protein complex 3 (AP-3) is a heterotetramer composed of two large adaptins (delta-type subunit AP3D1 and beta-type subunit AP3B1 or AP3B2), a medium adaptin (mu-type subunit AP3M1 or AP3M2) and a small adaptin (sigma-type subunit APS1 or AP3S2). Interacts with AGAP1. AP-3 associates with the BLOC-1 complex (By similarity). Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi complex. Belongs to the adaptor complexes medium subunit family. +Required for chromosome condensation and partitioning. Homodimer. Probably associated with the nucleoid. Contains large globular domains required for ATP hydrolysis at each terminus and a third globular domain forming a flexible SMC hinge near the middle of the molecule. These domains are separated by coiled-coil structures. Mutants produce anucleate cells and show defects in nucleoid structure and in chromosome partitioning. Belongs to the SMC family. +Gal / GalNAc-specific lectin. Agglutinates both native and trypsin-treated rabbit erythrocytes but not human erythrocytes irrespective of blood group type. Disulfide-linked heterodimer of A and B chains. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the LeuD family. LeuD type 2 subfamily. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Homopentamer. Belongs to the DMRL synthase family. +Molecular chaperone. Has ATPase activity. Homodimer. Belongs to the heat shock protein 90 family. +Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline. carbamoyl phosphate + L-ornithine = H(+) + L-citrulline + phosphate Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 1/3. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. OTCase family. +Expressed in the late phase of the viral replicative cycle. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. NifS/IscS subfamily. Although related to the NifS/IscS subfamily, lacks the conserved active site, suggesting it has no transferase activity. +Pectinolytic enzymes consist of four classes of enzymes: pectin lyase, polygalacturonase, pectin methylesterase and rhamnogalacturonase. Among pectinolytic enzymes, pectin lyase is the most important in depolymerization of pectin, since it cleaves internal glycosidic bonds of highly methylated pectins (By similarity). Eliminative cleavage of (1->4)-alpha-D-galacturonan methyl ester to give oligosaccharides with 4-deoxy-6-O-methyl-alpha-D-galact-4-enuronosyl groups at their non-reducing ends. Belongs to the polysaccharide lyase 1 family. +(1,4-alpha-D-galacturonosyl)n+m + H2O = (1,4-alpha-D-galacturonosyl)n + (1,4-alpha-D-galacturonosyl)m. Belongs to the glycosyl hydrolase 28 family. +Required to protect lysosomal transporter MFSD1 from lysosomal proteolysis and for MFSD1 lysosomal localization. Interacts (via lumenal domain) with lysosomal protein MFSD1; the interaction starts while both proteins are still in the endoplasmic reticulum and is required for stability and lysosomal localization of MFSD1. Highly N-glycosylated. N-glycosylation is essential for GLMP stability and for MFSD1 lysosomal localization. Belongs to the GLMP family. +Binds to activated (phosphorylated) protein-Tyr kinases, through its SH2 domain, and acts as an adapter, mediating the association of the p110 catalytic unit to the plasma membrane. Necessary for the insulin-stimulated increase in glucose uptake and glycogen synthesis in insulin-sensitive tissues. Plays an important role in signaling in response to FGFR1, FGFR2, FGFR3, FGFR4, KITLG/SCF, KIT, PDGFRA and PDGFRB. Likewise, plays a role in ITGB2 signaling. Modulates the cellular response to ER stress by promoting nuclear translocation of XBP1 in a ER stress- and/or insulin-dependent manner during metabolic overloading in the liver and hence plays a role in glucose tolerance improvement (By similarity). Heterodimer of a regulatory subunit PIK3R1 and a p110 catalytic subunit (PIK3CA, PIK3CB or PIK3CD). Interacts (via SH2 domains) with CCDC88A/GIV (tyrosine-phosphorylated form); the interaction enables recruitment of PIK3R1 to the EGFR receptor, enhancing PI3K activity and cell migration (By similarity). Interacts with phosphorylated LAT, LAX1, TRAT1 and LIME1 upon TCR and/or activation. Interacts with phosphorylated TOM1L1. Interacts with CBLB. The SH2 domains interact with the YTHM motif of phosphorylated INSR in vitro. Also interacts with tyrosine-phosphorylated IGF1R in vitro. Interacts with CD28 and CD3Z upon T-cell activation. Interacts with NISCH, SOCS7 and HCST. Interacts with RUFY3. Interacts with AXL, FASLG, FER, FGR, HCK, KIT and BCR. Interacts with PDGFRA (tyrosine phosphorylated) and PDGFRB (tyrosine phosphorylated). Interacts (via SH2 domain) with CSF1R (tyrosine phosphorylated). Interacts with ERBB4 (phosphorylated). Interacts (via SH2 domain) with TEK/TIE2 (tyrosine phosphorylated). Interacts with LYN (via SH3 domain); this enhances enzyme activity. Interacts with NTRK1 (phosphorylated upon ligand-binding). Interacts with PIK3R2; the interaction is dissociated in an insulin-dependent manner. Interacts with XBP1; the interaction is direct and induces translocation of XBP1 into the nucleus in a ER stress- and/or insulin-dependent but PI3K-independent manner (By similarity). Interacts with FGFR1, FGFR2, FGFR3 and FGFR4 (phosphorylated) (Probable). Interacts with IRS1 and phosphorylated IRS4 (PubMed:8628286). Interacts with PTK2/FAK1 (PubMed:8824286). Interacts with FAM83B; activates the PI3K/AKT signaling cascade (By similarity). Interacts with APPL1 and APPL2 (By similarity). Interacts with SRC (By similarity). Interacts with ALOX5; this interaction bridges ALOX5 with CD40 after CD40 ligation in B cells and leads to the production of reactive oxygen species (ROS) (By similarity). Interacts with TYK2 (By similarity). The P85-alpha isoform is widely expressed. Expression of the P55-alpha isoform is highest in brain and skeletal muscle. The P50-alpha isoform is abundant in liver with lower levels in brain and muscle. The SH3 domain mediates the binding to CBLB. Polyubiquitinated in T-cells by CBLB; which does not promote proteasomal degradation but impairs association with CD28 and CD3Z upon T-cell activation. Phosphorylated. Tyrosine phosphorylated in response to signaling by FGFR1, FGFR2, FGFR3 and FGFR4. Phosphorylated by CSF1R. Phosphorylated on tyrosine residues by TEK/TIE2. Dephosphorylated by PTPRJ. Phosphorylated by PIK3CA at Ser-608; phosphorylation is stimulated by insulin and PDGF. The relevance of phosphorylation by PIK3CA is however unclear. Phosphorylated in response to KIT and KITLG/SCF. Phosphorylated by FGR and ERBB4 (By similarity). Belongs to the PI3K p85 subunit family. +Part of the endoplasmic reticulum membrane protein complex (EMC) that enables the energy-independent insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins. Preferentially accommodates proteins with transmembrane domains that are weakly hydrophobic or contain destabilizing features such as charged and aromatic residues. Involved in the cotranslational insertion of multi-pass membrane proteins in which stop-transfer membrane-anchor sequences become ER membrane spanning helices. It is also required for the post-translational insertion of tail-anchored/TA proteins in endoplasmic reticulum membranes. By mediating the proper cotranslational insertion of N-terminal transmembrane domains in an N-exo topology, with translocated N-terminus in the lumen of the ER, controls the topology of multi-pass membrane proteins like the G protein-coupled receptors. By regulating the insertion of various proteins in membranes, it is indirectly involved in many cellular processes. Promotes angiogenesis and tissue repair in the heart after myocardial infarction. Stimulates cardiac endothelial cell migration and outgrowth via the activation of p38 MAPK, PAK and MAPK2 signaling pathways. Component of the ER membrane protein complex (EMC). Belongs to the EMC10 family. +Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins (By similarity). Heterohexamer of two PFD-alpha type and four PFD-beta type subunits. Belongs to the prefoldin subunit beta family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin. di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available. Belongs to the UppP family. +Nitrate reductase is a key enzyme involved in the first step of nitrate assimilation in plants, fungi and bacteria. H2O + NAD(+) + nitrite = H(+) + NADH + nitrate H2O + NADP(+) + nitrite = H(+) + NADPH + nitrate Binds 1 FAD per subunit. Binds 1 heme group per subunit. Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit. Homodimer. By nitrate. Belongs to the nitrate reductase family. +Catalyzes the insertion of one atom of molecular oxygen into position 2 of the phenyl ring of 3-(3-hydroxyphenyl)propionate (3-HPP) and hydroxycinnamic acid (3HCI). 3-(3-hydroxyphenyl)propanoate + H(+) + NADH + O2 = 3-(2,3-dihydroxyphenyl)propanoate + H2O + NAD(+) (2E)-3-(3-hydroxyphenyl)prop-2-enoate + H(+) + NADH + O2 = (2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate + H2O + NAD(+) Aromatic compound metabolism; 3-phenylpropanoate degradation. Belongs to the PheA/TfdB FAD monooxygenase family. +Belongs to the UPF0297 family. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homotetramer; dimer of dimers. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA (By similarity). Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding. Interacts with PCNA. PCNA stimulates the nuclease activity without altering cleavage specificity. Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily. +Regulates arginine biosynthesis genes. Amino-acid biosynthesis; L-arginine biosynthesis [regulation]. Belongs to the ArgR family. +Plays a role in splicing of the U12-type introns (PubMed:29617656). Implicated also in removal of U2 introns positioned adjacent to a U12 intron (PubMed:29617656). Interacts with SF3B1 (PubMed:29617656). Interacts with ZCRB1 (PubMed:29617656). Highest expression levels are detected in the brain, and lower expression levels in other tissues like epididymis, testis, bone marrow or muscle (PubMed:29617656). In testis, expressed in both Sertoli and spermatogenic cell (PubMed:29617656). Expressed at the 2-cell stage, and at the morula and blastocyst stages. No visible phenotype, possibly because of the compensating effects of one or more of the other 3 paralogs (U2AF1, U2AF1L4, ZRSR2). Maternally imprinted. Active paternal allele is unmethylated whereas the inactive maternal allele is highly methylated. +Initiates complex N-linked carbohydrate formation. Essential for the conversion of high-mannose to hybrid and complex N-glycans (By similarity). N(4)-(alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 5A1,2) + UDP-N-acetyl-alpha-D-glucosamine = H(+) + N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP The cofactor is mostly bound to the substrate. Protein modification; protein glycosylation. Expressed throughout development. Belongs to the glycosyltransferase 13 family. +Channel that permits osmotically driven movement of water in both directions. Aquaporins contain two tandem repeats each containing three membrane-spanning domains and a pore-forming loop with the signature motif Asn-Pro-Ala (NPA). Belongs to the MIP/aquaporin (TC 1.A.8) family. +Serine/threonine protein kinase which activates checkpoint signaling upon genotoxic stresses such as ionizing radiation (IR), ultraviolet light (UV), or DNA replication stalling, thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]-Q. Recruited by the MRX-complex to sites of DNA lesions immediately after damage to initiate non-homologous end-joining (NHEJ). Subsequently displaced by the RPA complex in a reaction probably involving the SAE2 protein. Phosphorylates MRE11 and XRS2, 2 subunits of the MRX-complex. The phosphorylation of MRE11 is a feedback response from the checkpoint signaling pathway. Phosphorylates RAD9, CHK1 and RAD53, leading to the activation of the CHK1 and RAD23 kinases involved in the DNA damage response cascade. Phosphorylates histone H2A to form H2AS128ph (gamma-H2A) at sites of DNA damage, also involved in the regulation of DNA damage response mechanism. Phosphorylates also SLX4 and RTT107 which are involved in genome stability. Required for the control of telomere length and genome stability. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts with XRS2 and associates with DNA double-strand breaks. Localizes to nuclear DNA repair foci in response to DNA double strand breaks. Belongs to the PI3/PI4-kinase family. ATM subfamily. +Stimulates synthesis of ecdysteroid in the testes of larvae and pupae. +Belongs to the AIM41 family. +Forms a fork protection complex (FPC) with TOF1 and which is required for chromosome segregation during meiosis and DNA damage repair. FPC coordinates leading and lagging strand synthesis and moves with the replication fork. FPC stabilizes replication forks in a configuration that is recognized by replication checkpoint sensors (By similarity). Component of the fork protection complex (FPC) consisting of TOF1 and CSM3. Belongs to the CSM3 family. +Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. [protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family. +ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate + H(+) Light regulated via thioredoxin by reversible oxidation/reduction of sulfhydryl/disulfide groups. Carbohydrate biosynthesis; Calvin cycle. Belongs to the phosphoribulokinase family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Involved in chemotaxis. Part of a chemotaxis signal transduction system that modulates chemotaxis in response to various stimuli. Catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins or MCP) by CheR. Also mediates the irreversible deamidation of specific glutamine residues to glutamic acid. [protein]-L-glutamate 5-O-methyl ester + H2O = H(+) + L-glutamyl-[protein] + methanol H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Contains a C-terminal catalytic domain, and an N-terminal region which modulates catalytic activity. Phosphorylated by CheA. Phosphorylation of the N-terminal regulatory domain activates the methylesterase activity. Belongs to the CheB family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (By similarity). Belongs to the snRNP core protein family. +Forms a complex with host RAN and probably binds to exportins carrying activated MAPK in order to mediate the hyperphosphorylation of host Phe/Gly containing nuclear pore proteins (Nups) resulting in cessation of active nucleocytoplasmic transport (PubMed:19073724, PubMed:20881039, PubMed:16888036, PubMed:26492198, PubMed:26115166). Proteins with NLS signals fail to import, cellular mRNAs fail to export, and some proteins small enough for diffusion are not retained anymore (efflux) (PubMed:19073724, PubMed:20881039, PubMed:16888036). The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (PubMed:19073724, PubMed:20881039, PubMed:16888036). Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. Together they form an icosahedral capsid composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms.VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. Together they form an icosahedral capsid composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms.VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. Together they form an icosahedral capsid composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms.VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. Lies on the inner surface of the capsid shell (By similarity). After binding to the host receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP4 is released, capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm (By similarity). After genome has been released, the channel shrinks (By similarity). VP0 precursor is a component of immature procapsids. Involved in host translation shutoff by inhibiting cap-dependent mRNA translation (PubMed:12921995, PubMed:21145089). Nuclear localization is required for this function (PubMed:12921995, PubMed:21145089). The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (Probable). Inhibits the phosphorylation of the leader protein (PubMed:25210192). Binds to the RNA stem-loop essential for the ribosomal frameshift event and trans-activates the production of protein 2B* (By similarity). Affects membrane integrity and causes an increase in membrane permeability. Associates with and induces structural rearrangements of intracellular membranes (By similarity). It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Interacts with IFIH1/MDA5 to inhibit the induction of the IFN-beta signal pathway (By similarity). Serves as membrane anchor via its hydrophobic domain. Forms a primer, VPg-pU, which is utilized by the polymerase for the initiation of RNA chains. Cysteine protease that generates mature viral proteins from the precursor polyprotein (By similarity). In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate cooperatively bind to the protease. Cleaves host PABP1, this cleavage is important for viral replication (By similarity). Cleaves host TANK and disrupts the TANK-TBK1-IKKepsilon-IRF3 complex, thereby inhibiting the induction of the IFN-beta signal pathway (By similarity). Replicates the genomic and antigenomic RNAs by recognizing replications specific signals (By similarity). Performs VPg uridylylation (By similarity). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) ATP + H2O = ADP + H(+) + phosphate Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. Interacts with host TRIM22; this interaction leads to the ubiquitination of protease 3C and may restrict the virus replication (By similarity). Interacts with host EIF4E (PubMed:21145089). Interacts with the leader protein (PubMed:25210192). Interacts with host RAN; the complex L-RAN recruits cellular kinases responsible for the L-induced nucleocytoplasmic trafficking inhibition (PubMed:16888036). The complex L-RAN can further bind to the host exportins XPO1/CRM1 and CSE1L/CAS (PubMed:26492198). Interacts with the protein 2A (PubMed:25210192). Interacts with host IFIH1/MDA5; this interaction inhibits the induction of the IFN-beta signal pathway (By similarity). Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are probably autophagosome-like vesicles. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are probably autophagosome-like vesicles. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are probably autophagosome-like vesicles. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are probably autophagosome-like vesicles. Phosphorylated. Specific enzymatic cleavages by the viral protease in vivo yield a variety of precursors and mature proteins (By similarity). The polyprotein seems to be cotranslationally cleaved at the 2A/2B junction by a ribosomal skip from one codon to the next without formation of a peptide bond (By similarity). This process would release the P1-2A peptide from the translational complex (By similarity). During virion maturation, immature virions are rendered infectious following cleavage of VP0 into VP4 and VP2. This maturation seems to be an autocatalytic event triggered by the presence of RNA in the capsid and is followed by a conformational change of the particle. Uridylylated by the polymerase and is covalently linked to the 5'-end of genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase. Myristoylation is required during RNA encapsidation and formation of the mature virus particle. Produced by conventional translation. Belongs to the picornaviruses polyprotein family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate (beta-HBP) intermediate into D-glycero-beta-D-manno-heptose 1-phosphate by removing the phosphate group at the C-7 position. D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O = D-glycero-beta-D-manno-heptose 1-phosphate + phosphate Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate: step 2/4. Bacterial outer membrane biogenesis; LPS core biosynthesis. Monomer. Belongs to the gmhB family. +Metallothioneins have a high content of cysteine residues that bind various heavy metals. Class I MTS in marine crustacea are involved in the sequestration of elevated levels of heavy-metal ions. By cadmium. Belongs to the metallothionein superfamily. Type 3 family. +GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Homomer. Belongs to the GTP cyclohydrolase I family. +Histones H1 are necessary for the condensation of nucleosome chains into higher-order structures. Macronuclei. Cell-growth/division-associated phosphorylation by a CDC2-like kinase (By similarity). Is additionally phosphorylated on either Ser-33, Thr-34 or Thr-35, and on either Thr-39 or Ser-40. +Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I. di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 4 family. MraY subfamily. +Has weak lytic activity toward S.aureus cells. Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. Belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. +Component of the packaging machinery which encapsidates the viral DNA into preformed capsids and transcriptional activator of the viral major late promoter (MLP). Binds, along with packaging proteins 1 and 3, to the specific packaging sequence on the left end of viral genomic DNA and plays an active role in packaging of the viral genome into preformed capsids. Specifically binds to the 5'-TTTG-3' nucleotides of the repeats making up the packaging sequence. Forms a transcription factor called DEF-A through cooperative binding with packaging protein 1 (Probable). DEF-A binds to downstream elements of the major late promoter (MLP) and stimulates transcription from the MLP after initiation of viral DNA replication. Simultaneously suppresses early gene expression and is thus likely to participate in the early-late switch in the expression pattern of the late viral proteins. May as well enhance transcription from IVa2 and pIX promoters. Part of a genome packaging complex composed of packaging proteins 1, 2 and 3; this complex specifically binds to the packaging sequence on the left end of viral genomic DNA and performs packaging of the viral genome. Self-assembles into higher-order structures. Expressed at the late phase of the viral replicative cycle. Probably already expressed from the early to late transition. All late proteins expressed from the major late promoter are produced by alternative splicing and alternative polyadenylation of the same gene giving rise to non-overlapping ORFs. Expression of packaging protein 2 and splicing factor is controlled by a L4 promoter distinct from the major late promoter. Unspliced isoform. Belongs to the adenoviridae splicing factor family. +Serine protease (PubMed:10103041, PubMed:7763554). Hydrolyzes azocasein (PubMed:10103041). Cleaves peptide bonds of the oxidized insulin B chain preferably at 15-Leu-|-Tyr-16, but also at 4-Gln-|-His-5 and 24-Phe-|-Phe-25, and to a lesser extent at 5-His-|-Leu-6 and 25-Phe-|-Tyr-26. Hydrolyzes amide bonds between amino acids and 7-amino-4-methylcoumarin (AMC) in vitro (PubMed:7763554). Inhibited by 0.1 mM diisopropyl fluorophosphate (DFP), phenylmethanesulfonyl fluoride (PMSF), chymostatin and elastatinal. Not inhibited by N-alpha-p-tosyl-L-lysine chloromethylketone (TLCK), N-tosyl-L-phenylalanyl chloromethyl ketone (TPCK) or N-carbobenzoxy-L-phenylalanine chloromethylketone (ZPCK). Active at pH 7 (up to 40 degrees Celsius for 30 min) and at pH 11 (up to 25 degrees Celsius). Protease activity is retained up to 40 degrees Celsius for 30 min, but completely inactivated at 50 degrees Celsius (at pH 7). Activity is retained up to 25 degrees Celsius, and completely inactivated at 40 degrees Celsius (at pH 11). Expression is induced in mycelia after 24 hours of growth. Maximal expression is reached at about 42 hours and expression is slightly decayed after 48 hours. Causes an allergic reaction in human. Binds to IgE. Belongs to the peptidase S8 family. +Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine. H(+) + L-aspartate = beta-alanine + CO2 Binds 1 pyruvoyl group covalently per subunit. Cofactor biosynthesis; (R)-pantothenate biosynthesis; beta-alanine from L-aspartate: step 1/1. Heterooctamer of four alpha and four beta subunits. Is synthesized initially as an inactive proenzyme, which is activated by self-cleavage at a specific serine bond to produce a beta-subunit with a hydroxyl group at its C-terminus and an alpha-subunit with a pyruvoyl group at its N-terminus. Belongs to the PanD family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +Part of the ABC transporter DppABCDF involved in dipeptide transport (PubMed:7536291). Responsible for energy coupling to the transport system (Probable). When a foreign outer membrane heme receptor is expressed in E.coli, DppABCDF can also transport heme and its precursor, 5-aminolevulinic acid (ALA), from the periplasm into the cytoplasm. a dipeptide(out) + ATP + H2O = a dipeptide(in) + ADP + H(+) + phosphate The complex is composed of two ATP-binding proteins (DppD and DppF), two transmembrane proteins (DppB and DppC) and a solute-binding protein (DppA) (PubMed:7536291, PubMed:16905647). MppA can replace DppA as binding protein for heme and ALA transport (PubMed:16905647). Inactivation of the gene abolishes use of heme as an iron source. Belongs to the ABC transporter superfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a(1), b(1), b'(1) and c(9-12). Belongs to the ATPase alpha/beta chains family. +Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P). S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 1/6. Belongs to the eIF-2B alpha/beta/delta subunits family. MtnA subfamily. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Potential odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Allosterically activated by GTP. Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +Involved in the biosynthesis of osmoregulated periplasmic glucans (OPGs). Glycan metabolism; osmoregulated periplasmic glucan (OPG) biosynthesis. Belongs to the OpgD/OpgG family. +Belongs to the SUI1 family. +Participates in the detoxification of a plethora of hydrazine and arylamine drugs. acetyl-CoA + an arylamine = an N-acetylarylamine + CoA Belongs to the arylamine N-acetyltransferase family. +Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-methyl-D-erythritol + diphosphate Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. Belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily. +Integrin alpha-5/beta-1 (ITGA5:ITGB1) is a receptor for fibronectin. It recognizes the sequence R-G-D in its ligands. ITGA5:ITGB1 acts as a receptor for fibrillin-1 (FBN1) and mediates R-G-D-dependent cell adhesion to FBN1. ITGA5:ITGB1 is a receptor for IL1B and binding is essential for IL1B signaling. ITGA5:ITGB3 is a receptor for soluble CD40LG and is required for CD40/CD40LG signaling (By similarity). Heterodimer of an alpha and a beta subunit. The alpha subunit is composed of a heavy and a light chain linked by a disulfide bond. Alpha-5 associates with beta-1. Belongs to the integrin alpha chain family. +Belongs to the CinA family. +Transcriptional regulator that controls a genetic switch in male development. It is necessary and sufficient for initiating male sex determination by directing the development of supporting cell precursors (pre-Sertoli cells) as Sertoli rather than granulosa cells. Involved in different aspects of gene regulation including promoter activation or repression. Binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SRY HMG box recognizes DNA by partial intercalation in the minor groove and promotes DNA bending. Also involved in pre-mRNA splicing (By similarity). In male adult brain involved in the maintenance of motor functions of dopaminergic neurons (By similarity). Interacts with CALM, EP300, HDAC3, KPNB1, ZNF208 isoform KRAB-O, PARP1, SLC9A3R2 and WT1. The interaction with EP300 modulates its DNA-binding activity. The interaction with KPNB1 is sensitive to dissociation by Ran in the GTP-bound form. Interaction with PARP1 impaired its DNA-binding activity. Belongs to the SRY family. The tenuous nature of sex - Issue 80 of March 2007 +ATPase component of the INO80 complex which remodels chromatin by shifting nucleosomes and is involved in DNA repair. ATP + H2O = ADP + H(+) + phosphate Component of the INO80 chromatin-remodeling complex. The DBINO region is involved in binding to DNA. Belongs to the SNF2/RAD54 helicase family. +Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA. a fatty acyl-[ACP] + phosphate = an acyl phosphate + holo-[ACP] Lipid metabolism; phospholipid metabolism. Homodimer. Probably interacts with PlsY. Associated with the membrane possibly through PlsY. Belongs to the PlsX family. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + H(+) + holo-[ACP] Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxD subfamily. +Dual endothelin-1/angiotensin-2 receptor that is functionally coupled to a calcium-mobilizing transduction system, responding equivalently to both endothelin-1/EDN1 and angiotensin-2 v in a highly specific manner (PubMed:16293765). Also binds the signal peptide of VEGFA (PubMed:16293765). May play a role in angiogenesis with a significant role in cardiovascular and neural development (PubMed:16293765). Widely expressed with higher levels in kidney and aorta. At 9.5 dpc, expressed predominantly in the heart, yolk sac mesodermal layer and endothelium, fetal vascular endothelium in the placenta, dorsal aorta, and ependymal layer of the neural tube. Expression that persists at 12.5 dpc, where expression is increased in some hemangioblasts in yolk sac blood islands, as well as more prominent expression in the ependymal layer of the neuroepithelium and in perineural blood vessels. Embryonic lethal at 12.5 dpc. Mice exhibit impaired angiogenesis and dysregulated neuroepithelial development. +Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 19 (CSTX) family. 03 subfamily. +Placental lactogen I is expressed in mid-pregnancy, while placental lactogen II is expressed throughout the later half of pregnancy. Belongs to the somatotropin/prolactin family. +Expressed in cauline leaves, stems, rosette leaves, immature siliques and primary inflorescences. Contains a PAM2-like motif, which seems to be involved in the binding to the PABC/CTC domain of PAB proteins. +A probable RNA chaperone. Forms a complex with KhpB which binds to cellular RNA and controls its expression. Plays a role in peptidoglycan (PG) homeostasis and cell length regulation. Probably plays a role in PG homeostasis and regulating peripheral PG synthesis. Forms a complex with KhpB. Grows slowly and is smaller than wild-type; estimated to be about 50% of the volume of wild-type cells. Belongs to the KhpA RNA-binding protein family. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Belongs to the SlyX family. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts with IRKI. Highly expressed in root tips, shoot apices and developing flowers. Autophosphorylated. No visible phenotype under normal growth conditions. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +Catalyzes the sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine. H2O + L-histidinol + 2 NAD(+) = 3 H(+) + L-histidine + 2 NADH Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 9/9. Belongs to the histidinol dehydrogenase family. +GTP-binding protein involved in transport from the endoplasmic reticulum to the Golgi apparatus (PubMed:11149932, PubMed:8138575). Activated by the guanine nucleotide exchange factor PREB (PubMed:11149932, PubMed:8138575). Involved in the selection of the protein cargo and the assembly of the COPII coat complex (PubMed:11149932, PubMed:8138575). Synergizes with the cargo receptor SURF4 to mediate the export of lipoproteins from the endoplasmic reticulum, thereby regulating lipoprotein delivery and the maintenance of lipid homeostasis (By similarity). Homodimer (PubMed:11739406). Binds PREB (PubMed:11739406). Part of the COPII coat complex (PubMed:11739406). Binds to the cytoplasmic tails of target proteins in the endoplasmic reticulum (PubMed:11739406). Interacts with SURF4 (By similarity). Associated with the endoplasmic reticulum and Golgi stacks, in particular in the juxta-nuclear Golgi region. Belongs to the small GTPase superfamily. SAR1 family. +5-phospho-beta-D-ribosylamine + ATP + glycine = ADP + H(+) + N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate Binds 1 Mg(2+) or Mn(2+) ion per subunit. Purine metabolism; IMP biosynthesis via de novo pathway; N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-diphosphate: step 2/2. Belongs to the GARS family. +Belongs to the Smg family. +Catalyzes the formation of N(4)-acetylcytidine (ac(4)C) at the wobble position of elongator tRNA(Met), using acetate and ATP as substrates. First activates an acetate ion to form acetyladenylate (Ac-AMP) and then transfers the acetyl group to tRNA to form ac(4)C34. acetate + ATP + cytidine(34) in elongator tRNA(Met) = AMP + diphosphate + N(4)-acetylcytidine(34) in elongator tRNA(Met) Belongs to the TmcAL family. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine. L-leucyl-tRNA(Leu) + N-terminal L-lysyl-[protein] = H(+) + N-terminal L-leucyl-L-lysyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-arginyl-[protein] = H(+) + N-terminal L-leucyl-L-arginyl-[protein] + tRNA(Leu) an N-terminal L-alpha-aminoacyl-[protein] + L-phenylalanyl-tRNA(Phe) = an N-terminal L-phenylalanyl-L-alpha-aminoacyl-[protein] + tRNA(Phe) Belongs to the L/F-transferase family. +Belongs to the TACO1 family. +Probably forms part of a two-component regulatory system RegX3/SenX3. Phosphorylated by SenX3. +Catalyzes the formation of an amide bond between tyramine and the gamma carboxy group of L-glutamate. The enzyme also accepts phenylethylamine in vitro. ATP + L-glutamate + tyramine = ADP + gamma-L-glutamyltyramine + H(+) + phosphate Binds 2 magnesium or manganese ions per subunit. kcat is 4.8 sec(-1) toward tyramine. kcat is 5.8 sec(-1) toward L-glutamate. kcat is 5.9 sec(-1) toward ATP. Optimum pH is 6.7. Cofactor biosynthesis; methanofuran biosynthesis. +Catalyzes the terminal and only committed step in triacylglycerol synthesis by using diacylglycerol and fatty acyl CoA as substrates. Required for storage lipid synthesis (By similarity). a 1,2-diacyl-sn-glycerol + an acyl-CoA = a triacyl-sn-glycerol + CoA all-trans-retinol + an acyl-CoA = an all-trans-retinyl ester + CoA (9Z)-octadecenoyl-CoA + 2-(9Z-octadecenoyl)-glycerol = 1,2-di-(9Z-octadecenoyl)-sn-glycerol + CoA (9Z)-octadecenoyl-CoA + 1,2-di-(9Z-octadecenoyl)-sn-glycerol = 1,2,3-tri-(9Z-octadecenoyl)-glycerol + CoA all-trans-retinol + hexadecanoyl-CoA = all-trans-retinyl hexadecanoate + CoA (9Z)-octadecenoyl-CoA + 1-O-(9Z-octadecenyl)-glycerol = 1-O-(9Z-octadecenyl)-mono-(9Z-octadecenoyl)-glycerol + CoA (9Z)-octadecenoyl-CoA + 1-(9Z-octadecenoyl)-glycerol = 1,2-di-(9Z-octadecenoyl)-glycerol + CoA 1,2-di-(9Z-octadecenoyl)-sn-glycerol + hexadecanoyl-CoA = 1,2-di-(9Z)-octadecenoyl-3-hexadecanoyl-sn-glycerol + CoA (9Z)-octadecenoyl-CoA + 1,3-di-(9Z-octadecenoyl)-glycerol = 1,2,3-tri-(9Z-octadecenoyl)-glycerol + CoA (9Z)-octadecenoyl-CoA + 2,3-di-(9Z)-octadecenoyl-sn-glycerol = 1,2,3-tri-(9Z-octadecenoyl)-glycerol + CoA 2-(9Z-octadecenoyl)-glycerol + hexadecanoyl-CoA = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycerol + CoA Glycerolipid metabolism; triacylglycerol biosynthesis. Belongs to the diacylglycerol acyltransferase family. +ATP-binding (A) component of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). Belongs to the ABC transporter superfamily. Energy-coupling factor EcfA family. +Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. Binds 1 [2Fe-2S] cluster. Belongs to the 2Fe2S plant-type ferredoxin family. +Probably participates in deamination of adenosine-34 to inosine in many tRNAs. adenosine(34) in tRNA + H(+) + H2O = inosine(34) in tRNA + NH4(+) Belongs to the cytidine and deoxycytidylate deaminase family. ADAT2 subfamily. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +High affinity, high specificity proton-dependent sulfate transporter, which mediates sulfate uptake. Provides the sulfur source for the cysteine synthesis pathway. Belongs to the CysZ family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily. +Catalyzes the deamination of dCTP to dUTP. dCTP + H(+) + H2O = dUTP + NH4(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 1/2. Homotrimer. Belongs to the dCTP deaminase family. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +Repressor involved in the biosynthesis of the osmoprotectant glycine betaine. It represses transcription of the choline transporter BetT and the genes of BetAB involved in the synthesis of glycine betaine (By similarity). Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway [regulation]. +Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX. (6R)-NADHX = (6S)-NADHX (6R)-NADPHX = (6S)-NADPHX Binds 1 potassium ion per subunit. Belongs to the NnrE/AIBP family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase delta chain family. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Part of the ABC transporter complex TagGH involved in teichoic acids export. Responsible for energy coupling to the transport system. ATP + H2O + teichoic acidSide 1 = ADP + phosphate + teichoic acidSide 2. The complex is composed of two ATP-binding proteins (TagH) and two transmembrane proteins (TagG). Belongs to the ABC transporter superfamily. Teichoic acids exporter (TC 3.A.1.104.1) family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Protein kinase which is a key regulator of the actin cytoskeleton and cell polarity (By similarity). Involved in regulation of smooth muscle contraction, actin cytoskeleton organization, stress fiber and focal adhesion formation, neurite retraction, cell adhesion and motility via phosphorylation of DAPK3, GFAP, LIMK1, LIMK2, MYL9/MLC2, TPPP, PFN1 and PPP1R12A (By similarity) (PubMed:9139666). Phosphorylates FHOD1 and acts synergistically with it to promote SRC-dependent non-apoptotic plasma membrane blebbing. Phosphorylates JIP3 and regulates the recruitment of JNK to JIP3 upon UVB-induced stress (By similarity). Acts as a suppressor of inflammatory cell migration by regulating PTEN phosphorylation and stability (By similarity). Acts as a negative regulator of VEGF-induced angiogenic endothelial cell activation. Required for centrosome positioning and centrosome-dependent exit from mitosis (By similarity). Plays a role in terminal erythroid differentiation (By similarity). Inhibits podocyte motility via regulation of actin cytoskeletal dynamics and phosphorylation of CFL1 (By similarity). Promotes keratinocyte terminal differentiation (By similarity). Involved in osteoblast compaction through the fibronectin fibrillogenesis cell-mediated matrix assembly process, essential for osteoblast mineralization (By similarity). May regulate closure of the eyelids and ventral body wall by inducing the assembly of actomyosin bundles (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by RHOA binding. Inhibited by Y-27632 (By similarity). Homodimer. Interacts with RHOA (activated by GTP), RHOB, RHOC, GEM, MYLC2B, RHOE, PPP1R12A, LIMK1, LIMK2, TSG101, CHORDC1, DAPK3, PFN1, PTEN and JIP3. Interacts with FHOD1 in a Src-dependent manner. Interacts with ITGB1BP1 (via N-terminus and PTB domain). Interacts with SHROOM3 (By similarity). A small proportion is associated with Golgi membranes (By similarity). Associated with the mother centriole and an intercentriolar linker (By similarity). Colocalizes with ITGB1BP1 and ITGB1 at the cell membrane predominantly in lamellipodia and membrane ruffles, but also in retraction fibers (By similarity). Localizes at the cell membrane in an ITGB1BP1-dependent manner (By similarity). Detected in corneal epithelium. The C-terminal auto-inhibitory domain interferes with kinase activity. RHOA binding leads to a conformation change and activation of the kinase. Truncated ROCK1 is constitutively activated. Autophosphorylated on serine and threonine residues. Cleaved by caspase-3 during apoptosis. This leads to constitutive activation of the kinase and membrane blebbing (By similarity). Belongs to the protein kinase superfamily. AGC Ser/Thr protein kinase family. +Belongs to the UPF0725 (EMB2204) family. +Transcription factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Facilitates transcription initiation by enhancing TATA-box recognition by TATA-box-binding protein (Tbp), and transcription factor B (Tfb) and RNA polymerase recruitment. Not absolutely required for transcription in vitro, but particularly important in cases where Tbp or Tfb function is not optimal. It dynamically alters the nucleic acid-binding properties of RNA polymerases by stabilizing the initiation complex and destabilizing elongation complexes. Seems to translocate with the RNA polymerase following initiation and acts by binding to the non template strand of the transcription bubble in elongation complexes. Monomer. Interaction with RNA polymerase subunits RpoF and RpoE is necessary for Tfe stimulatory transcription activity. Able to interact with Tbp and RNA polymerase in the absence of DNA promoter. Interacts both with the preinitiation and elongation complexes. The winged helix domain is involved in binding to DNA in the preinitiation complex. Belongs to the TFE family. +Belongs to the HupF/HypC family. +GTPase that may function in mitochondrial ribosome assembly (Probable). Involved in a variety of growth processes during vegetative development and promotes growth and cell division in the developing integuments (PubMed:10835408, PubMed:16849600). Expressed in seedlings, roots, leaves, stems, inflorescences and siliques. In contrast to other GTP-binding proteins, this family is characterized by a circular permutation of the GTPase motifs described by a G4-G1-G3 pattern. The DARXP motif is also sometime designated as G6 region. No visible phenotype when heterozygous, but completely female sterile when homozygous. Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Belongs to the MHC class II family. +DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) DNA polymerase delta is a heterotrimer of POL3, POL32 and HYS2. Present with 626 molecules/cell in log phase SD medium. Belongs to the DNA polymerase delta/II small subunit family. +Chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Has a low intrinsic ATPase activity which is markedly stimulated by HscB. Involved in the maturation of IscU. Belongs to the heat shock protein 70 family. +Associates with SNCA, RNF19A AND PRKN. Ubiquitinated; mediated by SIAH1 or RNF19A and leading to its subsequent proteasomal degradation. +Escorts unspliced or incompletely spliced viral pre-mRNAs (late transcripts) out of the nucleus of infected cells. These pre-mRNAs carry a recognition sequence called Rev responsive element (RRE) located in the env gene, that is not present in fully spliced viral mRNAs (early transcripts). This function is essential since most viral proteins are translated from unspliced or partially spliced pre-mRNAs which cannot exit the nucleus by the pathway used by fully processed cellular mRNAs. Rev itself is translated from a fully spliced mRNA that readily exits the nucleus. Rev's nuclear localization signal (NLS) binds directly to KPNB1/Importin beta-1 without previous binding to KPNA1/Importin alpha-1. KPNB1 binds to the GDP bound form of RAN (Ran-GDP) and targets Rev to the nucleus. In the nucleus, the conversion from Ran-GDP to Ran-GTP dissociates Rev from KPNB1 and allows Rev's binding to the RRE in viral pre-mRNAs. Rev multimerization on the RRE via cooperative assembly exposes its nuclear export signal (NES) to the surface. Rev can then form a complex with XPO1/CRM1 and Ran-GTP, leading to nuclear export of the complex. Conversion from Ran-GTP to Ran-GDP mediates dissociation of the Rev/RRE/XPO1/RAN complex, so that Rev can return to the nucleus for a subsequent round of export. Beside KPNB1, also seems to interact with TNPO1/Transportin-1, RANBP5/IPO5 and IPO7/RANBP7 for nuclear import. The nucleoporin-like HRB/RIP is an essential cofactor that probably indirectly interacts with Rev to release HIV RNAs from the perinuclear region to the cytoplasm. Homomultimer; when bound to the RRE. Multimeric assembly is essential for activity and may involve XPO1. Binds to human KPNB1, XPO1, TNPO1, RANBP5 and IPO7. Interacts with the viral Integrase. Interacts with human KHDRBS1. Interacts with human NAP1; this interaction decreases Rev multimerization and stimulates its activity. Interacts with human DEAD-box helicases DDX3 and DDX24; these interactions may serve for viral RNA export to the cytoplasm and packaging, respectively. Interacts with human PSIP1; this interaction may inhibit HIV-1 DNA integration by promoting dissociation of the Integrase-LEDGF/p75 complex. The presence of both nuclear import and nuclear export signals leads to continuous shuttling between the nucleus and cytoplasm. The RNA-binding motif binds to the RRE, a 240 bp stem-and-loop structure present in incompletely spliced viral pre-mRNAs. This region also contains the NLS which mediates nuclear localization via KPNB1 binding and, when the N-terminal sequence is present, nucleolar targeting. These overlapping functions prevent Rev bound to RRE from undesirable return to the nucleus. When Rev binds the RRE, the NLS becomes masked while the NES remains accessible. The leucine-rich NES mediates binding to human XPO1. Asymmetrically arginine dimethylated at one site by host PRMT6. Methylation impairs the RNA-binding activity and export of viral RNA from the nucleus to the cytoplasm. Phosphorylated by protein kinase CK2. Presence of, and maybe binding to the N-terminus of the regulatory beta subunit of CK2 is necessary for CK2-mediated Rev's phosphorylation. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Belongs to the HIV-1 REV protein family. +FMRFamide-like neuropeptides (PubMed:15809090, PubMed:24533288). Involved in mediating arousal from the sleep-like state called lethargus, which occurs during molting between larval and adult stages, in part by regulating touch sensitivity, and working in concert with neuropeptide pdf-1 (PubMed:27585848). Involved in neural modulation of systemic mitochondrial unfolded protein response (PubMed:27767096). Acts as a ligand to FMRFamide peptide receptor frpr-18 in vitro. Acts as a ligand to FMRFamide peptide receptor frpr-18 in vitro. Knockouts generated by CRISPR-Cas9-mediated gene editing strongly inhibited the peripheral induction of the mitochondrial unfolded protein response. +Belongs to the cysteine-rich repeat secretory protein family. +a quinone + H(+) + NADH = a quinol + NAD(+) a quinone + H(+) + NADPH = a quinol + NADP(+) Binds 1 FMN per monomer. Belongs to the WrbA family. +Sugar kinase that catalyzes the ATP-dependent phosphorylation of N-acetylmuramate (MurNAc) and N-acetylglucosamine (GlcNAc) at its C1 hydroxyl group, leading to MurNAc alpha-1P and GlcNAc alpha-1P, respectively (By similarity). Is involved in peptidoglycan recycling as part of a cell wall recycling pathway that bypasses de novo biosynthesis of the peptidoglycan precursor UDP-MurNAc (PubMed:24819062). Plays a role in intrinsic resistance to fosfomycin, which targets the de novo synthesis of UDP-MurNAc (PubMed:24819062). ATP + N-acetyl-D-muramate = ADP + H(+) + N-acetyl-alpha-D-muramate 1-phosphate ATP + N-acetyl-D-glucosamine = ADP + H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate Cell wall biogenesis; peptidoglycan recycling. Cells lacking this gene accumulate MurNAc. Deletion of this gene increases fosfomycin sensitivity. Growth rate is not affected. Belongs to the kinase AmgK family. +Hydrolyzes the pyrophosphate bond of UDP-2,3-diacylglucosamine to form 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom. Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipooligosaccharide (LOS) to the outer membrane of the cell. Can functionally complement lpxH deficiency in E.coli. Overexpression of LpxG results in toxic accumulation of lipid X and profoundly reduces the infectivity of C.trachomatis. Can utilize UDP-2-N,3-O-bis((3R)-3-hydroxytetradecanoyl)-alpha-D-glucosamine as substrate in vitro, but the substrate is likely UDP-2-N-((3R)-3-hydroxyicosanoyl),3-O-(tetradecanoyl)-alpha-D-glucosamine in vivo. H2O + UDP-2,3-diacyl-alpha-D-glucosamine = 2,3-diacyl-alpha-D-glucosaminyl 1-phosphate + 2 H(+) + UMP Binds 2 divalent metal cations. Glycolipid biosynthesis; lipid IV(A) biosynthesis. Belongs to the metallophosphoesterase superfamily. LpxG family. +Homohexamer. Assembles into a hexameric ring structure. Belongs to the AAA ATPase family. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +Belongs to the UPF0303 family. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +Plays critical roles in virus replication, from virus entry and uncoating to assembly and budding of the virus particle. M1 binding to ribonucleocapsids (RNPs) in nucleus seems to inhibit viral transcription. Interaction of viral NEP with M1-RNP is thought to promote nuclear export of the complex, which is targeted to the virion assembly site at the apical plasma membrane in polarized epithelial cells. Interactions with NA and HA may bring M1, a non-raft-associated protein, into lipid rafts. Forms a continuous shell on the inner side of the lipid bilayer in virion, where it binds the RNP. During virus entry into cell, the M2 ion channel acidifies the internal virion core, inducing M1 dissociation from the RNP. M1-free RNPs are transported to the nucleus, where viral transcription and replication can take place. Determines the virion's shape: spherical or filamentous. Clinical isolates of influenza are characterized by the presence of significant proportion of filamentous virions, whereas after multiple passage on eggs or cell culture, virions have only spherical morphology. Filamentous virions are thought to be important to infect neighboring cells, and spherical virions more suited to spread through aerosol between hosts organisms. Homodimer and homomultimer. Interacts with NEP. Binds ribonucleocapsid by both interacting with genomic RNA and NP protein. May interact with HA and NA. Cannot bind NP without genomic RNA. Only the first 9 residues are shared by the 2 isoforms. Most abundant protein in virion. When expressed alone can form virus-like particles in transfected cells. Belongs to the influenza viruses Matrix protein M1 family. +Muscle-specific filamin, which plays a central role in sarcomere assembly and organization (By similarity). Critical for normal myogenesis, it probably functions as a large actin-cross-linking protein with structural functions at the Z lines in muscle cells. May be involved in reorganizing the actin cytoskeleton in response to signaling events (PubMed:16914736). Homodimer; the filamin repeat 24 and the second hinge domain are important for dimer formation (By similarity). Interacts with FLNB, INPPL1, ITGB1A, KCND2, MYOT, MYOZ1 and MYOZ3. Interacts with sarcoglycans SGCD and SGCG. Interacts (via filament repeats 17-18, 20-21 and 24) with USP25 (isoform USP25m only). Interacts with FBLIM1 (By similarity). Interacts with XIRP1; this interaction is mediated by filamin 20 repeat (By similarity). Interacts with KY. Interacts with IGFN1. Interacts with MICALL2. Interacts with ANK3. Interacts with MICALL2 (By similarity). Interacts with ANK3. Interacts with SYNPO2 (By similarity). A small amount localizes at membranes. In striated muscle cells, it predominantly localizes in myofibrillar Z lines, while a minor fraction localizes with subsarcolemme (By similarity). Targeting to developing and mature Z lines is mediated by the intradomain insert (By similarity). During myogenesis, isoform 1 is expressed the first day, then is replaced by isoform 2. Ubiquitinated by FBXL22, leading to proteasomal degradation. Belongs to the filamin family. +5-dehydro-4-deoxy-D-glucarate + H(+) = 2,5-dioxopentanoate + CO2 + H2O Carbohydrate acid metabolism; D-glucarate degradation; 2,5-dioxopentanoate from D-glucarate: step 2/2. Belongs to the DapA family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +Probably functions as a manganese efflux pump. Belongs to the MntP (TC 9.B.29) family. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the eIF-3 subunit C family. +GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Toroid-shaped homodecamer, composed of two pentamers of five dimers. Belongs to the GTP cyclohydrolase I family. +Specifically methylates the N7 position of a guanine in 16S rRNA. Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Usually encoded in the trnK tRNA gene intron. Probably assists in splicing its own and other chloroplast group II introns. Belongs to the intron maturase 2 family. MatK subfamily. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Binds 1 zinc ion per subunit. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. Zinc-binding uS14 subfamily. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Upon acetylcholine binding, the AChR responds by an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. Pentamer of two alpha chains, and one each of the beta, delta, and gamma chains. Belongs to the ligand-gated ion channel (TC 1.A.9) family. Acetylcholine receptor (TC 1.A.9.1) subfamily. Alpha-1/CHRNA1 sub-subfamily. +Functions in nuclear protein import as nuclear transport receptor. Serves as receptor for nuclear localization signals (NLS) in cargo substrates. Is thought to mediate docking of the importin/substrate complex to the nuclear pore complex (NPC) through binding to nucleoporin and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to the importin, the importin/substrate complex dissociates and importin is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus (By similarity). Mediates the nuclear import of RPL12, and of UBE2E3 (By similarity). Interacts with UBE2E3 and RPL12. Belongs to the importin beta family. +Ethanolamine-phosphate cytidylyltransferase that catalyzes the second step in the synthesis of phosphatidylethanolamine (PE) from ethanolamine via the CDP-ethanolamine pathway (PubMed:17325045). Phosphatidylethanolamine is a dominant inner-leaflet phospholipid in cell membranes, where it plays a role in membrane function by structurally stabilizing membrane-anchored proteins, and participates in important cellular processes such as cell division, cell fusion, blood coagulation, and apoptosis (PubMed:17325045). CTP + H(+) + phosphoethanolamine = CDP-ethanolamine + diphosphate Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from ethanolamine: step 2/3. Homozygous knockout embryos die after implantation, prior to embryonic day 8.5. Belongs to the cytidylyltransferase family. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +This is a receptor for the anterior pituitary hormone prolactin. Interacts with SMARCA1. Interacts with NEK3 and VAV2 and this interaction is prolactin-dependent. Expressed in all tissues examined; liver, peripheral blood lymphocytes, endometrium, corpus luteum, intestine, fetal thymus, fetal spleen, fetal liver and fetal brain. The WSXWS motif appears to be necessary for proper protein folding and thereby efficient intracellular transport and cell-surface receptor binding. The box 1 motif is required for JAK interaction and/or activation. Belongs to the type I cytokine receptor family. Type 1 subfamily. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +3'-to-5' exoribonuclease specific for small oligoribonucleotides. Belongs to the oligoribonuclease family. +Required for chromosomal synapsis and meiotic recombination in males and females. ATP + H2O = ADP + H(+) + phosphate Interacts with Morc2a. Protein is abundant in testes but not detected in other adult tissues examined (at protein level). Detected in germ cells with a distinct developmental-specific expression pattern but not in somatic cells such as Sertoli cells. In juvenile testes, expression is absent prior to postnatal day 12, is detected at a low level at day 12, and increased significantly at day 14 and beyond. In adul testes, expressed in meiotic spermatocytes, abundant in post-meiotic haploid round spermatids, and absent from elongated spermatids. Knockouts are viable and appear to be grossly normal. Mutant males and females show meiotic arrest and sterility. Males have significantly smaller testes than control males. Their testes weigh approximately 70% less than control testes. Their spermatocytes and oocytes exhibit failures in chromosomal synapsis, blockades in meiotic recombination, and increased apoptosis (PubMed:29329290). The ovaries of adult female mutant mice are much smaller than those from heterozygous littermates and are devoid of oocytes (PubMed:29329290). Retrotransposed homolog of Morc2a. +Plays a role in the regulation of the cell surface expression of TLR4. Interacts with TLR4. Highly expressed in lung, spleen, thymus, and uterus. Moderately expressed in kidney, stomach and placenta. Weakly expressed in brain, heart, liver, small intestine, skeletal muscle and testis. Belongs to the canopy family. +Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Could accept sulfur from TusD (By similarity). Interacts with the TusBCD complex. Interacts with MnmA (By similarity). Belongs to the DsrC/TusE family. +This putative ketoacyl synthase lacks the active site cysteine. Belongs to the thiolase-like superfamily. Beta-ketoacyl-ACP synthases family. +Catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1). 7-aminomethyl-7-carbaguanine + 2 NADP(+) = 7-cyano-7-deazaguanine + 3 H(+) + 2 NADPH tRNA modification; tRNA-queuosine biosynthesis. Belongs to the GTP cyclohydrolase I family. QueF type 1 subfamily. +Catalyzes the formation of methylglyoxal from dihydroxyacetone phosphate. dihydroxyacetone phosphate = methylglyoxal + phosphate Belongs to the methylglyoxal synthase family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +Proton-dependent permease that transports di- and tripeptides. Belongs to the major facilitator superfamily. Proton-dependent oligopeptide transporter (POT/PTR) (TC 2.A.17) family. DtpB subfamily. +Does not exhibit any ribonuclease activity. Belongs to the pancreatic ribonuclease family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Belongs to the bacterial ribosomal protein bL34 family. +Catalyzes oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs. AH2 + O2 + uridine(34) in tRNA = 5-hydroxyuridine(34) in tRNA + A + H2O Belongs to the TrhO family. +Provides the (R)-glutamate required for cell wall biosynthesis. L-glutamate = D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the aspartate/glutamate racemases family. +Component of the large ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Component of the large ribosomal subunit. Detected on cytosolic polysomes (By similarity). Detected in ribosomes that are associated with the rough endoplasmic reticulum (By similarity). Belongs to the eukaryotic ribosomal protein eL21 family. +Belongs to the FAM184 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be a menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 15 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Belongs to the bacterial ribosomal protein bL35 family. +Molecular chaperone. Has ATPase activity. Homodimer. Belongs to the heat shock protein 90 family. +Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpA that pull DNA away from mid-cell into both cell halves. Homodimer. Homodimerization may be required to stabilize the binding of ScpA to the Smc head domains. Component of a cohesin-like complex composed of ScpA, ScpB and the Smc homodimer, in which ScpA and ScpB bind to the head domain of Smc. The presence of the three proteins is required for the association of the complex with DNA. Associated with two foci at the outer edges of the nucleoid region in young cells, and at four foci within both cell halves in older cells. Belongs to the ScpB family. +Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate + tRNA(n) Homohexameric ring arranged as a trimer of dimers. Belongs to the RNase PH family. +Involved in oxygen transport from gills to the various peripheral tissues. Heterotetramer of two alpha chains and two beta chains. Red blood cells. Belongs to the globin family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Promotes RNA polymerase (RNAP) assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. Part of the processive rRNA transcription and antitermination complex (rrnTAC). The complex forms an RNA-chaperone ring around the RNA exit tunnel of RNAP. It supports rapid transcription and antitermination of rRNA operons, cotranscriptional rRNA folding, and annealing of distal rRNA regions to allow correct ribosome biogenesis. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The rRNA transcription and antitermination complex (rrnTAC) consists of RNAP, NusA, NusB, NusE (rpsJ), NusG, SubB, ribosomal protein S4, DNA and precursor rRNA; S4 is more flexible than other subunits (PubMed:32871103). Belongs to the RNA polymerase subunit omega family. +Belongs to the UPF0324 family. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homotetramer; dimer of dimers. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Probable transcription factor. Expressed exclusively in a few inner cell layers of the inner integuments of the ovules. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system. ATP + H2O + L-methionine(out) = ADP + H(+) + L-methionine(in) + phosphate ATP + D-methionine(out) + H2O = ADP + D-methionine(in) + H(+) + phosphate The complex is composed of two ATP-binding proteins (MetN), two transmembrane proteins (MetI) and a solute-binding protein (MetQ). Belongs to the ABC transporter superfamily. Methionine importer (TC 3.A.1.24) family. +Catalyzes the attachment of asparagine to tRNA(Asn) in a two-step reaction: asparagine is first activated by ATP to form Asn-AMP and then transferred to the acceptor end of tRNA(Asn) (PubMed:9421509, PubMed:32738225, PubMed:32788587). In addition to its essential role in protein synthesis, acts as a signaling molecule that induced migration of CCR3-expressing cells (PubMed:30171954, PubMed:12235211). Has an essential role in the development of the cerebral cortex, being required for proper proliferation of radial glial cells (PubMed:32788587). ATP + L-asparagine + tRNA(Asn) = AMP + diphosphate + H(+) + L-asparaginyl-tRNA(Asn) Homodimer. The N-terminal domain (1-77) recruits and activates specific immune cells by interacting with CCR3-expressing cells. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Autoantibodies to NARS1, are often detected in sera from patients with interstitial lung disease (ILD). Belongs to the class-II aminoacyl-tRNA synthetase family. +Binds 2 divalent metal cations per subunit. Belongs to the peptidase M42 family. Extended N-terminus. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Belongs to the carbohydrate kinase PfkB family. +Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA). S-adenosyl-L-methionine + uridine(54) in tRNA = 5-methyluridine(54) in tRNA + H(+) + S-adenosyl-L-homocysteine S-adenosyl-L-methionine + uridine(341) in tmRNA = 5-methyluridine(341) in tmRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. TrmA subfamily. +Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. ATP + NAD(+) = ADP + H(+) + NADP(+) Belongs to the NAD kinase family. +As a result of hemolysis, hemoglobin is found to accumulate in the kidney and is secreted in the urine. Haptoglobin captures, and combines with free plasma hemoglobin to allow hepatic recycling of heme iron and to prevent kidney damage. Haptoglobin also acts as an antioxidant, has antibacterial activity and plays a role in modulating many aspects of the acute phase response. Hemoglobin/haptoglobin complexes are rapidly cleared by the macrophage CD163 scavenger receptor expressed on the surface of liver Kupfer cells through an endocytic lysosomal degradation pathway (By similarity). Tetramer of two alpha and two beta chains; disulfide-linked (By similarity). The hemoglobin/haptoglobin complex is composed of a haptoglobin dimer bound to two hemoglobin alpha-beta dimers (By similarity). Interacts with CD163 (By similarity). Interacts with ERGIC3 (By similarity). Expressed by the liver and secreted in plasma. The beta chain mediates most of the interactions with both subunits of hemoglobin, while the alpha chain forms the homodimeric interface. Belongs to the peptidase S1 family. Although homologous to serine proteases, it has lost all essential catalytic residues and has no enzymatic activity. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Exerts its effect at some terminal stage of cytochrome c oxidase synthesis, probably by being involved in the insertion of the copper B into subunit I. Belongs to the COX11/CtaG (TC 3.D.4.8) family. +Involved in oxygen transport from gills to the various peripheral tissues. Heterotetramer of two alpha chains and two beta chains. Red blood cells. This hemoglobin differs from other fish hemoglobins in lacking a residue between 121 and 122. Belongs to the globin family. +Belongs to the PsiE family. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +Necessary for abscisic acid (ABA) binding on the cell membrane and activation of the ABA signaling pathway in granulocytes. Interacts with an array of inositol phospholipids such as phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 5-phosphate (PI5P). PIP-binding enhances membrane association. Localizes to the juxta-nuclear vesicles (PubMed:16979580). Associates with the cortical actin cytoskeleton (PubMed:16979580). Cholesterol depletion by methyl-beta-cyclodextrin causes partial dissociation from the cell membrane in vitro and an enhanced cell detachment from the matrix in vivo (PubMed:16979580). Membrane-association is important for the increased cellular sensitivity to an anticancer drug (adriamycin) (PubMed:16979580). Expressed in brain and testis. Myristoylated. Essential for membrane association. Its exogenous expression in a sarcoma cell line decreases the expression of ABCB1 (P-glycoprotein 1) and increases cellular sensitivity to an anticancer drug (adriamycin). Belongs to the LanC-like protein family. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +Plant non-specific lipid-transfer proteins transfer phospholipids as well as galactolipids across membranes. May play a role in wax or cutin deposition in the cell walls of expanding epidermal cells and certain secretory tissues (By similarity). Causes an allergic reaction in human. Binds to IgE. Belongs to the plant LTP family. +Forms an icosahedral capsid with a T=7 symmetry and a 50 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. Binds to heparan sulfate proteoglycans on cell surface of basal layer keratinocytes to provide initial virion attachment. This binding mediates a conformational change in the virus capsid that facilitates efficient infection. The virion enters the host cell via endocytosis. During virus trafficking, L1 protein dissociates from the viral DNA and the genomic DNA is released to the host nucleus. The virion assembly takes place within the cell nucleus. Encapsulates the genomic DNA together with protein L2. Self-assembles into homopentamers. The capsid has an icosahedral symmetry and consists of 72 capsomers, with each capsomer being a pentamer of L1. Interacts with the minor capsid protein L2; this interaction is necessary for viral genome encapsidation. Interacts with protein E2; this interaction enhances E2-dependent replication and transcription activation. Belongs to the papillomaviridae L1 protein family. +Specifically methylates the N7 position of guanine in position 535 of 16S rRNA. Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Acyl carrier protein involved in the formation of acyl-S-ACP intermediates within the mycobactin biosynthesis process. Siderophore biosynthesis; mycobactin biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP, leading to the activated holo-ACP form. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. ATP + NAD(+) = ADP + H(+) + NADP(+) Belongs to the NAD kinase family. +Has dual roles in initiation of DNA replication, and regulation of checkpoint responses. Required for DNA replication initiation but not for the formation of pre-replicative complexes or the elongation stages. Necessary for the loading of replication factors onto chromatin, including gemc1, cdc45, DNA polymerases and components of the GINS complex such as ginsl/sld5. Binds chromatin in both S-phase cyclin-dependent kinase (S-CDK)-independent and S-CDK-dependent modes. Chromatin binding is required for the action of S-CDK, which in turn triggers the formation of preinitiation complexes of DNA replication. Its role in checkpoint activation is independent of the DNA replication role. In response to DNA damage, triggers the recruitment of checkpoint signaling proteins on chromatin, which activate the chek1 signaling pathway and block S-phase progression. Increases the kinase activity of atr to numerous substrates, and is required for the phosphorylation of Rad1. Interacts with cdc45. Interacts (via BRCT domains) with ticrr; interaction is cdk2-dependent. Interacts with atr in the presence of atrip. Interacts with recql4 (via N-terminus). Associates with chromatin. The N-terminal half is sufficient for DNA replication. Phosphorylation at 1131 is essential for phosphorylation of chek1, and thus for checkpoint regulation. +Catalyzes the interconversion through a 2-keto intermediate of uridine diphosphogalactopyranose (UDP-GalP) into uridine diphosphogalactofuranose (UDP-GalF) which is a key building block for cell wall construction in Mycobacterium tuberculosis. UDP-alpha-D-galactose = UDP-alpha-D-galactofuranose Cell wall biogenesis; cell wall polysaccharide biosynthesis. Homotetramer. Belongs to the UDP-galactopyranose/dTDP-fucopyranose mutase family. +RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Functions alone and as part of the erh1-mmi1 complex, to recruit the CCR4-NOT complex and the NURS complex to target RNAs (PubMed:26942678, PubMed:30651569, PubMed:31974447). Suppresses the meiotic program during vegetative growth and promotes the meiotic program during mating (PubMed:31974447). Binds to DSR (determinant of selective removal) regions in meiotic mRNA, and recruits the NURS complex to targets (PubMed:16823445, PubMed:26942678). Recruitment of NURS complex to target mRNAs promotes mRNA decay by engagement of the nuclear exosome, and formation of heterochromatin islands at meiotic genes silenced by the exosome (PubMed:16823445, PubMed:26942678). Recruitment of the CCR4-NOT complex to target RNAs promotes heterochromatin formation at RNAi-dependent heterochromatin domains (HOODs), including a subset of meiotic genes, lncRNAs and retrotransposons (PubMed:26942678). Recruitment of the CCR4-NOT complex to rDNA promotes rDNA heterochromatin assembly (PubMed:26942678). Promotes non-canonical transcription termination at meiotic genes and prevents lncRNA transcription from invading and repressing adjacent genes (PubMed:16823445, PubMed:30651569). Component of the erh1-mmi1 complex composed of mmi1 and erh1 (PubMed:26942678, PubMed:31974447, PubMed:30651569). Interacts (via N-terminus) with erh1 in a 2:2 stoichiometry (PubMed:26942678, PubMed:31974447, PubMed:30651569). Interacts with rrp6 (PubMed:16823445). Read-through transcription of regulatory lncRNAs (long non-coding RNAs) (PubMed:30651569). Decreases premature pre-mRNA 3'-end formation of ssm4 (PubMed:30651569). Increases levels and cytoplasmic localization of mating and meiosis specific transcripts during vegetative growth (PubMed:30651569). Decreases heterochromatin formation at meiotic heterochromatin islands (PubMed:26942678). +Catalyzes the condensation of ribulose 5-phosphate with formaldehyde to form 3-hexulose 6-phosphate. D-ribulose 5-phosphate + formaldehyde = D-arabino-hex-3-ulose 6-phosphate One-carbon metabolism; formaldehyde assimilation via RuMP pathway; D-fructose 6-phosphate from D-ribulose 5-phosphate and formaldehyde: step 1/2. By methanol or methylamine. Belongs to the HPS/KGPDC family. HPS subfamily. +Specifically methylates the adenine in position 37 of tRNA(1)(Val) (anticodon cmo5UAC). adenosine(37) in tRNA1(Val) + S-adenosyl-L-methionine = H(+) + N(6)-methyladenosine(37) in tRNA1(Val) + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. tRNA (adenine-N(6)-)-methyltransferase family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Glycosyltransferase that participates in the transfer of N-acetylglucosamine (GlcNAc) to the core mannose residues of N-linked glycans. Catalyzes the formation of the GlcNAcbeta1-4 branch on the GlcNAcbeta1-2Manalpha1-3 arm of the core structure of N-linked glycans. Essential for the production of tri- and tetra-antennary N-linked sugar chains. Does not catalyze the transfer of GlcNAc to the Manalpha1-6 arm to form GlcNAcBeta1-4Manalpha1-6 linkage ('GnT-VI' activity) (By similarity). N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = H(+) + N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAcl-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP Protein modification; protein glycosylation. Belongs to the glycosyltransferase 54 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 30 kDa subunit family. +Belongs to the chlamydial CPn_0705/CT_671/TC_0042 family. +Catalyzes the formation of the pentaglycine interpeptide bridge, which is characteristic of the S.aureus peptidoglycan. Adds glycines 2 and 3 of the pentaglycine bridge, using glycyl-tRNA(Gly) as donor (By similarity). beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-D-isoglutaminyl-L-Lys-(N(6)-Gly)-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + 2 glycyl-tRNA(Gly) = 2 H(+) + MurNAc-L-Ala-D-isoglutaminyl-L-Lys-(N(6)-tri-Gly)-D-Ala-D-Ala-diphospho-di-trans,octa-cis-undecaprenyl-GlcNAc + 2 tRNA(Gly) Homodimer. Interacts with FemB (By similarity). Belongs to the FemABX family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'-nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Magnesium is required for nucleotidyltransferase activity. Nickel for phosphatase activity. Monomer. Can also form homodimers and oligomers. Comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain associated with both phosphodiesterase and phosphatase activities. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 1 subfamily. +Modifies, by uridylylation and deuridylylation, the PII regulatory proteins (GlnB and homologs), in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen assimilation and metabolism. [protein-PII]-L-tyrosine + UTP = [protein-PII]-uridylyl-L-tyrosine + diphosphate [protein-PII]-uridylyl-L-tyrosine + H2O = [protein-PII]-L-tyrosine + H(+) + UMP Uridylyltransferase (UTase) activity is inhibited by glutamine, while glutamine activates uridylyl-removing (UR) activity. Has four distinct domains: an N-terminal nucleotidyltransferase (NT) domain responsible for UTase activity, a central HD domain that encodes UR activity, and two C-terminal ACT domains that seem to have a role in glutamine sensing. Belongs to the GlnD family. +Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication. Homotrimer. The subunits circularize to form a toroid; DNA passes through its center. Replication factor C (RFC) is required to load the toroid on the DNA. Belongs to the PCNA family. +Part of the ABC transporter complex RbsABC involved in ribose import. Responsible for energy coupling to the transport system. ATP + D-ribose(out) + H2O = ADP + D-ribose(in) + H(+) + phosphate The complex is composed of an ATP-binding protein (RbsA), two transmembrane proteins (RbsC) and a solute-binding protein (RbsB). Belongs to the ABC transporter superfamily. Ribose importer (TC 3.A.1.2.1) family. +Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Component of the primosome. Belongs to the helicase family. PriA subfamily. +Positively regulates the expression of ver-1 in the amphid sheath glia of amphid sensory neurons (PubMed:22298710). Together with ehn-3, plays a role in somatic gonad development and is required for proper gonadal primordium assembly and somatic gonad precursor cell morphology (PubMed:20026024). Expressed in the somatic gonad, hypodermis and cells in the head and tail (PubMed:20026024). Expressed in amphid and phasmid sheath glia, amphid and phasmid socket glia, and in neurons in the head (PubMed:22298710). Expressed from embryos to adults (PubMed:20026024). First expressed in somatic gonadal precursor cells during embryogenesis (PubMed:20026024). In the L2 larval stage of development, expressed in Z1.pa and Z4.ap distal tip cells and their descendants (PubMed:20026024). RNAi-mediated knockdown does not cause defects in somatic gonad development (PubMed:20026024). RNAi-mediated knockdown in a ehn-3 rd2 mutant background enhances the defects in gonadal development in the ehn-3 single mutant (PubMed:20026024). Belongs to the Ikaros C2H2-type zinc-finger protein family. +Belongs to the FHIP family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Belongs to the multi antimicrobial extrusion (MATE) (TC 2.A.66.1) family. +Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P). alpha-D-galactose + ATP = ADP + alpha-D-galactose 1-phosphate + H(+) Carbohydrate metabolism; galactose metabolism. Belongs to the GHMP kinase family. GalK subfamily. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 magnesium or manganese ions per subunit. Belongs to the PP2C family. +Multidrug resistance efflux protein. Belongs to the multi antimicrobial extrusion (MATE) (TC 2.A.66.1) family. MepA subfamily. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for the sorting of endocytic ubiquitinated cargos into multivesicular bodies. May be involved in cell growth and differentiation. Component of the ESCRT-I complex (endosomal sorting complex required for transport I) which consists of TSG101, VPS28, a VPS37 protein (VPS37A to -D) and MVB12A or MVB12B in a 1:1:1:1 stoichiometry. Interacts with TSG101, VPS28, MVB12A and MVB12B. Component of the ESCRT-I complex (endosomal sorting complex required for transport I) which consists of TSG101, VPS28, a VPS37 protein (VPS37A to -D) and UBAP1 in a 1:1:1:1 stoichiometry. Interacts with HGS and STAM2. Interacts with CEP55. Probably associates with membranes. Recruited to the plasma membrane by HIV-1. Phosphorylated by TBK1. Belongs to the VPS37 family. Extended N-terminus. +Catalyzes oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs. AH2 + O2 + uridine(34) in tRNA = 5-hydroxyuridine(34) in tRNA + A + H2O Belongs to the TrhO family. +Component of the BAT3 complex, a multiprotein complex involved in the post-translational delivery of tail-anchored (TA) membrane proteins to the endoplasmic reticulum membrane. TA membrane proteins, also named type II transmembrane proteins, contain a single C-terminal transmembrane region (By similarity). Component of the BAT3 complex. +RNA-free RNase P that catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Belongs to the HARP family. +May be responsible for the transport of glucosides into the cell, with the concomitant uptake of protons (symport system). Does not seem to transport sucrose. Glycan biosynthesis; sucrose metabolism. A number of isoforms are produced. According to EST sequences. Expressed in anthers. Belongs to the glycoside-pentoside-hexuronide (GPH) cation symporter transporter (TC 2.A.2.4) family. +Glycine receptors are ligand-gated chloride channels. Channel opening is triggered by extracellular glycine (PubMed:10188956, PubMed:26344198). Plays an important role in the down-regulation of neuronal excitability. Contributes to the generation of inhibitory postsynaptic currents. Channel activity is potentiated by ethanol (By similarity). Activated by glycine and taurine. Inhibited by strychnine (PubMed:10188956, PubMed:26344198). Allosterically activated by ivermectin (PubMed:26344198). Inhibited by picrotoxinin (PubMed:26344198). Strychnine binding locks the channel in a closed conformation and prevents channel opening in response to extracellular glycine (PubMed:26344198). Can also be activated by GABA and inhibited by bicuculline, but this requires heterologous expression in human cells (PubMed:10188956). Homopentamer (in vitro) (PubMed:26344198). Heteropentamer composed of glra1 and glrb (By similarity). Both homopentamers and heteropentamers form functional ion channels (By similarity). Expressed in brain. The channel pore is formed by pentameric assembly of the second transmembrane domain from all five subunits. Channel opening is effected by an outward rotation of the transmembrane domains that increases the diameter of the pore. Highly sensitive to activation by taurine despite the presence of Val in position 135. In mammals, Val-135 causes a drastic loss of taurine efficacy. The alpha subunit binds strychnine. Belongs to the ligand-gated ion channel (TC 1.A.9) family. Glycine receptor (TC 1.A.9.3) subfamily. GLRA1 sub-subfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase epsilon chain family. +Regulatory subunit of lactose synthase, changes the substrate specificity of galactosyltransferase in the mammary gland making glucose a good acceptor substrate for this enzyme. This enables LS to synthesize lactose, the major carbohydrate component of milk. In other tissues, galactosyltransferase transfers galactose onto the N-acetylglucosamine of the oligosaccharide chains in glycoproteins. Lactose synthase (LS) is a heterodimer of a catalytic component, beta1,4-galactosyltransferase (beta4Gal-T1) and a regulatory component, alpha-lactalbumin (LA). Mammary gland specific. Secreted in milk. Belongs to the glycosyl hydrolase 22 family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +May help in the organization of the PsaL subunit. Belongs to the PsaI family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Belongs to the HflD family. +Belongs to the WEB family. +Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine. (2S,6S)-2,6-diaminoheptanedioate = meso-2,6-diaminoheptanedioate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. Homodimer. Belongs to the diaminopimelate epimerase family. +Glucosyltransferase that glucosylates benzoates and benzoate derivatives in vitro. Belongs to the UDP-glycosyltransferase family. +Controls the transcription of genes involved in arginine and lysine metabolism. Homodimer. Belongs to the LysR transcriptional regulatory family. +Plays a role in erythroid cell differentiation. Mainly nuclear. The disease is caused by variants affecting the gene represented in this entry. Based on sequence similarity, it has been suggested that C15orf41 might encode a divalent metal-ion dependent restriction endonuclease, although nuclease activity could not be experimentally proven. Truncated N-terminus. +Cytoplasmic polyadenylation element binding protein that binds to and regulates the translation of specific mRNAs. Essential for progression through meiosis. Involved in spermatogenesis (By similarity). Interacts with fbf-1. +Released during platelet aggregation. Neutralizes the anticoagulant effect of heparin because it binds more strongly to heparin than to the chondroitin-4-sulfate chains of the carrier molecule. Chemotactic for neutrophils and monocytes. Inhibits endothelial cell proliferation (By similarity). Homotetramer. Interacts with TNFAIP6 (via Link domain). Binds non-covalently to a proteoglycan molecule. Belongs to the intercrine alpha (chemokine CxC) family. +Catalyzes the ATP-dependent phosphorylation of N-acetyl-L-glutamate. ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamyl 5-phosphate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 2/4. Belongs to the acetylglutamate kinase family. ArgB subfamily. +Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. AH2 + H2O2 = A + 2 H2O 2 H2O2 = 2 H2O + O2 Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit. Homodimer. Formation of the three residue Trp-Tyr-Met cross-link is important for the catalase, but not the peroxidase activity of the enzyme. Belongs to the peroxidase family. Peroxidase/catalase subfamily. +Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP). (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate Cofactor biosynthesis; molybdopterin biosynthesis. Homohexamer; trimer of dimers. Belongs to the MoaC family. +Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids. L-alanine = D-alanine Amino-acid biosynthesis; D-alanine biosynthesis; D-alanine from L-alanine: step 1/1. Belongs to the alanine racemase family. +Involved in arsenical resistance. Thought to form the channel of an arsenite pump. Belongs to the ArsB family. +D-glucuronate = D-fructuronate aldehydo-D-galacturonate = keto-D-tagaturonate Carbohydrate metabolism; pentose and glucuronate interconversion. Belongs to the metallo-dependent hydrolases superfamily. Uronate isomerase family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel. Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL. Belongs to the GroES chaperonin family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Involved in DNA repair and RecF pathway recombination. Belongs to the RecO family. +Involved in the intranuclear transport of ribosomal precursors. Interacts with MAK21/NOC1 and NOC3. Forms a nucleolar complex with MAK21 that binds to 90S and 66S pre-ribosomes, as well as a nuclear complex with NOC3 that binds to 66S pre-ribosomes. Present with 29000 molecules/cell in log phase SD medium. Belongs to the NOC2 family. Was originally thought to be RAD4. +Probable catalytic subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral membrane proteins such as Notch receptors. Requires the other members of the gamma-secretase complex to have a protease activity (By similarity). Homodimer. Component of the gamma-secretase complex, a complex composed of a presenilin homodimer, nicastrin, aph1 and pen2 (By similarity). The PAL motif is required for normal active site conformation. Belongs to the peptidase A22A family. +Reduces FMN, organic nitro compounds and disulfide DTNB. Involved in maintenance of the cellular redox state and the disulfide stress response (By similarity). Belongs to the flavin oxidoreductase frp family. +Snaclec that strongly induces platelet aggregation, in a dose-dependent manner. Tetramer of 4 heterodimers of alpha and beta subunits; disulfide-linked. Expressed by the venom gland. Belongs to the snaclec family. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product. Stimulates poly(A) polymerase (PAPOLA) conferring processivity on the poly(A) tail elongation reaction and controls also the poly(A) tail length. Increases the affinity of poly(A) polymerase for RNA. Binds to poly(A) and to poly(G) with high affinity. May protect the poly(A) tail from degradation. Monomer and homooligomer (PubMed:18479511). Binds RNA as a monomer and oligomerizes when bound to poly(A) (By similarity). Forms a complex with cleavage and polyadenylation specificity factor (CPSF) subunits FIPS5, PABN3 and PAPS4 (PubMed:16282318, PubMed:18479511). Interacts with CSP3 (PubMed:23334891). Shuttles between the nucleus and the cytoplasm but predominantly found in the nucleus. A number of isoforms are produced. According to EST sequences. The RRM domain is essential for the recognition of specific adenine bases in the poly(A) tail, but not sufficient for poly(A) binding. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the anticodon-binding domain and the C-terminal extension. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily. +Low-potential electron donor to a number of redox enzymes. NifF is the electron donor to nitrogenase. Belongs to the flavodoxin family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Catalyzes the migration of the L-beta-lysine and D-lysine epsilon amino group to the delta carbon to produce 3,5-diaminohexanoate and 2,5-diaminohexanoate, respectively. (3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate D-lysine = (2R,5S)-2,5-diaminohexanoate Rapidly inactivated in the presence of D-lysine and to a lesser extent in the absence of adenosylcobalamin (Adocbl). Activity is stable in the presence of Adocbl when D-lysine is absent. Adocbl imparts thermal stability at 37 degrees Celsius. Amino-acid metabolism; lysine degradation. Heterotetramer of 2 alpha and 2 beta subunits. Belongs to the KamD family. Truncated N-terminus. +Amphipathic alpha-helical antimicrobial peptide with potent activity against Gram-positive bacteria, weak activity against Gram-negative bacteria, and moderate activity against fungi (PubMed:9022710, PubMed:15513914, PubMed:16867990, PubMed:18255189, PubMed:18370376). Mainly acts by causing membrane permeabilization (Probable). Is also able to kill S.aureus (both wild-type and MRSA) that are internalized in human keratinocytes without injuring host cells (PubMed:24514087). Rapidly inactivates both channel catfish herpesvirus (ED(50)=15 uM) and frog virus 3 (ED(50)=58 uM) over a wide temperature range (PubMed:15193922). Also displays anti-leishmania activity by damaging parasite membrane (PubMed:15513914, PubMed:25668079). Acts synergistically with temporin-L which improves temporin-1Ta activity by preventing its self-association in lipopolysaccharides (LPS) (PubMed:16867990). Does not show hemolytic activity (PubMed:15513914). In vitro, stimulates insulin release from pancreatic beta-cells in a dose-dependent manner without increasing intracellular calcium, protects beta-cells against cytokine-induced apoptosis and augments beta-cells proliferation (PubMed:29349894). In vivo, intraperitoneal injection together with a glucose load into mice does not have effect on plasma glucose levels (PubMed:29349894). In vivo, when tested on mice with methicillin-resistant S.aureus (MRSA)-infected wounds, this peptide inhibits bacterial growth and shows wound healing effect (PubMed:18255189). In vitro, promotes cell migration and wound healing (PubMed:24514087). Forms helical oligomeric structures in LPS lipids, the major constituent of Gram-negative bacteria outer membrane (Probable). Adopts monomeric helical conformations when bound to bacterial (anionic) and eukaryotic (zwitterionic) model membranes (PubMed:18370376). In Gram-positive bacterial mimetic membranes, the aggregation is weakly pronounced, and penetration proceeds more rapidly and is deeper than in Gram-negative bacterial mimetic membranes where aggregation is high (By similarity). Self-association is prevented by temporin-L (PubMed:16867990). Expressed by the skin glands. Adopts helical conformation in LPS micelles fro residues L4-I12. Could be used to protect potato plants from fungi Phytophthora infestans, Phytophthora erythroseptica and bacterium Erwinia carotovora, since the analog N-terminally modified MsrA3 (F1MASRHMF), when expressed in potato plants, conveys strong resistance to late blight and pink rot phytopathogens in addition to the bacterial pathogen Erwinia carotovora. Transgenic tubers remained disease-free during storage for more than 2 years. Is an attractive candidate for the generation of new therapeutics to treat S.aureus-related epithelial (skin) infections. It has (i) a long-lasting existence in nature as active molecule which is able to exert a direct antimicrobial activity, which should guarantee the success of the antimicrobial efficacy of temporin-based anti-infective agents; (ii) a membrane-perturbing activity on bacteria, which should limit the induction of microbial resistance; (iii) the ability to kill both reference S.aureus and MRSA strains, once internalized by human epidermal cells and to treat them; (iv) the ability to stimulate migration of these cells; (v) a chemoattractic property for human monocytes; (vi) an exogenous (nonmammalian) nature, which should allow beneficial effects in clinical medicine, reducing the possible risk of inducing an autoimmune response; and, (vii) a small size, which should allow a low production cost. Belongs to the frog skin active peptide (FSAP) family. Temporin subfamily. +With CysN forms the ATP sulfurylase (ATPS) that catalyzes the adenylation of sulfate producing adenosine 5'-phosphosulfate (APS) and diphosphate, the first enzymatic step in sulfur assimilation pathway. APS synthesis involves the formation of a high-energy phosphoric-sulfuric acid anhydride bond driven by GTP hydrolysis by CysN coupled to ATP hydrolysis by CysD. ATP + H(+) + sulfate = adenosine 5'-phosphosulfate + diphosphate Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 1/3. Heterodimer composed of CysD, the smaller subunit, and CysN. Belongs to the PAPS reductase family. CysD subfamily. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Binds 1 zinc ion per subunit. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. Zinc-binding uS14 subfamily. +Blocks human and/or rat Kv11.1/KCNH2/ERG1, Kv11.2/KCNH6/ERG2 and Kv11.3/KCNH7/ERG3 by binding to channel outer vestibule (S5P domain) with a 1:1 stoichiometry. Inhibition data are the following: hERG1 (reversible, Kd=7.7 nM (PubMed:16497878), IC(50)=3.3 nM (PubMed:11136720), IC(50)=11.9 nM (PubMed:21205913)), rERG1 (reversible, Kd=19 nM) (PubMed:16497878), hERG2 (reversible, Kd=77 nM) (PubMed:16497878), rERG2 (irreversible, Kd=4.2 nM) (PubMed:16497878), hERG3 (reversible, Kd=11.5 nM) (PubMed:16497878) and rERG3 (reversible, Kd=747 nM) (PubMed:16497878) potassium channels. Has also a minimal effect on rat ELK1/KCNH4 potassium channels (9% inhibition at 100 nM (PubMed:15137031)). Both this toxin and CnErgTx1 (AC Q86QT3) share mechanism of action and have overlapping binding sites on ERG1 (PubMed:12719233). The potency of these two toxins is not affected by elevating potassium ion concentration from 2 to 98 mM (PubMed:12719233). In addition, at high toxin concentrations, block of ERG1 macroscopic currents by these two toxins is incomplete (88%) (PubMed:12719233). The blockade by this toxin is preferentially closed channel state-dependent, with a component of open, but not inactive state-dependent blockade (PubMed:12860380). This toxin produces a concentration-dependent prolongation of QTc in the isolated rabbit heart (16.3% at 100 nM) (PubMed:21205913). Expressed by the venom gland. Has the CSalpha/beta fold, which comprises one or two short alpha helices connected to anti-parallel beta-sheets stabilized by three or four disulfide bonds. The inhibition potency of the toxin for ERG1 decreases as temperature increases (IC(50)=7.6 nM and IC(50)=15.3 nM at room temperature and 37 degrees Celsius, respectively), likely due to changes in the structure of the channel binding site. The toxin (at 100 nM) does not inhibit hEAG1/KCNH1, hBK/KCa1.1/KCNMA1, hSK1/KCa2.1/KCNN1, rSK2/KCa2.2/KCNN2, hIK/KCa3.1/KCNN4, KCNQ1+KCNE1, KCNQ2+KCNQ3 and KCNQ4 channels (PubMed:11136720). The toxin (at 50 nM) does not inhibit Kv1.2/KCNA2, Kv1.4/KCNA4, Kv2.1/KCNB1, Kv4.3/KCND3, Kir1.1/KCNJ1 (PubMed:15137031). Belongs to the short scorpion toxin superfamily. Potassium channel inhibitor family. Gamma-KTx 2 subfamily. Has been classified as a gamma-KTx toxin due to its molecular target (Kv11/ERG), but may be classified as an alpha-KTx since it shares a high level of homology in both primary and 3D structures with other alpha-KTx scorpion toxins. However, it is noteworthy that surface by which BeKm-1 interacts with ERG1 is formed by residues located in the alpha-helix and the following loop, while the traditional functional site of other alpha-KTxs is formed by residues on the beta-sheet. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis. Belongs to the YciB family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be a menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 49 kDa subunit family. +a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) Belongs to the AB hydrolase superfamily. Lipase family. +Botulinum toxin causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of the eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure (PubMed:15394302, PubMed:7578132). Precursor of botulinum neurotoxin A which has 2 coreceptors; complex polysialylated gangliosides found on neural tissue and specific membrane-anchored proteins of synaptic vesicles. Receptor proteins are exposed on host presynaptic cell membrane during neurotransmitter release, when the toxin heavy chain (HC) binds to them. Upon synaptic vesicle recycling the toxin is taken up via the endocytic pathway. When the pH of the toxin-containing endosome drops a structural rearrangement occurs so that the N-terminus of the HC forms pores that allows the light chain (LC) to translocate into the cytosol (PubMed:17666397, PubMed:19096517). Once in the cytosol the disulfide bond linking the 2 subunits is reduced and LC cleaves its target protein on synaptic vesicles, preventing their fusion with the cytoplasmic membrane and thus neurotransmitter release. Toxin activity requires polysialylated gangliosides; GT1b supports activity better than GD1a (PubMed:12089155). Binds to host peripheral neuronal presynaptic membranes via the synaptic vesicle glycoproteins SV2A, SV2B and SV2C (PubMed:16543415). It binds directly to the largest lumenal (intravesicular) loop of SV2A, SV2B and SV2C that is transiently exposed outside of cells during exocytosis; gangliosides enhance binding (PubMed:16543415, PubMed:16545378, PubMed:18815274). Recognizes an N-linked glycan on SV2 proteins (PubMed:18815274, PubMed:27294781). May also use FGFR3 as a receptor (PubMed:23696738). Toxin uptake into neural cells requires stimulation (incubation with K(+) to stimulate receptor exposure) to be internalized by receptor-mediated endocytosis (PubMed:16543415, PubMed:19650874, PubMed:21632541, PubMed:21832053). Subsequently the toxin colocalizes with its receptor in host cells (PubMed:16543415, PubMed:19650874). Toxin uptake can be blocked by the appropriate SV2 protein fragments in cell culture (PubMed:16543415). Has proteolytic activity (PubMed:7578132). After translocation into the eukaryotic host cytosol LC hydrolyzes the '197-Gln-|-Arg-198' bond in SNAP25, blocking neurotransmitter release (PubMed:8243676, PubMed:7578132, PubMed:9886085, PubMed:10694409, PubMed:11700044, PubMed:11827515, PubMed:19351593). Recognizes the '146-Met--Gly-155' region of SNAP25, which confers substrate specificity (PubMed:9886085, PubMed:15592454). Hydrolyzes the '202-Thr-|-Arg-203' bond of mouse SNAP23, but not in human which has a different sequence (PubMed:9886085). Reduction of the interchain disulfide bond occurs in the host cytosol and probably prevents retrotranslocation into the synaptic vesicle (PubMed:17666397). Has slow (occurs over 4 weeks) autocatalytic cleavage, however it is not clear if this is physiologically relevant (PubMed:11565902). Responsible for host epithelial cell transcytosis, host nerve cell targeting and translocation of botulinum neurotoxin A light chain (LC) into host cytosol. Composed of 3 subdomains; the translocation domain (TD), and N-terminus and C-terminus of the receptor-binding domain (RBD) (PubMed:19096517). The RBD is responsible for binding to host epithelial cells and transcytosis across them; this uses different receptors than those on nerve cells (PubMed:21106906). RBD is also responsible for adherence of toxin to host nerve cell surface; HC alone prevents uptake of whole toxin by neural cells, and delays paralysis onset by 75% (PubMed:6694738, PubMed:10413679). Isolated RBD also delays paralysis onset (PubMed:21106906). The N-terminus of the RBD binds to phosphatidylinositol, which might play a role in membrane-binding (PubMed:19161982). Binds to host protein receptor synaptic vesicle glycoproteins SV2A, SV2B and SV2C via lumenal loop 4 (PubMed:16545378, PubMed:6370252, PubMed:27294781, PubMed:24240280, PubMed:19650874, PubMed:27313224). Binding can be inhibited by protein fragments from either the HC or SV2C (PubMed:24240280). Isolated HC significantly decreases uptake and toxicity of whole BoNT/A, but also interferes with uptake of BoNT/E and to a lesser extent BoNT/F (PubMed:19650874). The RBD recognizes the N-linked glycan on 'Asn-559' of SV2A, SV2B and SV2C; hydrogen-bonding occurs via 10 well-defined water molecules and stacking of hydrophobic residues (PubMed:27294781). Binds one host GT1b ganglioside, which serves as a coreceptor (PubMed:14731268, PubMed:18704164, PubMed:27958736). Modeling shows the HC can bind both coreceptors (a ganglioside and SV2 protein) simultaneously at different sites (PubMed:24240280). Crystals of the RBD with a GT1b analog can be grown at pH 5.5, indicating the toxin-ganglioside complex could be stable within the endosome (PubMed:18704164). Isolated RBD binds NTNHA (a bacterial protein that protects toxin) with high affinity at pH 6.0 but not at pH 7.5 (PubMed:22363010). The N-terminal belt (residues 449-545) wraps around the perimeter of the LC, probably protecting Zn(2+) in the active site; it is not required for channel formation by the TD domain but may serve to prevent premature LC dissociation from the translocation channel and to protect toxin prior to translocation (PubMed:22158863, PubMed:17907800, PubMed:19351593). The isolated TD forms transmembrane channels of about 15 Angstroms in the absence of a pH gradient; LC translocation requires a pH and redox gradient (pH 5.0/oxidizing in the cis compartment, pH 7.0/reducing in the trans compartment), LC does not unfold unless the cis pH is 6.0 or less (PubMed:2446925, PubMed:17666397, PubMed:19096517). Pores are presumably made by 1-2 toxin molecules (PubMed:23471747). While interaction with the RBD modulates the pH threshold for membrane insertion, the RBD is not essential for toxin degradation of SNAP25 in neural cells (PubMed:19096517). Limited hydrolysis of proteins of the neuroexocytosis apparatus, synaptobrevins, SNAP25 or syntaxin. No detected action on small molecule substrates. Binds 1 zinc ion per subunit (PubMed:1429690, PubMed:11700044, PubMed:15592454, PubMed:19351593, PubMed:22363010). Toxin internalization is inhibited by azide or dinitrophenol or at 4 degrees Celsius (PubMed:6694738). Dynamin (DNM) inhibitors abolish toxin uptake (PubMed:21832053). kcat is 140 min(-1) (PubMed:10694409). kcat is 1026 (-1) (PubMed:11827515). Heterodimer; disulfide-linked heterodimer of a light chain (LC) and heavy chain (HC) (PubMed:7578132). Interacts with glycosylated host synaptic vesicle glycoproteins SV2A, SV2B and SV2C which serve as coreceptors (PubMed:16543415, PubMed:18815274, PubMed:19650874, PubMed:24240280, PubMed:27313224). Glycosylation of 'Asn-559' in SV2C contributes a 12-fold increase in affinity to this interaction (PubMed:27313224). Depolarization of target tissue with high levels of K(+) leads to greater levels of receptor exposure (PubMed:16543415). In vitro addition of gangliosides increases SV2-toxin interaction (PubMed:16543415). Forms a highly interlocked heterodimer with NTNHA at pH 6.0 but not at pH 7.5 called the minimally functional progenitor toxin complex (M-PTC) (PubMed:22363010). The PTC is thought to protect toxin in the host acidic gastrointestinal tract, facilitate transcytosis across the intestinal barrier and release at neutral pH as is found in the bloodstream (PubMed:22363010). Whole toxin may be released from the bacteria during cell wall exfoliation (PubMed:7592120). There are estimated to be 150-500 toxin molecules per um(2) of non-myelinated mouse hemidiaphragm nerve membrane (PubMed:6694738). In mouse hemidiaphragm binds only to nerve terminals, and not to muscle, blood vessels, connective tissue Schwann cells or myelin, toxin can be internalized by this preparation (PubMed:6694738). Whole toxin may be released from the bacteria during cell wall exfoliation (PubMed:7592120). Colocalizes with its receptor SV2C (synaptic vesicle glycoprotein 2C) and VGAT (vesicular inhibitory amino acid transporter) in neurons (PubMed:24240280). In neurons HC colocalizes with synaptophysin or VAMP2 probably in synaptic vesicles, a portion also colocalizes with RAB5 and may be in synaptic vesicle protein sorting endosomes (PubMed:21632541, PubMed:21832053). Therefore there may be more than one uptake pathway at nerve terminals. Uptake of HC and whole toxin is slowed by dynamin inhibitors (PubMed:21832053). 1-2 molecules of HC are found in the host synaptic vesicle lumen, uptake and subsequent release of LC is very rapid (PubMed:21832053, PubMed:23471747). In cultured bacteria, first detected in late exponential growth (17 hours), reaches maximal levels at 24-25 hours and remains nearly constant for 5 days (at protein level). Has protease activity (PubMed:7578132). Has 3 functional domains; the translocation domain (TD) and the receptor-binding domain (RBD) which is further subdivided into N- and C-terminal domains (N-RBD and C-RBD). Upon trypsin digestion the isolated TD forms channels in bilayers when the cis side is acidic/oxidizing and the trans side is pH 7.0/reducing (PubMed:2446925, PubMed:17666397, PubMed:19096517). The RBD rotates 140 degrees around the TD in the presence of NTNHA (PubMed:22363010). The 3 major domains each serve as a chaperone for the other 2 to ensure they act only in the correct host cell context (PubMed:19096517). In BoNT/A structures the LC is separated from the RBD by the TD; the belt wraps around the perimeter of the LC, protecting Zn(2+) in the active site (PubMed:18032388, PubMed:19351593, PubMed:22363010). The belt region (449-545) may be a pseudosubstrate inhibitor which serves as an intramolecular chaperone for the LC prior to its translocation into the host cytosol (PubMed:17907800). In a bacterial culture the precursor chain is initally cleaved on the amino side of Gly-445 and is processed more slowly between Lys-448 and Ala-449 to give the final mature heavy chain sequence. Has slow autocatalytic activity, cleaves 250-Tyr-Tyr-251, 266-Phe-Gly-267, 419-Phe-Thr-420, 423-Phe-Glu-424, 430-Cys-Val-431, 432-Arg-Gly-433, 438-Lys-Thr-439, and probably 429-Leu-Cys-430 over a period of 4 weeks. Catalysis of the '197-Gln-|-Arg-198' bond in SNAP25 is estimated to be 10(5) more efficient than autocatalysis, leaving the physiological importance of autocatalysis in doubt (PubMed:11565902). Ubiquitinated by host HECD2. Deubiquitination by host VCPIP1 prevents degradation by the proteasome. Dynamin inhibitors slow toxin uptake by nerve cells, and might be used to prolong the treatment window for antitoxins. Replacement of the RBD by other proteins (such as wheat germ agglutinin) allows the rest of the toxin to be taken up by other cell types, and can be used for investigating synaptic vesicle docking-dependent processes in BoNT resistant cells (PubMed:10768948). LC retains protease activity (PubMed:10768948, PubMed:19351593). Isolated receptor-binding domain (RBD) can be used as a vaccine; a mutated form that is transcytosed into the general circulation but does not enter nerve cells (Leu-1266-1267-Ser) is as efficient as wild-type RBD (PubMed:21106906). Available under the name Botox (onabotulinumtoxinA, Allergan), Dysport (abobotulinumtoxinA, Ipsen Biopharmaceuticals) and Xeomin (incobotulinumtoxinA, Merz Pharmaceuticals) for the treatment of strabismus and blepharospasm associated with dystonia and cervical dystonia. Also used for the treatment of hemifacial spasm and a number of other neurological disorders characterized by abnormal muscle contraction. It is also used cosmetically to smooth facial wrinkles. There are seven antigenically distinct forms of botulinum neurotoxin: Types A, B, C, D, E, F, and G; new subtypes are quite frequent. Types A, B and E are the most frequent cause of adult human foodborne botulism; type A is the most severe, while type E has the shortest incubation period (PubMed:1431246). Neurotoxin type A is released from bacteria in the two-chain form (PubMed:6370252, PubMed:2126206). Botulism poisoning is usually food-borne, either by ingesting toxin or bacterial-contaminated food, or less frequently by inhalation poisoning. In both cases the neurotoxin binds to the apical surface of epithelial cells in the gut or airway. Toxin undergoes receptor-mediated endocytosis (using a different receptor than on target nerve cells), transcytosis across the epithelial cells and release into the general circulation. Once in the general circulation it binds to its target cells. Belongs to the peptidase M27 family. Contradictory results show that only SV2C is the receptor; in these experiments gangliosides do not improve toxin-coreceptor interaction (PubMed:16545378). From sausages to wrinkles - Issue 19 of February 2002 +Belongs to the HHV-5 UL15A protein family. +Transcription factor that binds to the DNA sequence 5'-AACAAT-3' (By similarity). Acts as a transcriptional activator (By similarity). Plays a role together with nlk in neural induction during early embryogenesis (By similarity). Interacts with nlk. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Belongs to the universal ribosomal protein uL30 family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Complex I is composed of 45 different subunits. Contains two C-X9-C motifs that are predicted to form a helix-coil-helix structure, permitting the formation of intramolecular disulfide bonds. Belongs to the complex I NDUFB7 subunit family. +Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress. These functions might be dependent on each isozyme/isoform in each plant tissue. 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit. Binds 2 calcium ions per subunit. There are 73 peroxidase genes in A.thaliana. Belongs to the peroxidase family. Classical plant (class III) peroxidase subfamily. +Hydrolyzes ureidoacrylate to form aminoacrylate and carbamate. The carbamate hydrolyzes spontaneously, thereby releasing one of the nitrogen atoms of the pyrimidine ring as ammonia and one of its carbon atoms as CO2. (Z)-3-ureidoacrylate + H(+) + H2O = (Z)-3-aminoacrylate + CO2 + NH4(+) (Z)-3-ureidoacrylate + H2O = (Z)-3-aminoacrylate + carbamate + H(+) (Z)-2-methylureidoacrylate + H(+) + H2O = (Z)-2-methylaminoacrylate + CO2 + NH4(+) Up-regulated by the nitrogen regulatory protein C (NtrC also called GlnG) and repressed by RutR. Belongs to the isochorismatase family. RutB subfamily. +Essential for recycling GMP and indirectly, cGMP. ATP + GMP = ADP + GDP Belongs to the guanylate kinase family. +GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Toroid-shaped homodecamer, composed of two pentamers of five dimers. Belongs to the GTP cyclohydrolase I family. +DNA-binding transcription regulator that regulates endothelial cell proliferation and G1/S cell-cycle progression. Specifically binds the 5'-[AT]NTNN[GT]GGCA[AGT]-3' core DNA sequence and acts by modulating expression of pRB-E2F cell-cycle target genes (By similarity). Belongs to the THAP1 family. +a quinone + H(+) + NADH = a quinol + NAD(+) a quinone + H(+) + NADPH = a quinol + NADP(+) Binds 1 FMN per monomer. Belongs to the WrbA family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP). (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate Cofactor biosynthesis; molybdopterin biosynthesis. Homohexamer; trimer of dimers. Belongs to the MoaC family. +Part of an ATP-dependent transport system LolCDE responsible for the release of lipoproteins targeted to the outer membrane from the inner membrane. Such a release is dependent of the sorting-signal (absence of an Asp at position 2 of the mature lipoprotein) and of LolA (By similarity). Belongs to the ABC-4 integral membrane protein family. LolC/E subfamily. +FMRFamides and FMRFamide-like peptides are neuropeptides. Belongs to the FARP (FMRF amide related peptide) family. +May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine. H2O + S-adenosyl-L-homocysteine = adenosine + L-homocysteine Binds 1 NAD(+) per subunit. Amino-acid biosynthesis; L-homocysteine biosynthesis; L-homocysteine from S-adenosyl-L-homocysteine: step 1/1. Belongs to the adenosylhomocysteinase family. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK (By similarity). Homohexamer. The oligomerization is ATP-dependent (By similarity). The N-terminal domain probably functions as a substrate-discriminating domain, recruiting aggregated proteins to the ClpB hexamer and/or stabilizing bound proteins. The NBD2 domain is responsible for oligomerization, whereas the NBD1 domain stabilizes the hexamer probably in an ATP-dependent manner. The movement of the coiled-coil domain is essential for ClpB ability to rescue proteins from an aggregated state, probably by pulling apart large aggregated proteins, which are bound between the coiled-coils motifs of adjacent ClpB subunits in the functional hexamer (By similarity). Belongs to the ClpA/ClpB family. +Ring cyclization and eight-electron oxidation of 3a-(2-amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline-7,9-dicarboxylic-acid to PQQ. 6-(2-amino-2-carboxyethyl)-7,8-dioxo-1,2,3,4,7,8-hexahydroquinoline-2,4-dicarboxylate + 3 O2 = H(+) + 2 H2O + 2 H2O2 + pyrroloquinoline quinone Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. Belongs to the PqqC family. +Together with LptD, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Required for the proper assembly of LptD. Binds LPS and may serve as the LPS recognition site at the outer membrane. Component of the lipopolysaccharide transport and assembly complex. Interacts with LptD. Belongs to the LptE lipoprotein family. +Catalyzes the decarboxylation of oxaloacetate into pyruvate. Seems to play a role in maintaining cellular concentrations of bicarbonate and pyruvate. H(+) + oxaloacetate = CO2 + pyruvate Binds 1 Mg(2+) ion per subunit. Homotetramer; dimer of dimers. Belongs to the isocitrate lyase/PEP mutase superfamily. Oxaloacetate decarboxylase family. +di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP Belongs to the glycosyltransferase 4 family. MraY subfamily. +Catalyzes an oxidative deamination of predominantly hydrophobic and aromatic L-amino acids, thus producing hydrogen peroxide that may contribute to the diverse toxic effects of this enzyme. Exhibits diverse biological activities, such as hemorrhage, hemolysis, edema, apoptosis of vascular endothelial cells or tumor cell lines, antibacterial and antiparasitic activities, as well as regulation of platelet aggregation. Effects of snake L-amino oxidases on platelets are controversial, since they either induce aggregation or inhibit agonist-induced aggregation. These different effects are probably due to different experimental conditions. an L-alpha-amino acid + H2O + O2 = a 2-oxocarboxylate + H2O2 + NH4(+) Homodimer; non-covalently linked. Expressed by the venom gland. Contains 2 disulfide bonds. N-glycosylated. Belongs to the flavin monoamine oxidase family. FIG1 subfamily. +Belongs to the universal ribosomal protein uS2 family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln). Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by MOCS3. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Also acts as a ubiquitin-like protein (UBL) that is covalently conjugated via an isopeptide bond to lysine residues of target proteins such as Jafrac1, Ciao1, Eip71CD and GILT1. The thiocarboxylated form serves as substrate for conjugation and oxidative stress specifically induces the formation of UBL-protein conjugates. tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis. Interacts with cer. C-terminal thiocarboxylation occurs in 2 steps, it is first acyl-adenylated (-COAMP) via the hesA/moeB/thiF part of the MOCS3 homolog, then thiocarboxylated (-COSH) via the rhodanese domain of the MOCS3 homolog. Belongs to the URM1 family. +Catalyzes the transfer of the acetyl group from acetyl coenzyme A to the free amino group of arylamines and hydrazines. Is able to utilize not only acetyl-CoA, but also n-propionyl-CoA and acetoacetyl-CoA as acyl donors, although at a lower rate. As acetyl-CoA and propionyl-CoA are products of cholesterol catabolism and the nat gene is likely present in the same operon than genes involved in cholesterol degradation, this enzyme could have a role in the utilization and regulation of these CoA species. acetyl-CoA + an arylamine = an N-acetylarylamine + CoA Homodimer and homotetramer. Belongs to the arylamine N-acetyltransferase family. +May function as a molecular transmitter linking various signaling pathways to transcriptional regulation. Negatively regulates the transcriptional repressor E4F1 and may function in cell growth. Inhibits the transcriptional activity of FOXO1 and its apoptotic function by enhancing the interaction of FOXO1 with SIRT1 and FOXO1 deacetylation (By similarity). Negatively regulates the calcineurin/NFAT signaling pathway in cardiomyocytes (PubMed:22851699). Interacts with ZNF638 and TTN/titin. Interacts with E4F1. Interacts with GRB7. Interacts with SIRT1 and FOXO1. Interacts with CEFIP (By similarity). Interacts with calcineurin (PubMed:22851699). Interacts with FOXK1 (PubMed:20013826). Highly expressed in heart but also detectable in brain and skeletal muscle. Up-regulated in hearts exposed to isoproterenol (at protein level). The third LIM zinc-binding mediates interaction with E4F1. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Required for neuronal survival during early development. Does not interact with CTNNB1. Expressed very early in development. Expression levels drop until shield stage and increase again during gastrulation and later development. Expressed abundantly in the developing brain, and at lower levels throughout the embryo. Belongs to the CTNNBIP1 family. +Folate-binding protein involved in regulating the level of ATP-DnaA and in the modification of some tRNAs. It is probably a key factor in regulatory networks that act via tRNA modification, such as initiation of chromosomal replication. Belongs to the tRNA-modifying YgfZ family. +2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + ADP + H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole from N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide: step 2/2. Belongs to the AIR synthase family. +Receptor for parathyroid hormone and for parathyroid hormone-related peptide. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase and also a phosphatidylinositol-calcium second messenger system. Interacts (via N-terminal extracellular domain) with PTHLH and PTH (PubMed:8688470). Homodimer in the absence of bound ligand. Peptide hormone binding leads to dissociation of the homodimer (By similarity). N-glycosylated. Belongs to the G-protein coupled receptor 2 family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +Belongs to the UPF0125 (RnfH) family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Methylated by PrmB. Belongs to the universal ribosomal protein uL3 family. +Involved in chemotaxis. Part of a chemotaxis signal transduction system that modulates chemotaxis in response to various stimuli. Catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins or MCP) by CheR. Also mediates the irreversible deamidation of specific glutamine residues to glutamic acid. [protein]-L-glutamate 5-O-methyl ester + H2O = H(+) + L-glutamyl-[protein] + methanol H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Contains a C-terminal catalytic domain, and an N-terminal region which modulates catalytic activity. Phosphorylated by CheA. Phosphorylation of the N-terminal regulatory domain activates the methylesterase activity. Belongs to the CheB family. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP = 7,8-dihydrofolate + dTMP Pyrimidine metabolism; dTTP biosynthesis. Homodimer. Belongs to the thymidylate synthase family. Bacterial-type ThyA subfamily. +Trans-acting factor that binds to glucocorticoid modulatory elements (GME) present in the TAT (tyrosine aminotransferase) promoter and increases sensitivity to low concentrations of glucocorticoids. Binds also to the transferrin receptor promoter. Essential auxiliary factor for the replication of parvoviruses. Homodimer, and heterodimer of GMEB1 and GMEB2. GMEB1 and GMEB2 form the parvovirus initiator complex (PIF). Interacts with the glucocorticoid receptor (NR3C1) and NCOA2/TIF2 (By similarity). May interact with HSP27 and CREB-binding protein (CBP). May be also cytoplasmic. +Catalyzes the final step of fatty acid oxidation in which acetyl-CoA is released and the CoA ester of a fatty acid two carbons shorter is formed. acetyl-CoA + an acyl-CoA = a 3-oxoacyl-CoA + CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadB) and two beta chains (FadA). Belongs to the thiolase-like superfamily. Thiolase family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Belongs to the UPF0336 family. +Nucleotidyltransferase involved in N-glycan biosynthetic pathway that takes place under low-salt conditions (1.75 M instead of 3.4 M). Participates in the formation of the tetrasaccharide present at 'Asn-532' of S-layer glycoprotein Csg, consisting of a sulfated hexose, 2 hexoses and rhamnose. Involved in the addition of final rhamnose (sugar 4) of the tetrasaccharide on the dolichol phosphate carrier. Binds 1 Mg(2+) ion per subunit. Protein modification; protein glycosylation. Cell surface structure biogenesis; S-layer biogenesis. Impaired formation of the tetrasaccharide present at 'Asn-532' of S-layer glycoprotein Csg. No effect on 'Asn-47' and 'Asn-117' glycosylation of S-layer glycoprotein Csg. Belongs to the glucose-1-phosphate thymidylyltransferase family. +Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of cognate toxin Rv2653c. +Atypical chemokine receptor that controls chemokine levels and localization via high-affinity chemokine binding that is uncoupled from classic ligand-driven signal transduction cascades, resulting instead in chemokine sequestration, degradation, or transcytosis. Also known as interceptor (internalizing receptor) or chemokine-scavenging receptor or chemokine decoy receptor. Has a promiscuous chemokine-binding profile, interacting with inflammatory chemokines of both the CXC and the CC subfamilies but not with homeostatic chemokines. Acts as a receptor for chemokines including CCL2, CCL5, CCL7, CCL11, CCL13, CCL14, CCL17, CXCL5, CXCL6, IL8/CXCL8, CXCL11, GRO, RANTES, MCP-1 and TARC. May regulate chemokine bioavailability and, consequently, leukocyte recruitment through two distinct mechanisms: when expressed in endothelial cells, it sustains the abluminal to luminal transcytosis of tissue-derived chemokines and their subsequent presentation to circulating leukocytes; when expressed in erythrocytes, serves as blood reservoir of cognate chemokines but also as a chemokine sink, buffering potential surges in plasma chemokine levels (By similarity). Predominantly localizes to endocytic vesicles, and upon stimulation by the ligand is internalized via caveolae. Once internalized, the ligand dissociates from the receptor, and is targeted to degradation while the receptor is recycled back to the cell membrane (By similarity). Belongs to the G-protein coupled receptor 1 family. Atypical chemokine receptor subfamily. +Required for growth and/or survival at acidic conditions. Proteolytic processing gives rise to the active protein. Belongs to the Asr family. +Catalyzes the reversible cleavage of L-rhamnulose-1-phosphate to dihydroxyacetone phosphate (DHAP) and L-lactaldehyde. L-rhamnulose 1-phosphate = (S)-lactaldehyde + dihydroxyacetone phosphate Binds 1 zinc ion per subunit. Carbohydrate degradation; L-rhamnose degradation; glycerone phosphate from L-rhamnose: step 3/3. Homotetramer. Belongs to the aldolase class II family. RhaD subfamily. +Binds to actin on the surface of endothelial cells; once bound, angiogenin is endocytosed and translocated to the nucleus. Stimulates ribosomal RNA synthesis including that containing the initiation site sequences of 45S rRNA. Cleaves tRNA within anticodon loops to produce tRNA-derived stress-induced fragments (tiRNAs) which inhibit protein synthesis and triggers the assembly of stress granules (SGs) (By similarity). Angiogenin induces vascularization of normal and malignant tissues. Angiogenic activity is regulated by interaction with RNH1 in vivo (By similarity). Homodimer. Interacts with and forms a tight 1:1 complex with RNH1. Dimerization of two such complexes may occur (By similarity). Rapidly endocytosed by target cells and translocated to the nucleus where it accumulates in the nucleolus and binds to DNA (By similarity). Belongs to the pancreatic ribonuclease family. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Serine/threonine-protein phosphatase that possesses phosphatase activity toward para-nitrophenyl phosphate (pNPP) in vitro. H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 manganese ions per subunit. Phosphatase activity is strongly reduced by the protein phosphatase inhibitor 2 (I-2). Expressed in roots, rosettes and flowers. Belongs to the PPP phosphatase family. PP-1 subfamily. +Belongs to the orthopoxviruses A37.5 protein family. +Belongs to the UPF0340 family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins (By similarity). Necessary for invasion of epithelial cells, secretion of invasion proteins and proliferation within macrophages. Binds 2 Zn(2+) ions per monomer. Homodimer. By heat shock under the control of the HtpR regulatory protein. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Part of the binding-protein-dependent transport system for oligopeptides; probably responsible for the translocation of the substrate across the membrane. Belongs to the binding-protein-dependent transport system permease family. OppBC subfamily. +Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Component of the 19S regulatory particle (RP/PA700) base subcomplex of the 26S proteasome. The 26S proteasome is composed of a core protease (CP), known as the 20S proteasome, capped at one or both ends by the 19S regulatory particle (RP/PA700). The RP/PA700 complex is composed of at least 17 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and distal to the 20S proteolytic core, respectively. Belongs to the proteasome subunit S1 family. +Nuclear serine protease which mediates apoptosis. Belongs to the peptidase S1C family. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine. L-leucyl-tRNA(Leu) + N-terminal L-lysyl-[protein] = H(+) + N-terminal L-leucyl-L-lysyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-arginyl-[protein] = H(+) + N-terminal L-leucyl-L-arginyl-[protein] + tRNA(Leu) an N-terminal L-alpha-aminoacyl-[protein] + L-phenylalanyl-tRNA(Phe) = an N-terminal L-phenylalanyl-L-alpha-aminoacyl-[protein] + tRNA(Phe) Belongs to the L/F-transferase family. +Does not interact with IDM1. Not regulated by heat. Belongs to the small heat shock protein (HSP20) family. +Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for photo-induced movements. Phosphorylates BLUS1, a kinase involved in stomatal opening. Mediates calcium spiking of extra- and intracellular origins in response to blue light. Involved in hypocotyl phototropism. Contributes to the chloroplast accumulation in low blue light and mediates their translocation (avoidance response) at high fluence. Regulates stomata opening and photomorphogenesis response of leaf tissue. Not involved in hypocotyl elongation inhibition, anthocyanin accumulation or cotyledon opening. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Binds 2 FMN per subunit. Exhibits a smaller absorbance peak at 350 nm. The broad fluorescence emission spectrum peaks at 490 nm. Homodimer. Interacts with PKS1, PKS2, RPT3 and PHOT1. Expressed in leaves, stems and flowers, and to a lower extent in roots. Light fluence rate-dependent induction, independent of light quality. The activation loop within the kinase domain is the target of phosphorylation (By similarity). The PAS (PER-ARNT-SIM) domains are required for the binding of FMN chromophores. Autophosphorylated in response to blue light irradiation. 2 molecules of FMN bind covalently to cysteines after exposure to blue light and are reversed in the dark. Undergoes a photocycle characterized by fluorescence and absorption changes induced by blue light. Half-time of photoproduct formation is 11 seconds and 15 seconds for dark regeneration. May be due to a competing acceptor splice site. Belongs to the protein kinase superfamily. AGC Ser/Thr protein kinase family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a(1), b(1), b'(1) and c(9-12). Belongs to the ATPase alpha/beta chains family. +Regulates arginine biosynthesis genes. Amino-acid biosynthesis; L-arginine biosynthesis [regulation]. Belongs to the ArgR family. +Catalytic subunit of the tagatose-1,6-bisphosphate aldolase GatYZ, which catalyzes the reversible aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to produce tagatose 1,6-bisphosphate (TBP). Requires GatZ subunit for full activity and stability. Is involved in the catabolism of galactitol. D-tagatofuranose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate Binds 1 zinc ion per subunit. Carbohydrate metabolism; D-tagatose 6-phosphate degradation; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-tagatose 6-phosphate: step 2/2. Forms a complex with GatZ. Belongs to the class II fructose-bisphosphate aldolase family. TagBP aldolase GatY subfamily. +Probably catalyzes the hydrolysis of L-ascorbate-6-P into 3-keto-L-gulonate-6-P. Is essential for L-ascorbate utilization under anaerobic conditions. H2O + L-ascorbate 6-phosphate = 3-dehydro-L-gulonate 6-phosphate Cofactor degradation; L-ascorbate degradation; D-xylulose 5-phosphate from L-ascorbate: step 1/4. Induced by L-ascorbate. Repressed by UlaR. Belongs to the UlaG family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved. Distribution is 50-50. Belongs to the SecA family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways. AMP + ATP = 2 ADP Monomer. Predominantly mitochondrial. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. AK2 subfamily. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +Belongs to the UPF0145 family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in the mitochondria. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Subunit of the heterotrimeric GatCAB amidotransferase (AdT) complex, composed of A, B and C subunits. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the GatC family. +Belongs to the ycf15 family. Could be the product of a pseudogene. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Component of the PELP1 complex involved in the nucleolar steps of 28S rRNA maturation and the subsequent nucleoplasmic transit of the pre-60S ribosomal subunit. Component of some MLL1/MLL complex. Component of the PELP1 complex, composed of at least PELP1, TEX10 and WDR18. The complex interacts with pre-60S ribosome particles. Belongs to the IPI1/TEX10 family. +Catalyzes the ferrous insertion into protoporphyrin IX. 2 H(+) + heme b = Fe(2+) + protoporphyrin IX Porphyrin-containing compound metabolism; protoheme biosynthesis; protoheme from protoporphyrin-IX: step 1/1. Belongs to the ferrochelatase family. +Overexpressed in acid environments. +Required for nuclear protein import and mediates docking of import substrate to distinct nucleoporins. Serves a receptor for nuclear localization signals. Mediates the nuclear import of TATA-binding protein (TBP) and of histones H2A and H2B (By similarity). +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Part of the ABC transporter complex TauABC involved in taurine import. Responsible for energy coupling to the transport system. ATP + H2O + taurine(out) = ADP + H(+) + phosphate + taurine(in) The complex is composed of two ATP-binding proteins (TauB), two transmembrane proteins (TauC) and a solute-binding protein (TauA). Belongs to the ABC transporter superfamily. Taurine importer (TC 3.A.1.17.1) family. +An FAD assembly protein, which accelerates covalent attachment of the cofactor into other proteins. Plays an essential role in the assembly of succinate dehydrogenase (SDH, respiratory complex II), an enzyme complex that is a component of both the tricarboxylic acid cycle and the electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. Required for flavinylation (covalent attachment of FAD) of the flavoprotein subunit SdhA of SDH and other flavinylated proteins as well. Belongs to the SdhE FAD assembly factor family. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner. ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) Monomer. ValRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated threonine is translocated from the active site to the editing site. The C-terminal coiled-coil domain is crucial for aminoacylation activity. Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily. +May be involved in recombination. Belongs to the RdgC family. +ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon (By similarity). ATP + H2O = ADP + H(+) + phosphate eIF4F is a multi-subunit complex, the composition of which varies with external and internal environmental conditions. It is composed of at least EIF4A, EIF4E and EIF4G (By similarity). Interacts with DRM2 (via UBA domains) (PubMed:23732981). Localizes to the nucleus when interacting with DRM2. The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis. Belongs to the DEAD box helicase family. eIF4A subfamily. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor. (S)-dihydroorotate + a quinone = a quinol + orotate Binds 1 FMN per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (quinone route): step 1/1. Monomer. Belongs to the dihydroorotate dehydrogenase family. Type 2 subfamily. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +This protein is required for primosome-dependent normal DNA replication; it is also involved in inducing stable DNA replication during SOS response. It forms, in concert with DnaB protein and other prepriming proteins DnaC, N, N', N'' a prepriming protein complex on the specific site of the template DNA recognized by protein N'. Belongs to the DnaT family. +Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA). NADP(+) + shikimate = 3-dehydroshikimate + H(+) + NADPH Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 4/7. Homodimer. Belongs to the shikimate dehydrogenase family. +Orphan nuclear receptor. Belongs to the nuclear hormone receptor family. +Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. This protein is an E3 ubiquitin ligase that interferes with host's ubiquitination pathway. Can ubiquitinate both ubiquitin and host TXN (thioredoxin). Leads to significant decrease of thioredoxin activity and increase of host cell death. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Interacts with host TXN. Secreted via type III secretion systems 1 and 2 (SPI-1 and SPI-2 TTSS), and delivered into the host cytoplasm. The LRR (leucine-rich repeat) domain forms a slightly curved solenoid and may mediate interaction with target proteins. Ubiquitinated in the presence of host E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme and ubiquitin. Belongs to the LRR-containing bacterial E3 ligase family. +Probable exonuclease that may be involved in enuclation of sieve elements. A number of isoforms are produced. Regulated by the transcription factors NAC045 and NAC086. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Has a neutrophil chemotactic activity. Also a positive regulator of chondrocyte proliferation (PubMed:9524238). Does not show metalloendopeptidase activity (PubMed:27334921). Interacts with MET. Highly expressed in adult and fetal liver and weakly in testis. Not expressed in bone marrow. By phytohemagglutinin (PHA). Belongs to the LECT2/MIM-1 family. +E3 ubiquitin-protein ligase that specifically binds poly-ADP-ribosylated proteins and mediates their ubiquitination and subsequent degradation. May regulate many important biological processes, such as cell survival and DNA damage response. Acts as an activator of the Wnt signaling pathway by mediating the ubiquitination of poly-ADP-ribosylated proteins. Neuroprotective protein. Protects against cell death induced by DNA damaging agents and rescues cells from G1 arrest. Promotes cell survival after gamma-irradiation. Facilitates DNA repair. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Translocates to the nucleus after DNA damage. The WWE domain mediates non-covalent poly(ADP-ribose)-binding. +Cell wall formation. ATP + L-alanine + UDP-N-acetyl-alpha-D-muramate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Belongs to the imidazoleglycerol-phosphate dehydratase family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Bacteriocin. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Involved in the morphogenesis of the adult appendages. GTPase-activating protein for p21-Rac. Promotes the exchange of Rac-bound GDP by GTP. In pupae, expressed in imaginal disks and only in the male gonad. In adults; isoform 1 is the predominant form in the testes and is expressed at a low level in the ovary and somatic tissues, and isoform 2 is very weakly expressed and is detectable solely in the testes. Expressed during spermatogenesis, in primary spermatocytes and imaginal disk morphogenesis. It is uncertain whether Met-1 or Met-23 is the initiator. +Mitochondrial outer membrane GTPase that mediates mitochondrial clustering and fusion (PubMed:12527753, PubMed:23921378, PubMed:24513856, PubMed:15297672). Membrane clustering requires GTPase activity (By similarity). It may involve a major rearrangement of the coiled coil domains (PubMed:15297672). Mitochondria are highly dynamic organelles, and their morphology is determined by the equilibrium between mitochondrial fusion and fission events (PubMed:12527753). Overexpression induces the formation of mitochondrial networks (in vitro). Has low GTPase activity (By similarity). GTP + H2O = GDP + H(+) + phosphate Homodimer, also in the absence of bound GTP (By similarity). Forms higher oligomers in the presence of a transition state GTP analog (By similarity). Forms homomultimers and heteromultimers with MFN2 (PubMed:12527753). Oligomerization is essential for mitochondrion fusion (PubMed:15297672). Component of a high molecular weight multiprotein complex (By similarity). Interacts with VAT1 (By similarity). Interacts with THG1L; THG1L probably functions as a guanyl-nucleotide exchange factor/GEF, activating MFN1. Detected in adult heart (PubMed:12759376). Detected in embryos (at protein level) (PubMed:12527753). Widely expressed (PubMed:11950885). Expressed in 8.5 dpc, 9.5 dpc, 10.5 dpc and 11.5 dpc embryos. A helix bundle is formed by helices from the N-terminal and the C-terminal part of the protein. The GTPase domain cannot be expressed by itself, without the helix bundle. Rearrangement of the helix bundle and/or of the coiled coil domains may bring membranes from adjacent mitochondria into close contact, and thereby play a role in mitochondrial fusion. Ubiquitinated by MARCHF5 (By similarity). When mitochondria are depolarized and dysfunctional, it is ubiquitinated by a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex that contains FBXO7 and PRKN. Ubiquitinated by non-degradative ubiquitin by PRKN, promoting mitochondrial fusion; deubiquitination by USP30 inhibits mitochondrial fusion (PubMed:24513856). Full embryonic lethality; nearly 90% of the mutant embryos have been resorbed at 11.5 dpc (PubMed:12527753). Contrary to wild-type embryonic fibroblasts that have elongated, tubular mitochondria, mutant embryonic fibroblasts contain only fragmented mitochondria (PubMed:12527753). In cultured cells, mutant mitochondria show a strongly decreased frequency of mitochondrial fusion events (PubMed:12527753). In spite of the aberrant mitochondrial morphology, there seem to be no gross defects in respiration (PubMed:12527753). Heart-specific disruption of Mfn1 does not impair heart function and has no effect on cardiomyocyte mitochondrial morphometry or respiratory function (PubMed:23620051). Belongs to the TRAFAC class dynamin-like GTPase superfamily. Dynamin/Fzo/YdjA family. Mitofusin subfamily. Extended N-terminus. Extended N-terminus. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +Belongs to the ABC-4 integral membrane protein family. +Necessary for efficient adipogenesis. Does not show ion channel activity. Belongs to the TMEM120 family. Truncated C-terminus. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine. H(+) + meso-2,6-diaminoheptanedioate = CO2 + L-lysine Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1. Homodimer. Belongs to the Orn/Lys/Arg decarboxylase class-II family. LysA subfamily. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. Belongs to the radical SAM superfamily. Lipoyl synthase family. +Na(+)/H(+) antiporter that extrudes sodium in exchange for external protons. 2 H(+)(out) + Na(+)(in) = 2 H(+)(in) + Na(+)(out) Belongs to the NhaA Na(+)/H(+) (TC 2.A.33) antiporter family. +Possibly a prophage capsid protein. Belongs to the encapsulin family. Family 3 subfamily. +May be involved in the regulation of growth and differentiation of liver cells. H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate Liver. Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily. +Component of the DNA-dependent RNA polymerase that catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit (By similarity). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Belongs to the RNA polymerase beta' chain family. +PhoP-regulated transcription is redox-sensitive, being activated when the periplasm becomes more reducing. MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway. Represses PhoP/PhoQ signaling, possibly by binding to the periplasmic domain of PhoQ, altering its activity and that of downstream effector PhoP. May form homooligomers. Probably interacts with the periplasmic domain of PhoQ. Belongs to the MgrB family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Involved in DNA mismatch repair and meiotic recombination processes. Facilitates crossovers between homologs during meiosis (By similarity). Heterooligomer of MSH4 and MSH5. Interacts with HJURP (By similarity). Belongs to the DNA mismatch repair MutS family. +Plays a role in viral genome replication by driving entry of quiescent cells into the cell cycle. Stimulation of progression from G1 to S phase allows the virus to efficiently use the cellular DNA replicating machinery to achieve viral genome replication. E7 protein has both transforming and trans-activating activities. Induces the disassembly of the E2F1 transcription factor from RB1, with subsequent transcriptional activation of E2F1-regulated S-phase genes. Interferes with host histone deacetylation mediated by HDAC1 and HDAC2, leading to transcription activation. Also plays a role in the inhibition of both antiviral and antiproliferative functions of host interferon alpha. Interaction with host TMEM173/STING impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta). Homodimer. Homooligomer. Interacts with host RB1; this interaction induces dissociation of RB1-E2F1 complex thereby disrupting RB1 activity. Interacts with host EP300; this interaction represses EP300 transcriptional activity. Interacts with protein E2; this interaction inhibits E7 oncogenic activity. Interacts with host TMEM173/STING; this interaction impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta). Predominantly found in the host nucleus. The E7 terminal domain is an intrinsically disordered domain, whose flexibility and conformational transitions confer target adaptability to the oncoprotein. It allows adaptation to a variety of protein targets and exposes the PEST degradation sequence that regulates its turnover in the cell. Highly phosphorylated. Belongs to the papillomaviridae E7 protein family. +Catalyzes the aminotransferase reaction from putrescine to 2-oxoglutarate, leading to glutamate and 4-aminobutanal, which spontaneously cyclizes to form 1-pyrroline. This is the first step in one of two pathways for putrescine degradation, where putrescine is converted into 4-aminobutanoate (gamma-aminobutyrate or GABA) via 4-aminobutanal. Also functions as a cadaverine transaminase in a a L-lysine degradation pathway to succinate that proceeds via cadaverine, glutarate and L-2-hydroxyglutarate. 2-oxoglutarate + an alkane-alpha,omega-diamine = an omega-aminoaldehyde + L-glutamate 2-oxoglutarate + putrescine = 1-pyrroline + H2O + L-glutamate 2-oxoglutarate + cadaverine = 5-aminopentanal + L-glutamate Amine and polyamine degradation; putrescine degradation; 4-aminobutanal from putrescine (transaminase route): step 1/1. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. Putrescine aminotransferase subfamily. +Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) with (2E,6E)-farnesyl diphosphate (E,E-FPP) to yield (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-undecaprenyl diphosphate (di-trans,octa-cis-UPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide. (2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = di-trans,octa-cis-undecaprenyl diphosphate + 8 diphosphate Binds 2 magnesium ions per subunit. Homodimer. Belongs to the UPP synthase family. +Transcription factor that binds to the site II motif (3'-TGGGCC/T-5') in the promoter of PCNA-2 and to 3'-GCCCG/A-5' elements in the promoters of cyclin CYCB1-1 and ribosomal protein genes. Interacts with PURA1 (PubMed:12631321). Interacts with SPL (PubMed:25527103). +Functions in xyloglucan synthesis by adding side chains to the xylosylated glucan backbone. Involved in the galactosylation of hemicellulose xyloglucan. Expressed in roots, hypocotyls, cotyledons, leaves, stems and sepals. Belongs to the glycosyltransferase 47 family. +Effector that enhances P.infestans colonization of Nicotiana benthamiana leaves. The RxLR-dEER motif acts to carry the protein into the host cell cytoplasm through binding to cell surface phosphatidylinositol-3-phosphate. Belongs to the RxLR effector family. +Belongs to the UPF0060 family. +Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins. Interacts with the Sec translocase complex via SecD. Specifically interacts with transmembrane segments of nascent integral membrane proteins during membrane integration. Belongs to the OXA1/ALB3/YidC family. Type 1 subfamily. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +Mu-conotoxins block voltage-gated sodium channels (Nav). This toxin inhibits tetrodotoxin(TTX)-sensitive sodium channels, but does not affect TTX-resistant sodium channels. Reduces the amplitude of currents without changing the activation and inactivation kinetics of currents. Expressed by the venom duct. The cysteine framework is V (CC-CC). Contains 2 disulfide bonds that can be either 'C1-C3, C2-C4' or 'C1-C4, C2-C3', since these disulfide connectivities have been observed for conotoxins with cysteine framework V (for examples, see AC P0DQQ7 and AC P81755). Does not have the ability to interact with the G-protein coupled somatostatin type 3 receptor (SSTR3). Belongs to the conotoxin T superfamily. +PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin or cytochrome c6. hnu + oxidized [2Fe-2S]-[ferredoxin] + reduced [plastocyanin] = oxidized [plastocyanin] + reduced [2Fe-2S]-[ferredoxin] PSI electron transfer chain: 5 divinyl chlorophyll a, 1 divinyl chlorophyll a', 2 phylloquinones and 3 4Fe-4S clusters. PSI core antenna: 90 divinyl chlorophyll a, 22 carotenoids, 3 phospholipids and 1 galactolipid. P700 is a divinyl chlorophyll a/divinyl chlorophyll a' dimer, A0 is one or more divinyl chlorophyll a, A1 is one or both phylloquinones and FX is a shared 4Fe-4S iron-sulfur center. The PsaA/B heterodimer binds the P700 divinyl chlorophyll special pair and subsequent electron acceptors. PSI consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The cyanobacterial PSI reaction center is composed of one copy each of PsaA,B,C,D,E,F,I,J,K,L,M and X, and forms trimeric complexes. Transcription decreases slightly upon iron starvation. Belongs to the PsaA/PsaB family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS. aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-phosphate H2O + L-glutamine = L-glutamate + NH4(+) Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis. In the presence of PdxS, forms a dodecamer of heterodimers. Only shows activity in the heterodimer. Belongs to the glutaminase PdxT/SNO family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Protease with a carboxypeptidase B-like function involved in the C-terminal processing of the lysine and arginine residues from protein precursors. Promotes cell fusion and is involved in the programmed cell death (By similarity). Preferential release of a C-terminal arginine or lysine residue. Belongs to the peptidase S10 family. +Probably participates in a plant defense mechanism. Has hemolytic activity. Expressed in leaves and petioles but not in petals, roots and runners (at protein level). The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. This is a cyclic peptide. Belongs to the cyclotide family. Moebius subfamily. This peptide is cyclic. The start position was chosen by similarity to OAK1 (kalata-B1) for which the DNA sequence is known. +Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine. [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(S)-S-oxide-[protein] [thioredoxin]-disulfide + H2O + L-methionine = [thioredoxin]-dithiol + L-methionine (S)-S-oxide Belongs to the MsrA Met sulfoxide reductase family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. [protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family. +Catalytic subunit of DNA primase, an RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. The small subunit contains the primase catalytic core and has DNA synthesis activity on its own. Binding to the large subunit stabilizes and modulates the activity, increasing the rate of DNA synthesis while decreasing the length of the DNA fragments, and conferring RNA synthesis capability. The DNA polymerase activity may enable DNA primase to also catalyze primer extension after primer synthesis. May also play a role in DNA repair. Heterodimer of a small subunit (PriS) and a large subunit (PriL). Belongs to the eukaryotic-type primase small subunit family. +Activates lipidic moieties required for mycobactin biosynthesis. Converts medium- to long-chain aliphatic fatty acids into acyl adenylate, which is further transferred on to the phosphopantetheine arm of the carrier protein MbtL. a long-chain fatty acid + ATP + holo-[ACP] = a long-chain fatty acyl-[ACP] + AMP + diphosphate a medium chain fatty acid + ATP + holo-[ACP] = a medium-chain fatty acyl-[ACP] + AMP + diphosphate Siderophore biosynthesis; mycobactin biosynthesis. Belongs to the ATP-dependent AMP-binding enzyme family. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +May function in the anterograde transport of protein from the endoplasmic reticulum (ER) to the Golgi complex and in the retrograde transport from the Golgi complex to the ER. Highly expressed in dry seeds. Expressed at low levels in roots, rosette and cauline leaves, stems and flowers. By salt and osmotic stresses. No visible phenotype under normal growth conditions. Belongs to the RINT1 family. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +Serine protease inhibitor. Expressed by the venom gland. Belongs to the venom Kunitz-type family. +Mediates visceral muscle contractile activity (myotropic activity). With pyroglutamate at Gln-1. Belongs to the periviscerokinin family. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +FAD-dependent monooxygenase; part of the gene cluster that mediates the biosynthesis of strobilurin A, an antifungal polyketide that contains a key beta-methoxyacrylate toxophore that targets the complex III of the mitochondrial electron transport chain (PubMed:30258052). Strobilurin biosynthesis begins with construction of benzoyl CoA by step-wise elimination of ammonia from phenylalanine by the phenylalanine ammonia-lyase str11, oxygenation by str8 and retro-Claisen reaction to form benzoic acid, which is activated to its CoA thiolester benzoyl CoA by the dedicated CoA ligase str10 (PubMed:30258052). Benzoyl CoA forms the starter unit for the highly reducing polyketide synthase stpks1 that produces the polyketide prestrobilutin A (PubMed:30258052). The FAD-dependent oxygenase str9 then catalyzes the key oxidative rearrangement responsible for the creation of the beta-methoxyacrylate toxophore (PubMed:30258052). Str9 performs epoxidation of the 2,3 olefin of prestrobilutin A, followed by Meinwald rearrangement to furnish the aldehyde intermediate (Probable). Rapid enolization of the aldehyde intermediate would give the beta-methoxyacrylate skeleton and methylations catalyzed by str2 and str3 complete the synthesis and lead to the peroduction of strobilurin A (Probable). The short-chain dehydrogenase stl2 and the dehydrogenase str4 play a role in the shunt pathway leading to the production of bolineol (PubMed:30258052). The cluster encodes no obvious halogenase gene that could be involved in production of strobilurin B, nor any obvious dimethylallyl-transferase that could be involved in the production of strobilurin G (Probable). It is possible that unknown proteins encoded in, or near, the cluster (such as str1 or stl1) may form new classes of halogenases or dimethylally-transferases, or that the responsible genes are located elsewhere on the genome (Probable). Similarly, proteins encoded by str5/str6 hydrolases appear to have no chemical role in the biosynthesis of strobilurin A (Probable). Finally, no obvious self-resistance gene is found within the cluster (Probable). Mycotoxin biosynthesis. Induced in strobilurin-producing conditions (on CGC medium after 6 days of growth). The structure of strobilurin A was used for the development of the major class of beta-methoxyacrylate agricultural fungicides since its beta-methoxyacrylate toxophore targets the Qo site of complex III of the mitochondrial electron transport chain and prevents adenosine triphosphate synthesis (PubMed:563391, PubMed:6271595). Compounds such as azoxystrobin (Syngenta) and Kresoxim methyl (BASF) are among the most widely used fungicides worldwide (PubMed:29711574, PubMed:12146165). This class of antifungals are used as effective treatments against a broad range of destructive fungal plant pathogens and make significant contributions to food security (PubMed:29711574, PubMed:12146165). The strobilurin fungicides are estimated to have been worth 3.4 billion dollars in 2015 and they make up 25% of the fungicide market and 6.7% of the total crop protection market (PubMed:30258052). Belongs to the paxM FAD-dependent monooxygenase family. +Catalyzes the addition of a mannose residue from GDP-D-mannose to the position 6 of the alpha-1,6-linked mannose residue of the triacyl phosphatidylinositol dimannoside (Ac3PIM2) to generate triacyl phosphatidylinositol trimannoside (Ac3PIM3). Phospholipid metabolism; phosphatidylinositol metabolism. Belongs to the glycosyltransferase group 1 family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +Part of the multicomponent 3-phenylpropionate dioxygenase, that converts 3-phenylpropionic acid (PP) and cinnamic acid (CI) into 3-phenylpropionate-dihydrodiol (PP-dihydrodiol) and cinnamic acid-dihydrodiol (CI-dihydrodiol), respectively. H(+) + NAD(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADH + 2 oxidized [2Fe-2S]-[ferredoxin] Aromatic compound metabolism; 3-phenylpropanoate degradation. This dioxygenase system consists of four proteins: the two subunits of the hydroxylase component (HcaE and HcaF), a ferredoxin (HcaC) and a ferredoxin reductase (HcaD). Belongs to the bacterial ring-hydroxylating dioxygenase ferredoxin reductase family. +May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the CWF19 family. It is uncertain whether Met-1 or Met-5 is the initiator. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +To T.pallidum TP_0127, TP_0315 and TP_0619. +Involved in the biosynthesis of ADP-glucose, a building block required for the elongation reactions to produce glycogen. Catalyzes the reaction between ATP and alpha-D-glucose 1-phosphate (G1P) to produce pyrophosphate and ADP-Glc. alpha-D-glucose 1-phosphate + ATP + H(+) = ADP-alpha-D-glucose + diphosphate Glycan biosynthesis; glycogen biosynthesis. Homotetramer. Belongs to the bacterial/plant glucose-1-phosphate adenylyltransferase family. +Cytokine produced by activated CD4-positive helper T-cells and to a lesser extend activated CD8-positive T-cells and natural killer (NK) cells that plays pivotal roles in the immune response and tolerance. Binds to a receptor complex composed of either the high-affinity trimeric IL-2R (IL2RA/CD25, IL2RB/CD122 and IL2RG/CD132) or the low-affinity dimeric IL-2R (IL2RB and IL2RG). Interaction with the receptor leads to oligomerization and conformation changes in the IL-2R subunits resulting in downstream signaling starting with phosphorylation of JAK1 and JAK3. In turn, JAK1 and JAK3 phosphorylate the receptor to form a docking site leading to the phosphorylation of several substrates including STAT5. This process leads to activation of several pathways including STAT, phosphoinositide-3-kinase/PI3K and mitogen-activated protein kinase/MAPK pathways. Functions as a T-cell growth factor and can increase NK-cell cytolytic activity as well. Promotes strong proliferation of activated B-cells and subsequently immunoglobulin production. Plays a pivotal role in regulating the adaptive immune system by controlling the survival and proliferation of regulatory T-cells, which are required for the maintenance of immune tolerance. Moreover, participates in the differentiation and homeostasis of effector T-cell subsets, including Th1, Th2, Th17 as well as memory CD8-positive T-cells. Belongs to the IL-2 family. +Belongs to the autoinducer-regulated transcriptional regulatory protein family. +Belongs to the bacterial ribosomal protein bS16 family. +Probable recombinase that does not seem to have a role in chromosome dimer resolution per se but rather may have some facilitative role during chromosome partitioning in general. Little effect on the percentage of cells with partition defects and no change in sporulation frequency. However, yopP disruption strongly increases the extent of the partitioning defects seen in codV mutant strains (by about two-fold) and, to a lesser extent, those seen in ripX and dif mutant strains. Belongs to the 'phage' integrase family. +Neurofilaments usually contain three intermediate filament proteins: NEFL, NEFM, and NEFH which are involved in the maintenance of neuronal caliber. May additionally cooperate with the neuronal intermediate filament proteins PRPH and INA to form neuronal filamentous networks (By similarity). Forms heterodimers with NEFL; which can further hetero-oligomerize (in vitro) (By similarity). Forms heterodimers with INA (in vitro) (By similarity). There are a number of repeats of the tripeptide K-S-P, NFM is phosphorylated on a number of the serines in this motif. It is thought that phosphorylation of NFM results in the formation of interfilament cross bridges that are important in the maintenance of axonal caliber. Phosphorylation seems to play a major role in the functioning of the larger neurofilament polypeptides (NF-M and NF-H), the levels of phosphorylation being altered developmentally and coincidentally with a change in the neurofilament function. Phosphorylated in the head and rod regions by the PKC kinase PKN1, leading to the inhibition of polymerization. Belongs to the intermediate filament family. +Adapter protein which modulates coupling of a number of cell surface receptor kinases with specific signaling pathways. Binds to, and suppress signals from, activated receptors tyrosine kinases, including the insulin (INSR) and insulin-like growth factor (IGF1R) receptors. The inhibitory effect can be achieved by 2 mechanisms: interference with the signaling pathway and increased receptor degradation. Delays and reduces AKT1 phosphorylation in response to insulin stimulation. Blocks association between INSR and IRS1 and IRS2 and prevents insulin-stimulated IRS1 and IRS2 tyrosine phosphorylation. Recruits NEDD4 to IGF1R, leading to IGF1R ubiquitination, increased internalization and degradation by both the proteasomal and lysosomal pathways. A similar role in the mediation of ubiquitination has also been suggested with INSR. Negatively regulates Wnt signaling by interacting with LRP6 intracellular portion and interfering with the binding of AXIN1 to LRP6. Positive regulator of the KDR/VEGFR-2 signaling pathway. May inhibit NEDD4-mediated degradation of KDR/VEGFR-2 (By similarity). Phosphorylation by mTORC1 stabilizes and activates GRB10 constituting a feedback pathway by which mTORC1 inhibits INSR-dependent signaling. Interacts with ligand-activated tyrosine kinase receptors, including FGFR1, INSR, IGF1R, MET and PDGFRB in a phosphotyrosine-dependent manner through the SH2 domain. Poorly binds to the EGFR. Directly interacts with MAP3K14/NIK and is recruited to the EGFR-ERBB2 complex. Interacts with GIGYF1/PERQ1 and GIGYF2/TNRC15. When unphosphorylated, interacts with AKT1 and when phosphorylated with YWHAE/14-3-3 epsilon. Interacts with NEDD4. Interacts with LRP6, thus interfering with the binding of AXIN1 to LRP6. Binds relatively non-specifically to several phosphoinositides, including PI(5)P, PI(4,5)P2, PI(3,4)P2 and PI(3,4,5)P3, with modest affinities through the PH domain. Binds to activated NRAS (By similarity). Phosphorylated on serine residues upon EGF, FGF and PDGF stimulation. Belongs to the GRB7/10/14 family. +Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair. Hydrolysis of Ala-|-Gly bond in repressor LexA. Homodimer. Belongs to the peptidase S24 family. +Has antibacterial activity against Gram-negative bacterium E.coli ATCC 25922 (MIC=300 uM) but not against S.pneumoniae ATCC 700603, S.choleraesuis ATCC 14028 or Gram-positive bacterium S.aureus ATCC 29313. Shows virtually no hemolytic activity and no cytotoxicity. Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Ocellatin subfamily. +Belongs to the major facilitator superfamily. DHA1 family. MdtH (TC 2.A.1.2.21) subfamily. +Belongs to the bacterial ribosomal protein bL28 family. +Binds 2 magnesium or manganese ions per subunit. Belongs to the RimK family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity and assembly of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 4 family. +alpha-D-xylose = alpha-D-xylulofuranose Binds 2 magnesium ions per subunit. Homotetramer. Belongs to the xylose isomerase family. +Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. It is subsequently lost, together with VP7, following virus entry into the host cell. Following entry into the host cell, low intracellular or intravesicular Ca(2+) concentration probably causes the calcium-stabilized VP7 trimers to dissociate from the virion. This step is probably necessary for the membrane-disrupting entry step and the release of VP4, which is locked onto the virion by VP7. During the virus exit from the host cell, VP4 seems to be required to target the newly formed virions to the host cell lipid rafts. Forms the spike 'foot' and 'body' and acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. During entry, the part of VP5* that protrudes from the virus folds back on itself and reorganizes from a local dimer to a trimer. This reorganization may be linked to membrane penetration by exposing VP5* hydrophobic region. In integrin-dependent strains, VP5* targets the integrin heterodimer ITGA2/ITGB1 for cell attachment. Forms the head of the spikes and mediates the recognition of specific host cell surface glycans. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact. In some other strains, VP8* mediates the attachment to histo-blood group antigens (HBGAs) for viral entry. Homotrimer. VP4 adopts a dimeric appearance above the capsid surface, while forming a trimeric base anchored inside the capsid layer. Only hints of the third molecule are observed above the capsid surface. It probably performs a series of molecular rearrangements during viral entry. Prior to trypsin cleavage, it is flexible. The priming trypsin cleavage triggers its rearrangement into rigid spikes with approximate two-fold symmetry of their protruding parts. After an unknown second triggering event, cleaved VP4 may undergo another rearrangement, in which two VP5* subunits fold back on themselves and join a third subunit to form a tightly associated trimer, shaped like a folded umbrella. Interacts with VP6. Interacts with VP7. Homotrimer. The trimer is coiled-coil stabilized by its C-terminus, however, its N-terminus, known as antigen domain or 'body', seems to be flexible allowing it to self-associate either as a dimer or a trimer. The outer layer contains 180 copies of VP4, grouped as 60 dimers. Immature double-layered particles assembled in the cytoplasm bud across the membrane of the endoplasmic reticulum, acquiring during this process a transient lipid membrane that is modified with the ER resident viral glycoproteins NSP4 and VP7; these enveloped particles also contain VP4. As the particles move towards the interior of the ER cisternae, the transient lipid membrane and the non-structural protein NSP4 are lost, while the virus surface proteins VP4 and VP7 rearrange to form the outermost virus protein layer, yielding mature infectious triple-layered particles. VP4 also seems to associate with lipid rafts of the host cell membrane probably for the exit of the virus from the infected cell by an alternate pathway. Outer capsid protein. Outer capsid protein. The VP4 spike is divided into a foot, a stalk and body, and a head. Proteolytic cleavage by trypsin results in activation of VP4 functions and greatly increases infectivity. The penetration into the host cell is dependent on trypsin treatment of VP4. It produces two peptides, VP5* and VP8* that remain associated with the virion. Cleavage of VP4 by trypsin probably occurs in vivo in the lumen of the intestine prior to infection of enterocytes. Trypsin seems to be incorporated into the three-layered viral particles but remains inactive as long as the viral outer capsid is intact and would only be activated upon the solubilization of the latter. This strain probably does not use sialic acid to attach to the host cell. In group A rotaviruses, VP4 defines the P serotype. Some rotavirus strains are neuraminidase-sensitive and require sialic acid to attach to the cell surface. Some rotavirus strains are integrin-dependent. Some rotavirus strains depend on ganglioside for their entry into the host cell. Hsp70 also seems to be involved in the entry of some strains. Belongs to the rotavirus VP4 family. +Hydrolase that can remove conjugated ubiquitin from target proteins such as p53/tp53. Acts as an essential regulator of p53/tp53 stability: in unstressed cells, specifically deubiquitinates p53/tp53 in the cytoplasm, leading to counteracts MDM2 action and stabilize p53/tp53. Following DNA damage, translocates to the nucleus and deubiquitinates p53/tp53, leading to regulate the p53/TP53-dependent DNA damage response. Component of a regulatory loop that controls autophagy and p53/tp53 levels (By similarity). Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Belongs to the peptidase C19 family. USP10 subfamily. +Belongs to the UPF0173 family. +Cell division protein that may be involved in stabilizing or promoting the assembly of the division complex. Localizes to the division septum. Belongs to the FtsQ/DivIB family. DivIB subfamily. +Probable ligand-activated transcriptional activator. Acts as a transcriptional regulator in GABAergic motor neuron cell fate specification and development. Promotes cell-type-specific expression of guanylate cyclase genes that have key roles in aggregation behavior and hyperoxia avoidance. Has no role in carbon dioxide avoidance. Interacts with daf-21/hsp90. Interacts with aha-1. Expressed in many distinct neuronal cells including RMED, RMEV, RMEL and RMER. Functions in URX neurons to promote aggregation behavior. Expressed during embryonic and larval development. Defects in neuronal differentiation, axon branching, aberrant cell migration and abnormal aggregation behavior on lawns of bacterial food. +Fimbriae (also called pili), polar filaments radiating from the surface of the bacterium to a length of 0.5-1.5 micrometers and numbering 100-300 per cell, enable bacteria to colonize the epithelium of specific host organs. At the tip of the pili. +Transforms N(2)-succinylglutamate into succinate and glutamate. H2O + N-succinyl-L-glutamate = L-glutamate + succinate Binds 1 zinc ion per subunit. Amino-acid degradation; L-arginine degradation via AST pathway; L-glutamate and succinate from L-arginine: step 5/5. Belongs to the AspA/AstE family. Succinylglutamate desuccinylase subfamily. +The MdtABC tripartite complex confers resistance against novobiocin and deoxycholate. Part of a tripartite efflux system composed of MdtA, MdtB and MdtC. MdtB forms a heteromultimer with MdtC. The mdtABC operon is transcriptionally activated by BaeR. Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family. MdtB subfamily. +Endothelial cell-specific membrane protein involved in the formation of the diaphragms that bridge endothelial fenestrae. It is also required for the formation of stomata of caveolae and transendothelial channels. Functions in microvascular permeability, endothelial fenestrae contributing to the passage of water and solutes and regulating transcellular versus paracellular flow in different organs. Plays a specific role in embryonic development. Homodimer. Membrane-associated protein of caveolae. Found in fenestral and stomatal diaphragms in fenestrated endothelia and transendothelial channels. Also colocalized with CAV1 in perinuclear region. Expressed in lung, kidney, spleen, heart, muscle, eye, pancreas, thyroid, thymus, submaxillary gland, prostate, epididymis, uterus and liver. Expressed in embryo at 7 dpc. Expressed in the brain vasculature at 12 up to 16 dpc, whereupon it disappears. Mutant animals result in lethality during prenatal development. Examination of the homozygous deficient embryos reveal subcutaneous edema, hemorrhages and defects in the vascular wall of subcutaneous capillaries. Hearts of deficient embryos show ventricular septal defects (VSDs) and thinner ventricular walls, as well as blood abnormalities. Analyses on protein expression and localization in endothelial cells of subcutaneous capillaries and endocardium show that the protein and caveolae with stomatal diaphragm were present in wild-type embryos, whereas the diaphragm is missing in the caveolae of deficient embryos. Deficient mice are viable after birth and survive up to 4 weeks on a mixed C57BL/6N/FVB-N background. Embryos on the mixed background show edema in neck and back, but no visible hemorrhages. Postnatal mutant mice display marked reduction in body size and kinked tails compare with wild-type, but no VSDs are observed in hearts. Detailed examination of the capillaries of kidneys and pancreas reveal that the knockout mice does not form fenestrae with diaphragm. +Guanine-nucleotide exchange factor (GEF) that acts as an activator of Rop (Rho of plants) GTPases by promoting the exchange of GDP for GTP. Interacts with ARAC11/ROP1 and ARAC10/ROP11. Interacts with PRK6 (PubMed:26961657). Localizes to the apical region of the pollen tube plasma membrane. Expressed in pollen grains and pollen tubes. The PRONE (plant-specific Rop nucleotide exchanger) domain is responsible for the GEF activity. Extended C-terminus. +Belongs to the nematode receptor-like protein sre family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseB family. +Acts as a positive regulator of ciliary hedgehog signaling. Required for centriole stability. Interacts with TEDC1. Found in a complex with TEDC1, TEDC2, TUBE1 and TUBD1. +Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain (By similarity). Interacts with ZNRF1 (By similarity). Part of a complex composed at least of ASCL2, EMSY, HCFC1, HSPA8, CCAR2, MATR3, MKI67, RBBP5, TUBB2A, WDR5 and ZNF335; this complex may have a histone H3-specific methyltransferase activity (By similarity). Dimer of alpha and beta chains. A typical microtubule is a hollow water-filled tube with an outer diameter of 25 nm and an inner diameter of 15 nM. Alpha-beta heterodimers associate head-to-tail to form protofilaments running lengthwise along the microtubule wall with the beta-tubulin subunit facing the microtubule plus end conferring a structural polarity. Microtubules usually have 13 protofilaments but different protofilament numbers can be found in some organisms and specialized cells. High expression in brain, where it represents 30% of all beta-tubulins. The MREI motif is common among all beta-tubulin isoforms and may be critical for tubulin autoregulation. Some glutamate residues at the C-terminus are polyglutamylated, resulting in polyglutamate chains on the gamma-carboxyl group (PubMed:26875866). Polyglutamylation plays a key role in microtubule severing by spastin (SPAST). SPAST preferentially recognizes and acts on microtubules decorated with short polyglutamate tails: severing activity by SPAST increases as the number of glutamates per tubulin rises from one to eight, but decreases beyond this glutamylation threshold (PubMed:26875866). Glutamylation is also involved in cilia motility (By similarity). Some glutamate residues at the C-terminus are monoglycylated but not polyglycylated due to the absence of functional TTLL10 in human. Monoglycylation is mainly limited to tubulin incorporated into cilia and flagella axonemes, which is required for their stability and maintenance. Flagella glycylation controls sperm motility. Both polyglutamylation and monoglycylation can coexist on the same protein on adjacent residues, and lowering glycylation levels increases polyglutamylation, and reciprocally. Phosphorylated on Ser-172 by CDK1 during the cell cycle, from metaphase to telophase, but not in interphase. This phosphorylation inhibits tubulin incorporation into microtubules. The disease is caused by variants affecting the gene represented in this entry. Belongs to the tubulin family. +May play a role in retrograde transport of proteins from the Golgi to the endoplasmic reticulum. May indirectly play a role in protein glycosylation in the Golgi. Homooligomer (PubMed:24806965). Interacts with COPB1 (PubMed:24806965). May interact with LMAN1 (PubMed:24806965). Interacts with the COG complex; probably through COG3 (PubMed:24806965). Expressed strongly in kidney and skeletal muscle, followed by liver, placenta, pancreas, and lung, with low amounts in heart and only traces in brain (PubMed:11085536). Widely expressed with ubiquitous expression in epithelial tissues (at protein level) (PubMed:17973242). Belongs to the TMEM115 family. +Tachykinins are active peptides which excite neurons, evoke behavioral responses, are potent vasodilators and secretagogues, and contract (directly or indirectly) many smooth muscles. Expressed by the skin glands. Belongs to the tachykinin family. +Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine (By similarity). Heterotetramer of two type I and two type II keratins. Associates with KRT8 (By similarity). Expressed predominantly in the intestinal epithelium in differentiated villus cells. Becomes apparent upon completion of villus formation at 20 days gestation (2 days before birth) and is expressed by the entire epithelium of the villus. Hyperphosphorylation at Ser-13 occurs during the early stages of apoptosis but becomes less prominent during the later stages. Phosphorylation at Ser-13 also increases in response to stress brought on by cell injury (By similarity). Proteolytically cleaved by caspases during apoptosis. Cleavage occurs at Asp-233 (By similarity). There are two types of cytoskeletal and microfibrillar keratin: I (acidic; 40-55 kDa) and II (neutral to basic; 56-70 kDa). Belongs to the intermediate filament family. +Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA). NADP(+) + shikimate = 3-dehydroshikimate + H(+) + NADPH Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 4/7. Homodimer. Belongs to the shikimate dehydrogenase family. +carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family. +Component of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane. Helps to maintain integrity of nuclear structures in response to mechanical stress. Nuclei are misshapen and disorganized, with irregularly condensed chromatin and centrosomal detachment from nuclei. Belongs to the intermediate filament family. +Essential for the assembly of the photosystem I (PSI) complex. May act as a chaperone-like factor to guide the assembly of the PSI subunits. Belongs to the Ycf3 family. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Part of a tripartite efflux system composed of MdtA, MdtB and MdtC. MdtB forms a heteromultimer with MdtC. Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family. MdtB subfamily. In strain 301 the corresponding sequence has an in-frame codon. The sequence has been checked and is believed to be correct. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +ATPase subunit of a proteasome-like degradation complex; this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the ClpX chaperone family. HslU subfamily. +Probably participates in a plant defense mechanism. Expressed in root, seed and nodule but not in flower, stem, shoot, leaf and pod (at protein level). The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Contains 3 disulfide bonds. This is a cyclic peptide. Belongs to the cyclotide family. Bracelet subfamily. +Belongs to the UPF0283 family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +By hydrolysis of the attached glycolipid, releases soluble variant surface glycoprotein containing phosphoinositol from the cell wall of T.brucei after cell lysis. It also cleaves similar membrane anchors on some mammalian proteins. VSG lipase may play a role in processes such as parasite differentiation or antigenic variation (By similarity). an alpha-D-GlcN-(1->6)-(1,2-diacyl-sn-glycero-3-phospho)-1D-myo-inositol = 6-(alpha-D-glucosaminyl)-1D-myo-inositol 1,2-cyclic phosphate + a 1,2-diacyl-sn-glycerol Monomer. +Sequence-specific endonuclease that cleaves unmethylated GATC sequences. It is involved in DNA mismatch repair. Belongs to the MutH family. +A subtype P restriction enzyme that recognizes the double-stranded sequence 5'-GAGCTC-3' and cleaves after T-5. Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. +alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 2/4. Belongs to the GPI family. +Belongs to the bacterial ribosomal protein bL36 family. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor, and NADPH and FADH(2) as the reductant. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP + H(+) + NADPH = (6S)-5,6,7,8-tetrahydrofolate + dTMP + NADP(+) Binds 4 FAD per tetramer. Each FAD binding site is formed by three monomers. Pyrimidine metabolism; dTTP biosynthesis. Homotetramer. Belongs to the thymidylate synthase ThyX family. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P. 4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + ADP + H(+) 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + ATP = 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + ADP Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole: step 2/3. Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole: step 3/3. Belongs to the ThiD family. +Is the anti-sigma factor for SigW. The presence of RsiW leads to the inactivation of SigW, and its proteolytic destruction to sigma-W activation (By similarity). Binds 1 Zn(2+) ion per subunit. Site-2 clipped RsiW is released from the membrane to the cytoplasm. Is processed by three successive proteolytic events. First, the extracellular region of RsiW is cleaved by PrsW (Site-1 cleavage) in response to cell envelope stresses. Next, it undergoes cleavage at an intramembrane site (Site-2 cleavage) mediated by RasP. This cleavage uncovers a cryptic proteolytic tag with conserved alanine residues in the transmembrane segment, that is recognized mainly by the ClpXP protease, which completely degrades the protein in the cytoplasm and leads to the induction of the sigma-W-controlled genes (By similarity). Belongs to the zinc-associated anti-sigma factor (ZAS) superfamily. Anti-sigma-W factor family. +AMP/ATP-binding subunit of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism. In response to reduction of intracellular ATP levels, AMPK activates energy-producing pathways and inhibits energy-consuming processes: inhibits protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation. AMPK acts via direct phosphorylation of metabolic enzymes, and by longer-term effects via phosphorylation of transcription regulators. Also acts as a regulator of cellular polarity by remodeling the actin cytoskeleton; probably by indirectly activating myosin. Gamma non-catalytic subunit mediates binding to AMP, ADP and ATP, leading to activate or inhibit AMPK: AMP-binding results in allosteric activation of alpha catalytic subunit (PRKAA1 or PRKAA2) both by inducing phosphorylation and preventing dephosphorylation of catalytic subunits. ADP also stimulates phosphorylation, without stimulating already phosphorylated catalytic subunit. ATP promotes dephosphorylation of catalytic subunit, rendering the AMPK enzyme inactive. AMPK is a heterotrimer of an alpha catalytic subunit (PRKAA1 or PRKAA2), a beta (PRKAB1 or PRKAB2) and a gamma non-catalytic subunits (PRKAG1, PRKAG2 or PRKAG3). Interacts with FNIP1 and FNIP2. Highly expressed in heart and brain, also found in kidney, white adipose tissue, lung and spleen. The AMPK pseudosubstrate motif resembles the sequence around sites phosphorylated on target proteins of AMPK, except the presence of a non-phosphorylatable residue in place of Ser. In the absence of AMP this pseudosubstrate sequence may bind to the active site groove on the alpha subunit (PRKAA1 or PRKAA2), preventing phosphorylation by the upstream activating kinase STK11/LKB1 (By similarity). The 4 CBS domains mediate binding to nucleotides. Of the 4 potential nucleotide-binding sites, 3 are occupied, designated as sites 1, 3, and 4 based on the CBS modules that provide the acidic residue for coordination with the 2'- and 3'-hydroxyl groups of the ribose of AMP. Of these, site 4 appears to be a structural site that retains a tightly held AMP molecule (AMP 3). The 2 remaining sites, 1 and 3, can bind either AMP, ADP or ATP. Site 1 (AMP, ADP or ATP 1) is the high-affinity binding site and likely accommodates AMP or ADP. Site 3 (AMP, ADP or ATP 2) is the weakest nucleotide-binding site on the gamma subunit, yet it is exquisitely sensitive to changes in nucleotide levels and this allows AMPK to respond rapidly to changes in cellular energy status. Site 3 is likely to be responsible for protection of a conserved threonine in the activation loop of the alpha catalytic subunit through conformational changes induced by binding of AMP or ADP. Phosphorylated by ULK1 and ULK2; leading to negatively regulate AMPK activity and suggesting the existence of a regulatory feedback loop between ULK1, ULK2 and AMPK. There is some ambiguity for a phosphosite: Ser-260/Thr-262. Belongs to the 5'-AMP-activated protein kinase gamma subunit family. +Has a role in vesicle-mediated transport but not with protein transport from Golgi to vesicle. Belongs to the syntaxin family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Plays a role in microtubule organization. Belongs to the CEP170 family. +Catalyzes the covalent attachment of the prokaryotic ubiquitin-like protein modifier Pup to the proteasomal substrate proteins, thereby targeting them for proteasomal degradation. This tagging system is termed pupylation. The ligation reaction involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a substrate lysine. ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N(6)-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine. Protein degradation; proteasomal Pup-dependent pathway. Protein modification; protein pupylation. The reaction mechanism probably proceeds via the activation of Pup by phosphorylation of its C-terminal glutamate, which is then subject to nucleophilic attack by the substrate lysine, resulting in an isopeptide bond and the release of phosphate as a good leaving group. Belongs to the Pup ligase/Pup deamidase family. Pup-conjugating enzyme subfamily. +Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions (By similarity). 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate H(+) + oxaloacetate = CO2 + pyruvate Divalent metal cation. Homotrimer. Belongs to the class II aldolase/RraA-like family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Belongs to the protease inhibitor I3 (leguminous Kunitz-type inhibitor) family. +This protein is involved in control of the biosynthesis of threonine. Belongs to the thr operon leader peptide family. +May be a regulator of microtubule physiology. Monomer and homodimer. Associated with microtubules. Detected in cilia of lung epithelium, and associated with the spermatid tail and manchette. Detected at very low levels in testis, lung and brain. Shows no detectable enzyme activity. Belongs to the NDK family. +May function in recognizing stalled ribosomes, interact with stem-loop structures in stalled mRNA molecules, and effect endonucleolytic cleavage of the mRNA. May play a role in the release non-functional ribosomes and degradation of damaged mRNAs. Has endoribonuclease activity. Monomer. The N-terminal domain has the RNA-binding Sm fold. It harbors the endoribonuclease activity. Belongs to the eukaryotic release factor 1 family. Pelota subfamily. +This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. cytidine + H(+) + H2O = NH4(+) + uridine 2'-deoxycytidine + H(+) + H2O = 2'-deoxyuridine + NH4(+) Binds 1 zinc ion. Homodimer. Belongs to the cytidine and deoxycytidylate deaminase family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Homodimer. Belongs to the GrpE family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +Required for spore cortex hydrolysis during germination. Appears to be required for either expression, localization, activation or function of SleB (By similarity). Belongs to the YpeB family. +[hyaluronan](n) = n 3-(4-deoxy-beta-D-gluc-4-enuronosyl)-N-acetyl-D-glucosamine + H2O Belongs to the polysaccharide lyase 8 family. Truncated N-terminus. Truncated N-terminus. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. Binds multiple chlorophylls and provides some of the ligands for the Ca-4Mn-5O cluster of the oxygen-evolving complex. It may also provide a ligand for a Cl- that is required for oxygen evolution. PSII binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbB/PsbC family. PsbC subfamily. +Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. (2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 4/5. Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface. Belongs to the enolase family. +Converts the free carboxyl group of a malonyl-thioester to its methyl ester by transfer of a methyl group from S-adenosyl-L-methionine (SAM). It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway. malonyl-[ACP] + S-adenosyl-L-methionine = malonyl-[ACP] methyl ester + S-adenosyl-L-homocysteine Cofactor biosynthesis; biotin biosynthesis. Belongs to the methyltransferase superfamily. +Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I. di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 4 family. MraY subfamily. +Lacks intrinsic GTPase activity. Has a low affinity for GDP, and constitutively binds GTP. Controls rearrangements of the actin cytoskeleton. Induces the Rac-dependent neuritic process formation in part by disruption of the cortical actin filaments. Causes the formation of many neuritic processes from the cell body with disruption of the cortical actin filaments (By similarity). Binds GRB7 and PLXNB1. Interacts with PLXNA2. Interacts with UBXD5 (By similarity). Belongs to the small GTPase superfamily. Rho family. +Component of the biogenesis of lysosome-related organelles complex-1 (BLOC-1) involved in endosomal cargo sorting. Component of the biogenesis of lysosome-related organelles complex-1 (BLOC-1) composed of at least BLI1, BLS1, CNL1, KXD1, SNN1 and VAB2. Belongs to the KXD1 family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Required during biogenesis of c-type cytochromes (cytochrome c6 and cytochrome f) at the step of heme attachment. May interact with Ccs1. Belongs to the CcmF/CycK/Ccl1/NrfE/CcsA family. +Belongs to the eukaryotic ribosomal protein eS10 family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +The glycine cleavage system catalyzes the degradation of glycine. (6S)-5,6,7,8-tetrahydrofolate + (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[protein] = (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + NH4(+) The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvT family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds 2 heme A groups non-covalently per subunit. Binds a copper B center. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). As a newly synthesized protein, rapidly incorporates into a multi-subunit assembly intermediate in the inner membrane, called MITRAC (mitochondrial translation regulation assembly intermediate of cytochrome c oxidase) complex, whose core components are COA3/MITRAC12 and COX14. Within the MITRAC complex, interacts with COA3 and with SMIM20/MITRAC7; the interaction with SMIM20 stabilizes the newly synthesized MT-CO1 and prevents its premature turnover. Interacts with TMEM177 in a COX20-dependent manner (By similarity). Belongs to the heme-copper respiratory oxidase family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Receptor for somatostatin-14 and -28. This receptor is coupled via pertussis toxin sensitive G proteins to inhibition of adenylyl cyclase. In addition it stimulates phosphotyrosine phosphatase and PLC via pertussis toxin insensitive as well as sensitive G proteins. Inhibits calcium entry by suppressing voltage-dependent calcium channels. Acts as the functionally dominant somatostatin receptor in pancreatic alpha- and beta-cells where it mediates the inhibitory effect of somatostatin-14 on hormone secretion. Inhibits cell growth through enhancement of MAPK1 and MAPK2 phosphorylation and subsequent up-regulation of CDKN1B. Stimulates neuronal migration and axon outgrowth and may participate in neuron development and maturation during brain development. Mediates negative regulation of insulin receptor signaling through PTPN6. Inactivates SSTR3 receptor function following heterodimerization. Homodimer and heterodimer with SSTR3 and SSTR5. Heterodimerization with SSTR3 inactivates SSTR3 receptor function. Heterodimerization with SSTR5 is enhanced by agonist stimulation of SSTR2 and increases SSTR2 cell growth inhibition activity. Following agonist stimulation, homodimers dissociate into monomers which is required for receptor internalization. Interacts with beta-arrestin; this interaction is necessary for receptor internalization and is destabilized by heterodimerization with SSTR5 which results in increased recycling of SSTR2 to the cell surface. Interacts (via C-terminus) with SHANK1 (via PDZ domain) (By similarity). Located mainly at the cell surface under basal conditions. Agonist stimulation results in internalization to the cytoplasm (By similarity). Cerebrum and kidney. Phosphorylated on serine and threonine residues in response to agonist stimulation, leading to receptor desensitization and rapid internalization. Phosphorylated to a greater extent on serine than threonine residues. Threonine phosphorylation is required for arrestin binding and receptor endocytosis but is not necessary for desensitization (By similarity). Belongs to the G-protein coupled receptor 1 family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Core component of the CAF-1 complex, a complex that is thought to mediate chromatin assembly in DNA replication and DNA repair. Assembles histone octamers onto replicating DNA in vitro. CAF-1 performs the first step of the nucleosome assembly process, bringing newly synthesized histones H3 and H4 to replicating DNA; histones H2A/H2B can bind to this chromatin precursor subsequent to DNA replication to complete the histone octamer. It may play a role in heterochromatin maintenance in proliferating cells by bringing newly synthesized cbx proteins to heterochromatic DNA replication foci. Homodimer. Part of the CAF-1 complex that contains RBBP4, CHAF1B and CHAF1A. CHAF1A binds directly to CHAF1B. Only minor amounts of RBBP4 are complexed with CHAF1A and CHAF1B in G1 phase. CHAF1A binds directly to PCNA and to CBX1. Interacts with MBD1. Interacts directly with CBX5 via the PxVxL motif. Interacts with CBX5. Interacts with histones H3.1, H3.2 and H3.1t (By similarity). DNA replication foci. Contains one Pro-Xaa-Val-Xaa-Leu (PxVxL) motif, which is required for interaction with chromoshadow domains. This motif requires additional residues -7, -6, +4 and +5 of the central Val which contact the chromoshadow domain (By similarity). Belongs to the CHAF1A family. +Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair. Hydrolysis of Ala-|-Gly bond in repressor LexA. Homodimer. Belongs to the peptidase S24 family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +Expressed in embryos and in adult animals. Belongs to the IAP family. +Required for the export of nuclear mRNAs and involved in mRNA trafficking in the cytoplasm (PubMed:27016737, PubMed:28554770, PubMed:33602059). Component of the nuclear pore complex (NPC)-associated TREX-2/AMEX complex (anchoring and mRNA export complex) which functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket), thereby enabling the export of mRNAs to the cytoplasm through the nuclear pores (PubMed:27016737, PubMed:28554770, PubMed:33602059). Within the complex, specifically promotes the association of factors involved in regulating nuclear mRNA export, such as Moe, sbr/NXF1 and the ORC complex, to the mRNPs particles (PubMed:27016737, PubMed:28554770, PubMed:33602059). In the cytoplasm, functions independently of its role in the TREX-2/AMEX complex, to promote cytoplasmic mRNA trafficking together with nudC (PubMed:33602059). Associates with translationally active polysomes (PubMed:18086857). Component of the nuclear pore complex (NPC)-associated TREX-2/AMEX complex (anchoring and mRNA export complex), composed of e(y)2, xmas and PCID2 (PubMed:27016737). Interaction between the TREX-2/AMEX complex and the ORC complex is required for ORC localization to mRNPs, and consequently mRNA export (PubMed:27016737). Within the TREX-2/AMEX-ORC complex, interacts with Orc3 and Orc4 (PubMed:27016737). Interacts with sbr/NXF1 (PubMed:18086857). Interacts with Moe (PubMed:28554770). Interacts with nudC; required to maintain stability in the cytoplasm (PubMed:33602059). Shuttles in and out of the nucleus by a emb/Crm1-dependent mechanism (PubMed:18086857). The ubiquitinated forms are localized to the cytoplasm, the nonubiquitinated forms are localized to the nucleus, and both forms are associated with the nuclear membrane (PubMed:33602059). Associated with cytoplasmic microtubules (PubMed:33602059). Associates with mRNA in the nucleus and cytoplasm (PubMed:33602059). Expressed in embryos (at protein level). PCI domain is required for interaction with polysomes but not the interaction with sbr. Mono- and poly-ubiquitinated. Belongs to the CSN12 family. +Its precise biological substrate is not known. Catalyzes C14-demethylation of lanosterol, 24,25-dihydrolanosterol and obtusifoliol which is critical for ergosterol biosynthesis. It transforms lanosterol into 4,4'-dimethyl cholesta-8,14,24-triene-3-beta-ol. a 14alpha-methyl steroid + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = a Delta(14) steroid + formate + 4 H(+) + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase] Steroid biosynthesis; zymosterol biosynthesis; zymosterol from lanosterol: step 1/6. Monomer. Belongs to the cytochrome P450 family. +Encapsidates the negative strand viral RNA, protecting it from nucleases. The encapsidated genomic RNA is termed the ribonucleoprotein (RNP) and serves as template for transcription and replication. The RNP needs to be localized in the host nucleus to start an infectious cycle, but is too large to diffuse through the nuclear pore complex. NP comprises at least 2 nuclear localization signals that are responsible for the active RNP import into the nucleus through cellular importin alpha/beta pathway. Later in the infection, nclear export of RNPs are mediated through viral proteins NEP interacting with M1 which binds nucleoproteins. It is possible that nucleoprotein binds directly host exportin-1/XPO1 and plays an active role in RNPs nuclear export. M1 interaction with RNP seems to hide nucleoprotein's nuclear localization signals. Soon after a virion infects a new cell, M1 dissociates from the RNP under acidification of the virion driven by M2 protein. Dissociation of M1 from RNP unmasks nucleoprotein's nuclear localization signals, targeting the RNP to the nucleus. Homomultimerizes to form the nucleocapsid. May bind host exportin-1/XPO1. Binds to viral genomic RNA. Protein-RNA contacts are mediated by a combination of electrostatic interactions between positively charged residues and the phosphate backbone and planar interactions between aromatic side chains and bases. Late in virus-infected cells, may be cleaved from a 56-kDa protein to a 53-kDa protein by a cellular caspase. This cleavage might be a marker for the onset of apoptosis in infected cells or have a specific function in virus host interaction. Belongs to the influenza viruses nucleoprotein family. +Catalyzes the ATP-dependent phosphorylation of L-homoserine to L-homoserine phosphate. ATP + L-homoserine = ADP + H(+) + O-phospho-L-homoserine Amino-acid biosynthesis; L-threonine biosynthesis; L-threonine from L-aspartate: step 4/5. Belongs to the GHMP kinase family. Homoserine kinase subfamily. +Probable ion channel inhibitor. Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 14 (magi-1) family. 01 (HNTX-16) subfamily. +Protease which cleaves the matured lantibiotic from the modified prepeptide. Antibiotic biosynthesis; epidermin biosynthesis. Belongs to the peptidase S8 family. +Blocks both the muscle-twitch response to nerve stimulation and the response to exogenous acetylcholine. Expressed by the venom gland. In contrast to other snake toxins the action of this toxin is reversible. Unusual amino acid sequence distinctly different from other short-chain type toxins. Is classified as a P-type cytotoxin, since a proline residue stands at position 30 (Pro-31 in standard classification). Belongs to the snake three-finger toxin family. Short-chain subfamily. Orphan group XVIII sub-subfamily. +Probable ion channel. Expressed in a range of tissues including cerebrum, cerebellum, retina, cochlea, lung, liver and heart. Also expressed in the apical, medial and basal portions of the basillar papilla. Belongs to the TMC family. +Required for maturation of urease via the functional incorporation of the urease nickel metallocenter. UreD, UreF and UreG form a complex that acts as a GTP-hydrolysis-dependent molecular chaperone, activating the urease apoprotein by helping to assemble the nickel containing metallocenter of UreC. The UreE protein probably delivers the nickel. Belongs to the UreF family. +Catalyzes the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH 5,10-methenyltetrahydrofolate + H2O = (6S)-10-formyltetrahydrofolate + H(+) One-carbon metabolism; tetrahydrofolate interconversion. Homodimer. Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family. +Belongs to the bacterial ribosomal protein bL36 family. +tRNA methylase which 2'-O-methylates cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His). cytidine(4) in tRNA(Pro) + S-adenosyl-L-methionine = 2'-O-methylcytidine(4) in tRNA(Pro) + H(+) + S-adenosyl-L-homocysteine cytidine(4) in tRNA(Gly)(GCC) + S-adenosyl-L-methionine = 2'-O-methylcytidine(4) in tRNA(Gly)(GCC) + H(+) + S-adenosyl-L-homocysteine adenosine(4) in tRNA(His) + S-adenosyl-L-methionine = 2'-O-methyladenosine(4) in tRNA(His) + H(+) + S-adenosyl-L-homocysteine Belongs to the methyltransferase TRM13 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) In plastids the minimal PEP RNA polymerase catalytic core is composed of four subunits: alpha, beta, beta', and beta''. When a (nuclear-encoded) sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Belongs to the urease beta subunit family. +Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-phosphate Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis. In the presence of PdxT, forms a dodecamer of heterodimers. Belongs to the PdxS/SNZ family. +Required for formate dehydrogenase (FDH) activity. Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH. Belongs to the FdhD family. +Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Belongs to the thiamine-phosphate synthase family. +May be involved as a ribosomal RNA processing factor in ribosome biogenesis. Binds to DNA (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the PpiC/parvulin rotamase family. PIN4 subfamily. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Probable regulator of exocrine pancreas development. Belongs to the PPDPF family. +Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. 2-oxoglutarate + O-phospho-L-serine = 3-phosphooxypyruvate + L-glutamate 2-oxoglutarate + 4-(phosphooxy)-L-threonine = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate Binds 1 pyridoxal phosphate per subunit. Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 2/3. Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 3/5. Homodimer. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. SerC subfamily. +Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity). (6S)-5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + H(+) + NADPH Cofactor biosynthesis; tetrahydrofolate biosynthesis; 5,6,7,8-tetrahydrofolate from 7,8-dihydrofolate: step 1/1. Belongs to the dihydrofolate reductase family. +Potential calcium sensor. Although assigned as a calmodulin family member by PubMed:17263873, it only contains EF-hand domains. +Expressed during stationary phase (at protein level). Encoded by the cryptic lambdoid prophage DLP12. To equivalent protein in phage 82. +Regulates arginine biosynthesis genes. Amino-acid biosynthesis; L-arginine biosynthesis [regulation]. Belongs to the ArgR family. +Cationic amphipathic alpha-helical peptide with antimicrobial activities against E.coli (MIC=3.1 uM), S.aureus (MIC=25 uM), and S.cerevisiae (MIC=50 uM). Also shows histamine-releasing activity (37.5% at 10 uM). Does not show hemolytic activity, even at 50 uM. Expressed by the venom gland. Truncated sequences of this peptide have also been found in the venom. It is possible they have been cleaved in the venom. Monoisotopic mass. Belongs to the formicidae venom precursor-01 superfamily. +Expressed by the venom gland. Belongs to the non-disulfide-bridged peptide (NDBP) superfamily. Long chain multifunctional peptide (group 2) family. +Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP. Allosterically activated by GTP. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uracil: step 1/1. Belongs to the UPRTase family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of replication as well as for processivity of DNA replication. Forms a ring-shaped head-to-tail homodimer around DNA which binds and tethers DNA polymerases and other proteins to the DNA (PubMed:25170813). The DNA replisome complex has a single clamp-loading complex (3 tau and 1 each of delta, delta', psi and chi subunits) which binds 3 Pol III cores (1 core on the leading strand and 2 on the lagging strand) each with a beta sliding clamp dimer. Additional proteins in the replisome are other copies of gamma, psi and chi, Ssb, DNA helicase and RNA primase (By similarity). Belongs to the beta sliding clamp family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseB family. +2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + ADP + H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole from N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide: step 2/2. Belongs to the AIR synthase family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. Binds multiple chlorophylls and provides some of the ligands for the Ca-4Mn-5O cluster of the oxygen-evolving complex. It may also provide a ligand for a Cl- that is required for oxygen evolution. PSII binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbB/PsbC family. PsbC subfamily. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +Removes the pyruvyl group from chorismate, with concomitant aromatization of the ring, to provide 4-hydroxybenzoate (4HB) for the ubiquinone pathway. chorismate = 4-hydroxybenzoate + pyruvate Cofactor biosynthesis; ubiquinone biosynthesis. Monomer. Belongs to the UbiC family. +Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). 5,6-dimethylbenzimidazole + nicotinate beta-D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate Nucleoside biosynthesis; alpha-ribazole biosynthesis; alpha-ribazole from 5,6-dimethylbenzimidazole: step 1/2. Belongs to the CobT family. +Belongs to the UPF0246 family. +Cell wall formation. ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) + phosphate Binds 2 magnesium or manganese ions per subunit. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the D-alanine--D-alanine ligase family. +Sigma factors are initiation factors that promote the attachment of RNA polymerase (RNAP) to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma-E controls the envelope stress response, responding to periplasmic protein stress, increased levels of periplasmic lipopolysaccharide (LPS) as well as heat shock and oxidative stress; it controls protein processing in the extracytoplasmic compartment (By similarity). ECF sigma-E is held in an inactive form by its cognate anti-sigma factor (RseA) until released by regulated intramembrane proteolysis (RIP). RIP occurs when an extracytoplasmic signal (periplasmic stress and excess LPS) triggers a concerted proteolytic cascade to transmit information and elicit cellular responses. The anti-sigma factor RseA is an inner membrane protein, binding sigma-E in the cytoplasm and RseB in the periplasm. RseA is first cut extracytoplasmically (site-1 protease, S1P, by DegS), then within the membrane itself (site-2 protease, S2P, by RseP), while cytoplasmic proteases (predominantly ClpX-ClpP) finish degrading the regulatory protein, liberating sigma-E. Degradation of RseA requires 2 signals to activate DegS; an outer membrane protein (OMP) signal activates DegS, while an LPS signal causes release of RseB from RseA, freeing RseA to be cleaved (By similarity). Interacts transiently with the RNAP catalytic core formed by RpoA, RpoB, RpoC and RpoZ (2 alpha, 1 beta, 1 beta' and 1 omega subunit) to form the RNAP holoenzyme that can initiate transcription. Interacts 1:1 with anti-sigma-E factor RseA which prevents binding to RNAP catalytic core (By similarity). Associates with the inner membrane via RseA. The sigma-70 factor domain-2 mediates sequence-specific interaction with the -10 element in promoter DNA, and plays an important role in melting the double-stranded DNA and the formation of the transcription bubble. The sigma-70 factor domain-2 mediates interaction with the RNA polymerase subunits RpoB and RpoC (By similarity). The sigma-70 factor domain-4 contains a helix-turn-helix (H-T-H) motif that mediates interaction with the -35 element in promoter DNA. The domain also mediates interaction with the RNA polymerase subunit RpoA. Interactions between sigma-70 factor domain-4 and anti-sigma factors prevents interaction of sigma factors with the RNA polymerase catalytic core (By similarity). Belongs to the sigma-70 factor family. ECF subfamily. +Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP). 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP Binds 1 divalent metal cation per subunit. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 4/6. Homotrimer. Belongs to the IspF family. +Belongs to the bacterial ribosomal protein bL32 family. +Avian ovomucoid consists of three homologous, tandem Kazal family inhibitory domains. +Binds ssDNA with nanomolar affinity but no sequence specificity. Homodimer; two homodimers can further weakly assemble into a homotetramer. Expressed in the early phase of the viral replicative cycle. Belongs to the skunalikevirus SSB protein family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Odorant signal transduction is probably mediated by a G-protein coupled cascade using cAMP as second messenger. The olfactory channel can be shown to be activated by cyclic nucleotides which leads to a depolarization of olfactory sensory neurons. Heterotetramer composed of two subunits of CNGA2, one of CNGA4 and one of CNGB1b. The complex forms the cyclic nucleotide-gated (CNG) channel of olfactory sensory neurons (By similarity). Olfactory neurons. The C-terminal coiled-coil domain mediates trimerization of CNGA subunits. The olfactory channel is activated by both cAMP and cGMP at similar concentrations, whereas the cGMP-gated channel is much less sensitive to cAMP. Belongs to the cyclic nucleotide-gated cation channel (TC 1.A.1.5) family. CNGA2 subfamily. +Forms a proton-selective ion channel that is necessary for the efficient release of the viral genome during virus entry. After attaching to the cell surface, the virion enters the cell by endocytosis. Acidification of the endosome triggers M2 ion channel activity. The influx of protons into virion interior is believed to disrupt interactions between the viral ribonucleoprotein (RNP), matrix protein 1 (M1), and lipid bilayers, thereby freeing the viral genome from interaction with viral proteins and enabling RNA segments to migrate to the host cell nucleus, where influenza virus RNA transcription and replication occur. Also plays a role in viral proteins secretory pathway. Elevates the intravesicular pH of normally acidic compartments, such as trans-Golgi network, preventing newly formed hemagglutinin from premature switching to the fusion-active conformation. The M2 protein from most influenza A strains is inhibited by amantadine and rimantadine, resulting in viral uncoating incapacity. Emergence of amantadine-resistant variants is usually rapid. Homotetramer; composed of two disulfide-linked dimers held together by non-covalent interactions. May interact with matrix protein 1. Abundantly expressed at the apical plasma membrane in infected polarized epithelial cells, in close proximity to budding and assembled virions. Minor component of virions (only 16-20 molecules/virion). Only the first 9 residues are shared by the 2 isoforms. Cytoplasmic tail plays an important role in virion assembly and morphogenesis. When the channel is activated, one or more imidazole moieties of His-37 probably become bi-protonated. Belongs to the influenza viruses matrix protein M2 family. +Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins. Interacts with the Sec translocase complex via SecD. Specifically interacts with transmembrane segments of nascent integral membrane proteins during membrane integration. Belongs to the OXA1/ALB3/YidC family. Type 1 subfamily. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity). Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically. Binds to both single-stranded guanine- and cytosine-rich strands within the nuclease hypersensitive element (NHE) III(1) region of the MYC gene promoter. Does not bind to duplex NHE III(1). Has G-quadruplex (G4) DNA-binding activity, which is independent of its nucleotide-binding and kinase activity. Binds both folded and unfolded G4 with similar low nanomolar affinities. Stabilizes folded G4s regardless of whether they are prefolded or not (By similarity). Exhibits histidine protein kinase activity (PubMed:12486123). a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. Hexamer of two different chains: A and B (A6, A5B, A4B2, A3B3, A2B4, AB5, B6) (By similarity). Interacts with CAPN8 (By similarity). Interacts with AKAP13 (By similarity). Interacts ITGB1BP1 (via C-terminal domain region) (By similarity). Interacts with BCL2L10 (By similarity). Colocalizes with ITGB1 and ITGB1BP1 at the edge or peripheral ruffles and lamellipodia during the early stages of cell spreading on fibronectin or collagen but not on vitronectin or laminin substrates. Belongs to the NDK family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Methyltransferase required for the conversion of demethylmenaquinol (DMKH2) to menaquinol (MKH2). a 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + H(+) + S-adenosyl-L-homocysteine Quinol/quinone metabolism; menaquinone biosynthesis; menaquinol from 1,4-dihydroxy-2-naphthoate: step 2/2. Belongs to the class I-like SAM-binding methyltransferase superfamily. MenG/UbiE family. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +Catalyzes the sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine. H2O + L-histidinol + 2 NAD(+) = 3 H(+) + L-histidine + 2 NADH Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 9/9. Belongs to the histidinol dehydrogenase family. +Transaminase; part of the gene clusters that mediate the biosynthesis of AM-toxins, host-selective toxins (HSTs) causing Alternaria blotch on apple, a worldwide distributed disease (By similarity). AM-toxins are cyclic depsipeptides containing the 3 residues 2-hydroxy-isovaleric acid (2-HIV), dehydroalanine, L-alanine which are common for all 3 AM-toxins I to III. The fourth precursor is L-alpha-amino-methoxyphenyl-valeric acid (L-Amv) for AM-toxin I, L-alpha-amino-phenyl-valeric acid (L-Apv) for AM-toxin II, and L-alpha-amino-hydroxyphenyl-valeric acid (L-Ahv) for AM-toxin III (Probable). AM-toxins have two target sites for affecting susceptible apple cells; they cause invagination of the plasma membrane and electrolyte loss and chloroplast disorganization (PubMed:22846083). The non-ribosomal peptide synthetase AMT1 contains 4 catalytic modules and is responsible for activation of each residue in AM-toxin (PubMed:10875335). The aldo-keto reductase AMT2 catalyzes the conversion of 2-keto-isovaleric acid (2-KIV) to 2-hydroxy-isovaleric acid (2-HIV), one of the precursor residues incorporated by AMT1 during AM-toxin biosynthesis, by reduction of its ketone to an alcohol (PubMed:15066029). The cytochrome P450 monooxygenase AMT3 and the thioesterase AMT4 are also important for AM-toxin production, but their exact function within the AM-toxin biosynthesis are not known yet (PubMed:17990954). Up to 21 proteins (including AMT1 to AMT4) are predicted to be involved in AM-toxin biosynthesis since their expression ishighly up-regulated in AM-toxin-producing cultures (PubMed:17990954). Mycotoxin biosynthesis. Gene clusters encoding host-selective toxins (HSTs) are localized on conditionally dispensable chromosomes (CDCs), also called supernumerary chromosomes, where they are present in multiple copies (PubMed:17990954). The CDCs are not essential for saprophytic growth but controls host-selective pathogenicity (PubMed:17990954). Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family. +Acts as one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. Cytoplasmic dynein 1 acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. May play a role in changing or maintaining the spatial distribution of cytoskeletal structures (By similarity). Binds and inhibits the catalytic activity of neuronal nitric oxide synthase. Promotes transactivation functions of ESR1 and plays a role in the nuclear localization of ESR1. Regulates apoptotic activities of BCL2L11 by sequestering it to microtubules. Upon apoptotic stimuli the BCL2L11-DYNLL1 complex dissociates from cytoplasmic dynein and translocates to mitochondria and sequesters BCL2 thus neutralizing its antiapoptotic activity (By similarity). Homodimer. Monomer; the monomeric form is incapable of binding to target proteins. The cytoplasmic dynein 1 complex consists of two catalytic heavy chains (HCs) and a number of non-catalytic subunits presented by intermediate chains (ICs), light intermediate chains (LICs) and light chains (LCs); the composition seems to vary in respect to the IC, LIC and LC composition. The heavy chain homodimer serves as a scaffold for the probable homodimeric assembly of the respective non-catalytic subunits. The ICs and LICs bind directly to the HC dimer and the LCs assemble on the IC dimer. Interacts with TXNDC17. Interacts with WWC1 and ESR1. The interaction with WWC1 is mandatory for the recruitment and transactivation functions of ESR1 or DYNLL1 to the target chromatin. Interacts with BCL2; the interaction is greatly enhanced in the nucleus and in mitochondria upon induction of apoptosis. Interacts with PAK1; the interaction requires dimeric DYNLL1. Interacts with MYZAP. Part of an astrin (SPAG5)-kinastrin (SKAP) complex containing KNSTRN, SPAG5, PLK1, DYNLL1 and SGO2. Interacts with ATMIN; this interaction inhibits ATMIN transcriptional activity and hence may play a role in a feedback loop whereby DYNLL1 inhibits transactivation of its own promoter by ATMIN. Interacts with NEK9 (not phosphorylated at 'Ser-944') (By similarity). Interacts with BCL2L11 (PubMed:21478148). Interacts with BICD2 (PubMed:22956769). Interacts with BCAS1 (By similarity). Interacts with Bassoon/BSN (By similarity). Interacts with HDAC6 (By similarity). Interacts with TPPP (By similarity). Interacts with AMBRA1 (via TQT motifs); tethering AMBRA1 to the cytoskeleton (By similarity). Interacts with FAM83D/CHICA (via C-terminus) (By similarity). Interacts with HMMR, SPAG5/Astrin and KNSTRN/Kinastrin (By similarity). Upon induction of apoptosis translocates together with BCL2L11 to mitochondria. Phosphorylation at Ser-88 appears to control the dimer-monomer transition. Belongs to the dynein light chain family. +Putative oxophytodienoate reductase that may be involved in the biosynthesis or metabolism of oxylipin signaling molecules. Belongs to the NADH:flavin oxidoreductase/NADH oxidase family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 2/3. Homotetramer. Belongs to the argininosuccinate synthase family. Type 1 subfamily. +Catalyzes the conversion of lactate to pyruvate. (S)-lactate + NAD(+) = H(+) + NADH + pyruvate Fermentation; pyruvate fermentation to lactate; (S)-lactate from pyruvate: step 1/1. Homotetramer. Belongs to the LDH/MDH superfamily. LDH family. +Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. It also functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. Sec13 is required for efficient mRNA export from the nucleus to the cytoplasm and for correct nuclear pore biogenesis and distribution (By similarity). The COPII coat is composed of at least 5 proteins: the sec23/24 complex, the sec13/31 complex, and the protein sar1. Component of the nuclear pore complex (NPC). NPC constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. Due to its 8-fold rotational symmetry, all subunits are present with 8 copies or multiples thereof. Belongs to the WD repeat SEC13 family. +Nucleoside triphosphate pyrophosphatase that hydrolyzes dTTP and UTP. Can also hydrolyze CTP and the modified nucleotides pseudo-UTP, 5-methyl-CTP (m(5)CTP) and 5-methyl-UTP (m(5)UTP) (PubMed:24210219). May have a dual role in cell division arrest and in preventing the incorporation of modified nucleotides into cellular nucleic acids (PubMed:24210219). dTTP + H2O = diphosphate + dTMP + H(+) H2O + UTP = diphosphate + H(+) + UMP CTP + H2O = CMP + diphosphate + H(+) H2O + psi-UTP = diphosphate + H(+) + psi-UMP 5-methyl-CTP + H2O = 5-methyl-CMP + diphosphate + H(+) H2O + TTP = 5-methyl-UMP + diphosphate + H(+) kcat is 11.6 sec(-1) with dTTP as substrate. kcat is 4.9 sec(-1) with UTP as substrate. kcat is 7.1 sec(-1) with CTP as substrate. kcat is 2.4 sec(-1) with m(5)UTP as substrate. kcat is 8.5 sec(-1) with m(5)CTP as substrate. kcat is 7.2 sec(-1) with pseudo-UTP as substrate. Homodimer. Not essential for cell division. Overexpression results in extensive filamentation caused by a disruption and subsequent inhibition of the septation process. Belongs to the Maf family. YhdE subfamily. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Transport of potassium into the cell. Belongs to the HAK/KUP transporter (TC 2.A.72) family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. The sequence shown here has been extracted from PDB entry 1SRV. +Carboxylesterase that acts as a key negative regulator of the Wnt signaling pathway by specifically mediating depalmitoleylation of WNT proteins. Serine palmitoleylation of WNT proteins is required for efficient binding to frizzled receptors. [Wnt protein]-O-(9Z)-hexadecenoyl-L-serine + H2O = (9Z)-hexadecenoate + [Wnt protein]-L-serine + H(+) Belongs to the pectinacetylesterase family. Notum subfamily. +Catalyzes thiolytic cleavage of beta-ketoadipyl-CoA to succinyl-CoA and acetyl-CoA. acetyl-CoA + succinyl-CoA = 3-oxoadipyl-CoA + CoA Aromatic compound metabolism; beta-ketoadipate pathway; acetyl-CoA and succinyl-CoA from 3-oxoadipate: step 2/2. Belongs to the thiolase-like superfamily. Thiolase family. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Belongs to the UPF0761 family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Homodimer. Belongs to the GrpE family. +May regulate immune response to the intracellular capsid in acting as a T-cell tolerogen, by having an immunoregulatory effect which prevents destruction of infected cells by cytotoxic T-cells. This immune regulation may predispose to chronicity during perinatal infections and prevent severe liver injury during adult infections. Homodimerizes. Phosphorylated. Cleaved by host furin. Belongs to the orthohepadnavirus precore antigen family. +Microtubule-associated force-producing protein that plays a role in organelle transport. Its motor activity is directed toward the microtubule's plus end (By similarity). May connect microtubules to actin filaments. Associates with actin-based structures in cells and is likely involved in the organization of actin cytoskeletons in such structures. Interacts with actin. Composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it hydrolyzes ATP and binds microtubule), a central alpha-helical coiled coil domain that mediates the heavy chain dimerization; and a small globular C-terminal domain which interacts with other proteins, vesicles and membranous organelles. Belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Kinesin family. Kinesin subfamily. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Probable transcriptional regulator involved in cell adhesion. Belongs to the adn1/SEU family. +Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Binds 1 potassium ion per subunit. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. +Oxidative deamination of D-amino acids. A + a D-alpha-amino acid + H2O = a 2-oxocarboxylate + AH2 + NH4(+) Belongs to the DadA oxidoreductase family. +Catalyzes efficient strand joining on a single nicked DNA. ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate. Belongs to the ATP-dependent DNA ligase family. Was originally proposed to code for two separate adjacent ORFs, HI_1182 and HI_1183. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Belongs to the bacterial ribosomal protein bL36 family. +Hydrolyzes fatty acids from S-acylated cysteine residues in proteins with a strong preference for palmitoylated G-alpha proteins over other acyl substrates. Mediates the deacylation of G-alpha proteins such as GPA1 in vivo, but has weak or no activity toward palmitoylated Ras proteins. Has weak lysophospholipase activity in vitro; however such activity may not exist in vivo. H2O + S-hexadecanoyl-L-cysteinyl-[protein] = H(+) + hexadecanoate + L-cysteinyl-[protein] Belongs to the AB hydrolase superfamily. AB hydrolase 2 family. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +Transcription factor that specifies expression of key genes in developing central nervous system (CNS). Essential for many, if not all, late developing neuroblastoma (NB) sublineages. Binds to the 5'-[CG]C[CT][CT]AAAAA[AT]-3' DNA sequence, like hb, suggesting that cas and hb act as a late regulators in early and late CNS NB sublineage, respectively. Acts by repressing expression of nub/pdm-1 and pdm2/pdm-2 POU genes, and restrict their pattern of expression in appropriate cells. Required for a full expression of vvl/drifter and acj6/I-POU; it is however unknown whether it directly activates these genes. Controls engrailed (en) expression in the ventral nerve chord. Expressed in a specific subset of neuroblasts in the ventral nerve cord and the procephalic region in the embryo. Expressed in many, if not all, late delaminating NBs, and in early NBs, but only after they have undergone several rounds of ganglion mother cell-producing divisions. Expressed in embryos. Expressed from blastoderm embryos. Not expressed in first and second instar larvae. Weakly expressed in third instar larvae. May be weakly expressed in adults. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Involved in oxygen transport from gills to the various peripheral tissues. Heterotetramer of two alpha chains and two beta chains. Red blood cells. Belongs to the globin family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form the product. After dissociation, two additional enzymatic reactions on the tRNA convert PreQ1 to queuine (Q), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine). 7-aminomethyl-7-carbaguanine + guanosine(34) in tRNA = 7-aminomethyl-7-carbaguanosine(34) in tRNA + guanine Binds 1 zinc ion per subunit. tRNA modification; tRNA-queuosine biosynthesis. Homodimer. Within each dimer, one monomer is responsible for RNA recognition and catalysis, while the other monomer binds to the replacement base PreQ1. Belongs to the queuine tRNA-ribosyltransferase family. +Tropomyosin, in association with the troponin complex, plays a central role in the calcium dependent regulation of muscle contraction. Homodimer. The molecule is in a coiled coil structure that is formed by 2 polypeptide chains. The sequence exhibits a prominent seven-residues periodicity. Causes an allergic reaction in human. Belongs to the tropomyosin family. +(6S)-10-formyltetrahydrofolate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide = (6S)-5,6,7,8-tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide H2O + IMP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide Purine metabolism; IMP biosynthesis via de novo pathway; 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide (10-formyl THF route): step 1/1. Purine metabolism; IMP biosynthesis via de novo pathway; IMP from 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide: step 1/1. The IMP cyclohydrolase activity resides in the N-terminal region. Belongs to the PurH family. +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Involved in protein export. Participates in an early event of protein translocation (By similarity). Belongs to the SecG family. +Component of the RACK1 regulatory proteins that play a role in multiple signal transduction pathways. Homodimer and heterodimer with RACK1A. Belongs to the WD repeat G protein beta family. Ribosomal protein RACK1 subfamily. +Used by the larvae to construct a supramolecular structure, the larval tube. Salivary gland. +Catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates. Cleaves off the terminal sialic acids on the glycosylated HA during virus budding to facilitate virus release. Additionally helps virus spread through the circulation by further removing sialic acids from the cell surface. These cleavages prevent self-aggregation and ensure the efficient spread of the progeny virus from cell to cell. Otherwise, infection would be limited to one round of replication. Described as a receptor-destroying enzyme because it cleaves a terminal sialic acid from the cellular receptors. May facilitate viral invasion of the upper airways by cleaving the sialic acid moieties on the mucin of the airway epithelial cells. Likely to plays a role in the budding process through its association with lipid rafts during intracellular transport. May additionally display a raft-association independent effect on budding. Plays a role in the determination of host range restriction on replication and virulence. Sialidase activity in late endosome/lysosome traffic seems to enhance virus replication. Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates. Inhibited by the neuraminidase inhibitors zanamivir (Relenza) and oseltamivir (Tamiflu). These drugs interfere with the release of progeny virus from infected cells and are effective against all influenza strains. Resistance to neuraminidase inhibitors is quite rare. Homotetramer. Preferentially accumulates at the apical plasma membrane in infected polarized epithelial cells, which is the virus assembly site. Uses lipid rafts for cell surface transport and apical sorting. In the virion, forms a mushroom-shaped spike on the surface of the membrane. Intact N-terminus is essential for virion morphogenesis. Possesses two apical sorting signals, one in the ectodomain, which is likely to be a glycan, and the other in the transmembrane domain. The transmembrane domain also plays a role in lipid raft association. N-glycosylated. The influenza A genome consist of 8 RNA segments. Genetic variation of hemagglutinin and/or neuraminidase genes results in the emergence of new influenza strains. The mechanism of variation can be the result of point mutations or the result of genetic reassortment between segments of two different strains. Belongs to the glycosyl hydrolase 34 family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Endo-1,4-mannanase that catalyzes the random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans and heteromannans. It is a crucial enzyme for depolymerization of seed galactomannans and wood galactoglucomannans. Active against locust bean gum and gum guar (PubMed:16844780). Also has efficient transglycosylation activity. Produces mainly mannopentaose and mannoheptaose out of mannotetraose. May even prefer sugars as acceptors instead of water (PubMed:24950755). Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans. Optimum pH is 6. Optimum temperature is 60 degrees Celsius. Monomer. Belongs to the glycosyl hydrolase 5 (cellulase A) family. +Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility. Component of a PRC1-like complex. The hPRC-H complex purification reported by PubMed:12167701 probably presents a mixture of different PRC1-like complexes. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Belongs to the thiamine-phosphate synthase family. +Converts GTP to 7,8-dihydroneopterin triphosphate. GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Belongs to the GTP cyclohydrolase IV family. +Catalyzes the formation of L-homocysteine from O-succinyl-L-homoserine (OSHS) and hydrogen sulfide. Cannot use the other activated form of L-homoserine, O-acetyl-L-homoserine, as a substrate. hydrogen sulfide + O-succinyl-L-homoserine = L-homocysteine + succinate Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-homocysteine from O-succinyl-L-homoserine: step 1/1. Homotetramer. Belongs to the trans-sulfuration enzymes family. MetZ subfamily. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. Extended N-terminus. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O H2O + L-histidinol phosphate = L-histidinol + phosphate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 8/9. In the N-terminal section; belongs to the histidinol-phosphatase family. In the C-terminal section; belongs to the imidazoleglycerol-phosphate dehydratase family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 1 subfamily. +Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Belongs to the Nudix hydrolase family. RppH subfamily. +Belongs to the SfsA family. +Insecticidal toxin. It inhibits insect voltage-gated sodium channels (Nav) by partially blocking the channel pore in DUM neurons from the American cockroach, not by acting as a gating modifier. The inhibition is only partially reversible after prolonged washout. In vivo, the toxin causes flaccid paralysis followed by death when injected into Heliothis virescens larvae. It also causes uncoordinated movements followed by full paralysis to sheep blowflies (Lucilia cuprina). When the toxin is fused to snowdrop lectin, it is orally active against larvae of the tomato moth (Laconobia oleracea), the rice brown planthopper (Nilaparvata lugens), and the peach-potato aphid (Myzus persicae). Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 16 (SFI) family. +Associates with aggregated proteins, together with IbpB, to stabilize and protect them from irreversible denaturation and extensive proteolysis during heat shock and oxidative stress. Aggregated proteins bound to the IbpAB complex are more efficiently refolded and reactivated by the ATP-dependent chaperone systems ClpB and DnaK/DnaJ/GrpE. Its activity is ATP-independent. Monomer. Forms homomultimers of about 100-150 subunits at optimal growth temperatures. Conformation changes to monomers at high temperatures or high ionic concentrations. Belongs to the small heat shock protein (HSP20) family. +Myristoyl-binding protein that acts as a cargo adapter: specifically binds the myristoyl moiety of a subset of N-terminally myristoylated proteins and is required for their localization. Plays a key role in localization of proteins to the primary cilium membrane (By similarity). Adopts an immunoglobulin-like beta-sandwich fold forming a hydrophobic cavity that capture N-terminally myristoylated target peptides. Phe residues within the hydrophobic beta sandwich are required for myristate binding (By similarity). Belongs to the PDE6D/unc-119 family. +ATP-binding (A) component of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). Belongs to the ABC transporter superfamily. Energy-coupling factor EcfA family. +Dimethyl sulfoxide (DMSO) reductase catalyzes the reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS) during anaerobic respiration; it can also use trimethylamine N-oxide (TMAO) as terminal electron acceptor. Subunit B is proposed to be involved in electron transfer. Binds 4 [4Fe-4S] clusters. Probable multiprotein complex that likely consists of DmsA, DmsB and DmsC. By anaerobic conditions. Its expression is under the control of DmsR. +Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Expressed in the developing limb buds. Belongs to the Abd-B homeobox family. It is uncertain whether Met-1 or Met-11 is the initiator. Truncated N-terminus. Truncated N-terminus. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Atypical MAPK protein that regulates several process such as autophagy, ciliogenesis, protein trafficking/secretion and genome integrity, in a kinase activity-dependent manner. Controls both, basal and starvation-induced autophagy throught its interaction with GABARAP, MAP1LC3B and GABARAPL1 leading to autophagosome formation, SQSTM1 degradation and reduced MAP1LC3B inhibitory phosphorylation. Regulates primary cilium formation and the localization of ciliary proteins involved in cilium structure, transport, and signaling. Prevents the relocation of the sugar-adding enzymes from the Golgi to the endoplasmic reticulum, thereby restricting the production of sugar-coated proteins. Upon amino-acid starvation, mediates transitional endoplasmic reticulum site disassembly and inhibition of secretion. Binds to chromatin leading to MAPK15 activation and interaction with PCNA, that which protects genomic integrity by inhibiting MDM2-mediated degradation of PCNA. Regulates DA transporter (DAT) activity and protein expression via activation of RhoA. In response to H(2)O(2) treatment phosphorylates ELAVL1, thus preventing it from binding to the PDCD4 3'UTR and rendering the PDCD4 mRNA accessible to miR-21 and leading to its degradation and loss of protein expression (By similarity). Also functions in a kinase activity-independent manner as a negative regulator of growth (PubMed:9891064). Phosphorylates in vitro FOS and MBP (PubMed:11875070). During oocyte maturation, plays a key role in the microtubule organization and mei- otic cell cycle progression in oocytes, fertilized eggs, and early embryos (By similarity). Interacts with ESRRA promoting its re-localization from the nucleus to the cytoplasm and then prevents its transcriptional activity (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by threonine and tyrosine phosphorylation. Inhibited by dual specificity phosphatases, such as DUSP1 (By similarity). Phosphorylation and activation in response to DNA damaging agents, serum stimulation. Constitutively activated when phosphorylated on Tyr-178. Activity depends on the relative rates of MAPK15 autophosphorylation and dephosphorylation by PTPN1 (By similarity). Interacts with CSK/c-Src, ABL1, RET and TGFB1I1. Interacts with GABARAP, MAP1LC3B and GABARAPL1; controls, in a kinase-dependent fashion, both basal and starvation-induced autophagy. Interacts with ESRRA; promotes re-localization of ESRRA to the cytoplasm through a XPO1-dependent mechanism then inhibits ESRRA transcriptional activity. Interacts with PCNA; the interaction is chromatin binding- and kinase activity-dependent and prevents MDM2-mediated PCNA destruction by inhibiting the association of PCNA with MDM2 (By similarity). Interacts with DVL2 (By similarity). Interacts with CLIC3; MAPK15 does not phosphorylates CLIC3 (PubMed:9880541). Co-localizes to the cytoplasm only in presence of ESRRA. Translocates to the nucleus upon activation (By similarity). At prometaphase I, metaphase I (MI), anaphase I, telophase I, and metaphase II (MII) stages, is stably detected at the spindle (By similarity). Ubiquitously expressed at a weak level. Highest expression is found in testis and to a lower extent in lung. C-terminal domain, rather than the kinase activity, is required for the full function of the enzyme. This region may be a protein interaction domain that regulates kinase localization, activation and transcriptional activity. When C-terminally truncated, the enzyme shows a reduction in the Thr-Glu-Tyr (TEY) phosphorylation level, in the in vitro kinase activity, in its nuclear localization and in its inhibitory effect on cell growth. The N-terminal region (1-20) is the minimal region necessary for ubiquitination and further proteasomal degradation. The TXY motif contains the threonine and tyrosine residues whose phosphorylation activates the MAP kinases. Autophosphorylated on Thr-176 and Tyr-178; activates the enzyme. Dephosphorylated by PTPN1. Ubiquitinated. Ubiquitination may allow its tight kinase activity regulation and rapid turnover. May be ubiquitinated by a SCF E3 ligase. Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. MAP kinase subfamily. +Involved in siroheme-dependent heme b biosynthesis. Catalyzes the decarboxylation of siroheme into didecarboxysiroheme (PubMed:24865947). Siroheme is decarboxylated to monodecarboxysiroheme, which is in turn decarboxylated to didecarboxysiroheme (PubMed:24865947). 2 H(+) + siroheme = 12,18-didecarboxysiroheme + 2 CO2 Porphyrin-containing compound metabolism; protoheme biosynthesis. Forms an heterodimer composed of AhbA and AhbB. Belongs to the Ahb/Nir family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. Belongs to the phosphatidylserine decarboxylase family. PSD-A subfamily. +Putative transcription factor. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Involved in the biosynthesis of the major light-harvesting pigment bacteriochlorophyll c (BChlc), which confers a significant competitive advantage to green sulfur bacteria living at limiting red and near-infrared light intensities. BchR is a methyltransferase that adds a single methyl group to the methyl carbon at the C-12(1) position of 8-ethyl-12-methyl-3-vinylbacteriochlorophyllide d to yield 8,12-diethyl-3-vinylbacteriochlorophyllide d. 8-ethyl-12-methyl-3-vinylbacteriochlorophyllide d + S-adenosyl-L-methionine = 8,12-diethyl-3-vinylbacteriochlorophyllide d + H(+) + S-adenosyl-L-homocysteine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Porphyrin-containing compound metabolism; bacteriochlorophyll biosynthesis (light-independent). Cells lacking this gene produce bacteriochlorophyll c (BChlc) that is not methylated at C-12(1) and show a growth rate that decreases to 53% of that of the wild-type at low light intensity. Double mutants lacking both bchR and bchQ produce bacteriochlorophyll c (BChlc) that is not methylated at C-8(2) and C-12(1), and show a growth rate that decreases to 41% of that of the wild-type at low light intensity. Belongs to the radical SAM superfamily. +Synthesizes alpha-1,4-glucan chains using ADP-glucose. [(1->4)-alpha-D-glucosyl](n) + ADP-alpha-D-glucose = [(1->4)-alpha-D-glucosyl](n+1) + ADP + H(+) Glycan biosynthesis; glycogen biosynthesis. Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily. +This protein catalyzes the penultimate step in bacteriochlorophyll a biosynthesis. Porphyrin-containing compound metabolism; bacteriochlorophyll biosynthesis (light-independent). +Belongs to the UPF0735 family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +Belongs to the UPF0266 family. +Polymerase responsible for protein-primed viral DNA replication by strand displacement with high processivity and fidelity. To start replication, the DNA polymerase forms a heterodimer with a free primer terminal protein (TP), recognizes the replication origins at both 5' ends of the linear chromosome, and initiates replication using as primer the OH-group of Ser-232 of the TP. This polymerase possesses three enzymatic activities: DNA synthesis (polymerase), primer terminal protein (TP) deoxynucleotidylation, which is the formation of a covalent linkage (phosphoester) between the hydroxyl group of a specific serine residue in TP and 5'-dAMP, a reaction directed by the second T at the 3' end, and 3' to 5' exonuclease activity. Exonuclease activity has a proofreading purpose. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Interacts with the primer terminal protein; this interaction allows the initiation of TP-primed DNA replication at both viral DNA ends. Interacts with DNA. The N-terminus contains the 3'-5' exonuclease activity and strand displacement ability. The C-terminus contains the protein-primed initiation, DNA polymerization and pyrophosphorolytic activities. This DNA polymerase requires a protein as a primer. Belongs to the DNA polymerase type-B family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Homodimer. Belongs to the GrpE family. +Belongs to the universal ribosomal protein uS2 family. +Catalyzes the reversible retro-aldol cleavage of 2-keto-3-deoxy-L-rhamnonate (KDR) to pyruvate and lactaldehyde. 2-dehydro-3-deoxy-L-rhamnonate = (S)-lactaldehyde + pyruvate Binds 1 Mg(2+) ion per subunit. Homohexamer. Belongs to the HpcH/HpaI aldolase family. KDR aldolase subfamily. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Belongs to the SecA family. +D-arabinose 5-phosphate + H2O + phosphoenolpyruvate = 3-deoxy-alpha-D-manno-2-octulosonate-8-phosphate + phosphate Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate: step 2/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsA family. +Involved in the positive regulation of the TOR signaling pathway (PubMed:21216945, PubMed:25399018). Acts as a negative regulator of PP2A catalytic activity (PubMed:10517853, PubMed:21216945, PubMed:24357600). Plays a positive role in the ABA-regulated inhibition of germination, probably throught its interaction with ABI5 (PubMed:24357600). Interacts with the 36 kDa catalytic subunit (subunit C) of PP2A (PubMed:10517853). Interacts with PP2A1 and PP2A2 (PubMed:24357600). Interacts with PP2A3, PPX1 and FYPP1 (PubMed:21216945, PubMed:24357600). Interacts with FYPP3 and ABI5 (PubMed:24357600). Interacts with ATPK1/S6K1 and ATPK2/S6K2 (PubMed:25399018). Interacts with TIP41L (By similarity). Ubiquitous (PubMed:10517853). Highly expressed in seed, and particularly in the embryo (PubMed:24357600). Highly expressed during seed maturation. By chilling (PubMed:10517853). By abscisic acid (ABA) (PubMed:24357600). Phosphorylated by TOR kinase in vitro. RNAi plants show the formation of spontaneous disease-like nectrotic lesions leading to premature cell death. The defective plants also display a strong reduction in protein synthesis, the induction of autophagy and nitrogen mobilization. Plants over-expressing TAP46 exhibit an increased abscisic acid (ABA) sensitivity in seed germination and a reduced PP2A activity (PubMed:24357600). Over-expression of TAP46 also leads to the stimulation of the overall plant growth and the increased nitrogen-assimilating activities (PubMed:25399018). Belongs to the IGBP1/TAP42 family. +Involved in the final reduction of the elongation cycle of fatty acid synthesis (FAS II). Catalyzes the reduction of a carbon-carbon double bond in an enoyl moiety that is covalently linked to an acyl carrier protein (ACP). a 2,3-saturated acyl-[ACP] + NAD(+) = a (2E)-enoyl-[ACP] + H(+) + NADH Lipid metabolism; fatty acid biosynthesis. Monomer. Belongs to the TER reductase family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 2 family. +Subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation. N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity. Protein modification; protein glycosylation. Component of the oligosaccharyltransferase (OST) complex. Belongs to the DAD/OST2 family. +Probable role in the clearance of triglyceride-rich lipoprotein from blood. Binds chylomicrons, LDL and VLDL in presence of free fatty acids and allows their subsequent uptake in the cells (PubMed:15265030). Maintains epithelial barrier function by recruiting MARVELD2/tricellulin to tricellular tight junctions (PubMed:21245199, PubMed:23239027). Homotrimer or homotetramer (By similarity). Assembles into cell-cell contacts (PubMed:21245199). Interacts (via the cytoplasmic domain) with MARVELD2 (via C-terminal cytoplasmic domain); the interaction is required to recruit MARVELD2 to tricellular contacts (PubMed:21245199, PubMed:23239027). Interacts with OCLN (PubMed:23239027). Located at tricellular contacts. Expressed in eptihelial tissues (at protein level) (PubMed:21245199). Specifically expressed in liver and to a lower extent in kidney (at protein level). Also detected in brain, testis, ovaries, adrenal gland, intestine, muscle, and lung. In colon, only expressed in the lower portion of crypts (PubMed:23239027). Expressed in liver, stomach, small intestine and colon. Also detected in other epithelial tissues. Expressed during embryogenesis (at protein level). Detected from 7.5 dpc to 17 dpc. Phosphorylation at Ser-308 by MAPK8/JNK1 and MAPK9/JNK2 may be required for exclusive localization at tricellular tight junstions. Death between 12.5 dpc and 15.5 dpc probably due to impaired liver and embryonic development. Belongs to the immunoglobulin superfamily. LISCH7 family. +Positive regulator of phosphatidylinositol 4,5-bisphosphate turnover and negatively regulates signaling through the cell integrity pathway. Involved in rDNA silencing (By similarity). Belongs to the IRS4 family. +Belongs to the UPF0319 family. +Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. Binds two Mg(2+) per subunit. Monomer. Belongs to the type IA topoisomerase family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Belongs to the PEP2 family. The predicted gene ATEG_07673 has been split into 2 genes: ATEG_07673.1 and ATEG_07673.2. +Mediates assembly of pili by forming soluble multimeric complexes with pili subunits as an intermediate step in the assembly process. Belongs to the periplasmic pilus chaperone family. +Plays a role in the dissolution of the outermost membrane of extracellular enveloped virions (EV) to allow virion entry into host cells. Participates also in wrapping mature virions (MV) to form enveloped virions (EV). Interacts with A33; this interaction is required for efficient targeting of A33 and B5 into enveloped virions. Interacts with A34; this interaction is required for the correct glycosylation, trafficking and stability of A34 and B5 incorporation into extracellular enveloped virions. Interacts with envelope phospholipase F13. B5 is found on enveloped virion (EV) membranes. Belongs to the receptors of complement activation (RCA) family. +ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys) Binds 3 Mg(2+) ions per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Belongs to the PRM5 family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +This enzyme metabolizes arachidonic acid predominantly via a NADPH-dependent olefin epoxidation mainly to 14,15-, 11,12-, and 8,9-epoxyeicosatrienoic acids (EET). It also acts as an omega-1-hydroxylase by metabolizing arachidonic acid to 19-hydroxyeicosatetraenoic acid (19-OH-AA). an organic molecule + O2 + reduced [NADPH--hemoprotein reductase] = an alcohol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Abundantly expressed in heart and liver. Belongs to the cytochrome P450 family. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. Monomer. Belongs to the IF-3 family. +Is able to cleave peptidoglycan. Belongs to the transglycosylase family. IsaA subfamily. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. 2 H(+) + 2 superoxide = H2O2 + O2 Binds 1 Fe cation per subunit. Homodimer. Belongs to the iron/manganese superoxide dismutase family. +Required for the assembly of cytochrome c oxidase. Belongs to the COX23 family. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The eIF-3 complex interacts with pix. Belongs to the eIF-3 subunit C family. +Belongs to the LyrA family. +Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair. Hydrolysis of Ala-|-Gly bond in repressor LexA. Homodimer. Belongs to the peptidase S24 family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the synthesis of IGP and AICAR. The resulting ammonia molecule is channeled to the active site of HisF. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate H2O + L-glutamine = L-glutamate + NH4(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 1 family. +Component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. Component of the nexin-dynein regulatory complex (N-DRC). Interacts with CFAP52 (By similarity). Belongs to the DRC10 family. +Required for defense response to Xanthomonas campestris pv. vesicatoria (Xcv). In heterologous systems, confers resistance to bacterial pathogens such as Pseudomonas syringae pv. tomato but susceptibility to pathogenic oomycetes such as Hylaloperonospora parasitica when expressed in Arabidopsis thaliana. May be involved in the regulation of responses to bitoic and abiotic stresses. Homodimer and heterodimers. Mostly expressed in stems and flowers. In leaves by X.campestris pv. vesicatoria, faster during compatible than incompatible interactions. Induced in leaves by treatments with ethylene, methyl jasmonate (MeJA), abscisic acid (ABA), beta-amino-n-butyric acid (BABA), NaCl, mechanical wounding, and low temperature, but not with salicylic acid (SA). Susceptibility to X.campestris pv. vesicatoria is enhanced upon virus induced gene silencing (VIGS). Belongs to the Casparian strip membrane proteins (CASP) family. +Belongs to the NIPA family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Catalyzes the oxidation 4-aminobutanal (gamma-aminobutyraldehyde) to 4-aminobutanoate (gamma-aminobutyrate or GABA). This is the second step in one of two pathways for putrescine degradation, where putrescine is converted into 4-aminobutanoate via 4-aminobutanal. Also functions as a 5-aminopentanal dehydrogenase in a a L-lysine degradation pathway to succinate that proceeds via cadaverine, glutarate and L-2-hydroxyglutarate. 4-aminobutanal + H2O + NAD(+) = 4-aminobutanoate + 2 H(+) + NADH 5-aminopentanal + H2O + NAD(+) = 5-aminopentanoate + 2 H(+) + NADH Amine and polyamine degradation; putrescine degradation; 4-aminobutanoate from 4-aminobutanal: step 1/1. Amino-acid degradation. Homotetramer. 4-aminobutanal can spontaneously cyclize to 1-pyrroline, and 5-aminopentanal to 1-piperideine. Belongs to the aldehyde dehydrogenase family. Gamma-aminobutyraldehyde dehydrogenase subfamily. +Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate. (S)-dihydroorotate + H2O = H(+) + N-carbamoyl-L-aspartate Binds 2 Zn(2+) ions per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 3/3. Belongs to the metallo-dependent hydrolases superfamily. DHOase family. Class I DHOase subfamily. +Vesicle trafficking protein that functions in the secretory pathway. Part of the t-SNARE complex. Belongs to the syntaxin family. +Binds 1 [2Fe-2S] cluster. Belongs to the CISD protein family. CISD2 subfamily. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Isopentenyl-diphosphate delta-isomerase; part of the second module of ergosterol biosynthesis pathway that includes the middle steps of the pathway (By similarity). IDI1 catalyzes the 1,3-allylic rearrangement of isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity). The second module is carried out in the vacuole and involves the formation of farnesyl diphosphate, which is also an important intermediate in the biosynthesis of ubiquinone, dolichol, heme and prenylated proteins. Activity by the mevalonate kinase ERG12 (FG05912) first converts mevalonate into 5-phosphomevalonate. 5-phosphomevalonate is then further converted to 5-diphosphomevalonate by the phosphomevalonate kinase ERG8 (FG09764). The diphosphomevalonate decarboxylase ERG19 (FG10424) then produces isopentenyl diphosphate. The isopentenyl-diphosphate delta-isomerase IDI1 (FG09722) then catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP). Finally the farnesyl diphosphate synthase ERG20 (FG06784) catalyzes the sequential condensation of isopentenyl pyrophosphate with dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate (Probable). isopentenyl diphosphate = dimethylallyl diphosphate Binds 1 Mg(2+) ion per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1. Belongs to the IPP isomerase type 1 family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase. Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Prokaryotic type I sub-subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +Can activate aflatoxin B1 to a genotoxic product. an organic molecule + O2 + reduced [NADPH--hemoprotein reductase] = an alcohol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] P450 can be induced to high levels in liver and other tissues by various foreign compounds, including drugs, pesticides, and carcinogens. Belongs to the cytochrome P450 family. +Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. 2-oxoglutarate + O-phospho-L-serine = 3-phosphooxypyruvate + L-glutamate 2-oxoglutarate + 4-(phosphooxy)-L-threonine = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate Binds 1 pyridoxal phosphate per subunit. Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 2/3. Homodimer. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. SerC subfamily. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Required for the assembly of the mitochondrial NADH:ubiquinone oxidoreductase complex (complex I). Involved in the assembly of the distal region of complex I. Interacts with incompletely assembled mitochondrial NADH:ubiquinone oxidoreductase complex (complex I). Belongs to the ATP synthase subunit s family. +Serine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]-Q. Phosphorylates 'Ser-139' of histone variant H2AX at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. After the introduction of DNA breaks by the RAG complex on one immunoglobulin allele, acts by mediating a repositioning of the second allele to pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. Also involved in signal transduction and cell cycle control. May function as a tumor suppressor. Necessary for activation of ABL1 and SAPK. Phosphorylates DYRK2, CHEK2, p53/TP53, FBXW7, FANCD2, NFKBIA, BRCA1, CTIP, nibrin (NBN), TERF1, UFL1, RAD9, UBQLN4 and DCLRE1C (PubMed:9843217, PubMed:9733515, PubMed:10550055, PubMed:10766245, PubMed:10839545, PubMed:10910365, PubMed:10802669, PubMed:10973490, PubMed:11375976, PubMed:12086603, PubMed:15456891, PubMed:19965871, PubMed:30612738, PubMed:30886146, PubMed:26774286). May play a role in vesicle and/or protein transport. Could play a role in T-cell development, gonad and neurological function. Plays a role in replication-dependent histone mRNA degradation. Binds DNA ends. Phosphorylation of DYRK2 in nucleus in response to genotoxic stress prevents its MDM2-mediated ubiquitination and subsequent proteasome degradation. Phosphorylates ATF2 which stimulates its function in DNA damage response. Phosphorylates ERCC6 which is essential for its chromatin remodeling activity at DNA double-strand breaks (PubMed:29203878). Phosphorylates TTC5/STRAP at 'Ser-203' in the cytoplasm in response to DNA damage, which promotes TTC5/STRAP nuclear localization (PubMed:15448695). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Inhibited by wortmannin. Homodimer (PubMed:28508083). Dimers or tetramers in inactive state. On DNA damage, autophosphorylation dissociates ATM into monomers rendering them catalytically active. Binds p53/TP53, ABL1, BRCA1, NBN/nibrin and TERF1. Part of the BRCA1-associated genome surveillance complex (BASC), which contains BRCA1, MSH2, MSH6, MLH1, ATM, BLM, PMS2 and the RAD50-MRE11-NBN protein complex. This association could be a dynamic process changing throughout the cell cycle and within subnuclear domains. Interacts with RAD17; DNA damage promotes the association. Interacts with EEF1E1; the interaction, induced on DNA damage, up-regulates TP53. Interacts with DCLRE1C, KAT8, KAT5, NABP2, ATMIN and CEP164. Interacts with AP2B1 and AP3B2; the interaction occurs in cytoplasmic vesicles (By similarity). Interacts with TELO2 and TTI1. Interacts with DDX1. Interacts with BRAT1. Interacts with CYREN (via XLF motif) (By similarity). Primarily nuclear. Found also in endocytic vesicles in association with beta-adaptin. Found in pancreas, kidney, skeletal muscle, liver, lung, placenta, brain, heart, spleen, thymus, testis, ovary, small intestine, colon and leukocytes. By ionizing radiation. The FATC domain is required for interaction with KAT5. Phosphorylated by NUAK1/ARK5 (PubMed:12409306). Autophosphorylation on Ser-367, Ser-1893, Ser-1981 correlates with DNA damage-mediated activation of the kinase (PubMed:12556884, PubMed:16141325, PubMed:16858402, PubMed:21144835, PubMed:27664052). During the late stages of DNA damage response, dephosphorylated following deacetylation by SIRT7, leading to ATM deactivation (PubMed:30944854). Acetylation, on DNA damage, is required for activation of the kinase activity, dimer-monomer transition, and subsequent autophosphorylation on Ser-1981 (PubMed:12556884, PubMed:16141325, PubMed:16858402, PubMed:17923702, PubMed:21144835). Acetylated in vitro by KAT5/TIP60 (PubMed:16141325). Deacetylated by SIRT7 during the late stages of DNA damage response, promoting ATM dephosphorylation and subsequent deactivation (PubMed:30944854). The disease is caused by variants affecting the gene represented in this entry. Defects in ATM may contribute to T-cell acute lymphoblastic leukemia (TALL) and T-prolymphocytic leukemia (TPLL). TPLL is characterized by a high white blood cell count, with a predominance of prolymphocytes, marked splenomegaly, lymphadenopathy, skin lesions and serous effusion. The clinical course is highly aggressive, with poor response to chemotherapy and short survival time. TPLL occurs both in adults as a sporadic disease and in younger AT patients. Defects in ATM may contribute to B-cell non-Hodgkin lymphomas (BNHL), including mantle cell lymphoma (MCL). Defects in ATM may contribute to B-cell chronic lymphocytic leukemia (BCLL). BCLL is the commonest form of leukemia in the elderly. It is characterized by the accumulation of mature CD5+ B-lymphocytes, lymphadenopathy, immunodeficiency and bone marrow failure. Belongs to the PI3/PI4-kinase family. ATM subfamily. Truncated N-terminus. Probable cloning artifact. Truncated N-terminus. Probable cloning artifact. Ataxia telangiectasia mutated entry +Part of the multicomponent 3-phenylpropionate dioxygenase. Converts 3-phenylpropionic acid (PP) and cinnamic acid (CI) into 3-phenylpropionate-dihydrodiol (PP-dihydrodiol) and cinnamic acid-dihydrodiol (CI-dihydrodiol), respectively. 3-phenylpropanoate + H(+) + NADH + O2 = 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate + NAD(+) (E)-cinnamate + H(+) + NADH + O2 = (2E)-3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)prop-2-enoate + NAD(+) Binds 1 Fe cation. Binds 1 [2Fe-2S] cluster per subunit. Aromatic compound metabolism; 3-phenylpropanoate degradation. This dioxygenase system consists of four proteins: the two subunits of the hydroxylase component (HcaE and HcaF), a ferredoxin (HcaC) and a ferredoxin reductase (HcaD). Belongs to the bacterial ring-hydroxylating dioxygenase alpha subunit family. +Modulates RecA activity. Belongs to the RecX family. +Belongs to the AIM39 family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccA family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Belongs to the UPF0246 family. +Inactive precursor of the viral replicase, which is activated by cleavages carried out by the viral protease nsP2. The early replication complex formed by the polyprotein P123 and nsP4 synthesizes the minus-strand RNAs (antigenome) (By similarity). Polyprotein P123 is a short-lived polyprotein that accumulates during early stage of infection (Probable). As soon P123 is cleaved into mature proteins, the plus-strand RNAs synthesis begins (By similarity). The early replication complex formed by the polyprotein P123' and nsP4 synthesizes minus-strand RNAs (antigenome) (Probable). Polyprotein P123' is a short-lived polyprotein that accumulates during early stage of infection (Probable). As soon P123' is cleaved into mature proteins, the plus-strand RNAs synthesis begins (Probable). Cytoplasmic capping enzyme that catalyzes two virus-specific reactions: methyltransferase and nsP1 guanylyltransferase (By similarity). mRNA-capping is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus (Probable). The enzymatic reaction involves a covalent link between 7-methyl-GMP and nsP1, whereas eukaryotic capping enzymes form a covalent complex only with GMP (Probable). NsP1 capping consists in the following reactions: GTP is first methylated into 7-methyl-GMP and then is covalently linked to nsP1 to form the m7GMp-nsP1 complex from which 7-methyl-GMP complex is transferred to the mRNA to create the cap structure (By similarity). NsP1 is also needed for the initiation of the minus-strand RNAs synthesis (By similarity). Probably serves as a membrane anchor for the replication complex composed of nsP1-nsP4 (By similarity). Nsp1 is needed for the initiation of the minus-strand RNAs synthesis (By similarity). Palmitoylated nsP1 is remodeling host cell cytoskeleton, and induces filopodium-like structure formation at the surface of the host cell (By similarity). Multifunctional protein whose N-terminus is part of the RNA polymerase complex and displays NTPase, RNA triphosphatase and helicase activities (By similarity). NTPase and RNA triphosphatase are involved in viral RNA capping and helicase keeps a check on the dsRNA replication intermediates (By similarity). The C-terminus harbors a protease that specifically cleaves the polyproteins and releases the mature proteins (By similarity). Required for the shutoff of minus-strand RNAs synthesis (By similarity). Inhibits host translation to ensure maximal viral gene expression and evade host immune response (By similarity). Seems to be essential for minus-strand RNAs and subgenomic 26S mRNAs synthesis (By similarity). Displays mono-ADP-ribosylhydrolase activity (By similarity). ADP-ribosylation is a post-translational modification that controls various processes of the host cell and the virus probably needs to revert it for optimal viral replication (By similarity). Binds proteins of FXR and G3BP families and sequesters them into the viral RNA replication complexes thereby inhibiting the formation of host stress granules on viral mRNAs (By similarity). The nsp3-FXR and nsp3-G3BP complexes bind viral RNAs and probably orchestrate the assembly of viral replication complexes, thanks to the ability of G3BP and FXR family members to self-assemble and bind DNA (By similarity). Seems to be essential for minus-strand RNAs and subgenomic 26S mRNAs synthesis (By similarity). Displays mono-ADP-ribosylhydrolase activity (Probable). ADP-ribosylation is a post-translational modification that controls various processes of the host cell and the virus probably needs to revert it for optimal viral replication (Probable). Binds proteins of FXR and G3BP families and sequesters them into the viral RNA replication complexes thereby inhibiting the formation of host stress granules on viral mRNAs (Probable). The nsp3'-FXR and nsp3-G3BP complexes bind viral RNAs and probably orchestrate the assembly of viral replication complexes, thanks to the ability of G3BP and FXR family members to self-assemble and bind DNA (Probable). RNA dependent RNA polymerase (By similarity). Replicates genomic and antigenomic RNA by recognizing replications specific signals. The early replication complex formed by the polyprotein P123 and nsP4 synthesizes minus-strand RNAs (By similarity). The late replication complex composed of fully processed nsP1-nsP4 is responsible for the production of genomic and subgenomic plus-strand RNAs (By similarity). GTP + S-adenosyl-L-methionine = N(7)-methyl-GTP + S-adenosyl-L-homocysteine [nsP1 protein]-L-histidine + N(7)-methyl-GTP = [nsP1 protein]-N(tele)-(N(7)-methylguanosine 5'-phospho)-L-histidine + diphosphate [nsP1 protein]-N(tele)-(N(7)-methylguanosine 5'-phospho)-L-histidine + a 5'-end diphospho-(purine-ribonucleoside) in mRNA + H(+) = [nsP1 protein]-L-histidine + a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(purine-ribonucleoside) in mRNA a 5'-end triphospho-(purine-ribonucleoside) in mRNA + H2O = a 5'-end diphospho-(purine-ribonucleoside) in mRNA + H(+) + phosphate a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate ATP + H2O = ADP + H(+) + phosphate a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) 4-O-(ADP-D-ribosyl)-L-aspartyl-[protein] + H2O = ADP-D-ribose + H(+) + L-aspartyl-[protein] 5-O-(ADP-D-ribosyl)-L-glutamyl-[protein] + H2O = ADP-D-ribose + H(+) + L-glutamyl-[protein] ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide ADP-beta-D-ribose 1''-phosphate + H2O = ADP-D-ribose + phosphate For nsP4 adenylyltransferase activity; Mn(2+) supports catalysis at 60% of the levels observed with Mg(2+). For nsP4 RNA-directed RNA polymerase activity. For nsP1 guanylylation. For nsP2 RNA triphosphatase activity. For nsP2 NTPase activity. Inhibited by sinefungin. Interacts with non-structural protein 3 (By similarity). Interacts with RNA-directed RNA polymerase nsP4 (By similarity). Interacts with protease nsP2 (By similarity). interacts with itself (By similarity). Interacts with mRNA-capping enzyme nsP1 (By similarity). Interacts with host DDX1 (By similarity). Interacts with host DDX3 (By similarity). Interacts (via C-terminus) with host FXR1; this interaction inhibits the formation of host stress granules on viral mRNAs and the nsp3-FXR1 complexes bind viral RNAs and probably orchestrate the assembly of viral replication complexes (By similarity). Interacts (via C-terminus) with host FXR2; this interaction inhibits the formation of host stress granules on viral mRNAs and the nsp3-FXR2 complexes bind viral RNAs and probably orchestrate the assembly of viral replication complexes (By similarity). Interacts (via C-terminus) with host FMR1; this interaction inhibits the formation of host stress granules on viral mRNAs and the nsp3-FMR1 complexes bind viral RNAs and probably orchestrate the assembly of viral replication complexes (By similarity). Interacts (via C-terminus) with host G3BP1; this interaction inhibits the formation of host stress granules on viral mRNAs and the nsp3-G3BP1 complexes bind viral RNAs and probably orchestrate the assembly of viral replication complexes (By similarity). Interacts (via C-terminus) with host G3BP2; this interaction inhibits the formation of host stress granules on viral mRNAs and the nsp3-G3BP2 complexes bind viral RNAs and probably orchestrate the assembly of viral replication complexes (By similarity). Interacts with mRNA-capping enzyme nsP1 (By similarity). Interacts with protease nsP2 (By similarity). interacts with itself (By similarity). Interacts with RNA-directed RNA polymerase nsP4 (By similarity). Interacts with mRNA-capping enzyme nsP1 (By similarity). Interacts with KPNA1/karyopherin-alpha1; this interaction probably allows the active transport of protease nsP2 into the host nucleus (By similarity). Part of cytoplasmic vesicles, which are probably formed at the plasma membrane and internalized leading to late endosomal/lysosomal spherules containing the replication complex. Part of cytoplasmic vesicles, which are probably formed at the plasma membrane and internalized leading to late endosomal/lysosomal spherules containing the replication complex. Part of cytoplasmic vesicles, which are probably formed at the plasma membrane and internalized leading to late endosomal/lysosomal spherules containing the replication complex. In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then a fraction of nsP1 localizes to the inner surface of the plasma membrane and its filopodial extensions. Only the palmitoylated nsP1 localizes to the host filopodia (By similarity). NsP1 is also part of cytoplasmic vesicles, which are probably formed at the plasma membrane and internalized leading to late endosomal/lysosomal spherules containing the replication complex (By similarity). In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then approximately half of nsP2 is found in the nucleus (By similarity). Shuttles between cytoplasm and nucleus (By similarity). NsP2 is also part of cytoplasmic vesicles, which are probably formed at the plasma membrane and internalized leading to late endosomal/lysosomal spherules containing the replication complex (By similarity). In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then nsP3 and nsP3' form aggregates in cytoplasm (By similarity). NsP3 is also part of cytoplasmic vesicles, which are probably formed at the plasma membrane and internalized leading to late endosomal/lysosomal spherules containing the replication complex (By similarity). In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then nsP3 and nsP3' form aggregates in cytoplasm (By similarity). NsP3' is also part of cytoplasmic vesicles, which are probably formed at the plasma membrane and internalized leading to late endosomal/lysosomal spherules containing the replication complex (Probable). NsP4 is part of cytoplasmic vesicles, which are probably formed at the plasma membrane and internalized leading to late endosomal/lysosomal spherules containing the replication complex. The N-terminus exhibits NTPase and RNA triphosphatase activities and is proposed to have helicase activity, whereas the C-terminus possesses protease activity (By similarity). Contains a nuclear localization signal and a nuclear export signal, these two motifs are probably involved in the shuttling between the cytoplasm and the nucleus of nsP2 (By similarity). In the N-terminus, the macro domain displays a mono-ADP-ribosylhydrolase activity (By similarity). The central part has a zinc-binding function (By similarity). The C-terminus contains two regions responsible for the formation of the nsP3/FXR and nsp3/G3BP complexes (By similarity). In the N-terminus, the macro domain displays a mono-ADP-ribosylhydrolase activity (By similarity). The central part has a zinc-binding function (By similarity). The C-terminus contains two regions responsible for the formation of the nsP3'/FXR and nsp3'/G3BP complexes (By similarity). Specific enzymatic cleavages in vivo yield mature proteins (By similarity). The processing of the polyprotein is temporally regulated (By similarity). In early stages (1.7 hpi), P1234 is first cleaved in trans through its nsP2 protease activity, releasing P123' and nsP4, which associate to form the early replication complex (By similarity). At the same time, P1234 is also cut at the nsP1/nsP2 site early in infection but with lower efficiency (By similarity). After replication of the viral minus-strand RNAs (4 hpi), the polyproteins are cut at the nsP1/nsP2 and nsP2/nsP3 sites very efficiently, preventing accumulation of P123' and P1234 and allowing the formation of the late replication complex (By similarity). NsP3'/nsP4 site is not cleaved anymore and P34 is produced rather than nsP4 (By similarity). Specific enzymatic cleavages in vivo yield mature proteins (By similarity). The processing of the polyprotein is temporally regulated (By similarity). In early stages (1.7 hpi), P123 is cleaved at the nsP1/nsP2 site with low efficiency (By similarity). After replication of the viral minus-strand RNAs (4 hpi), the polyproteins are cut at the nsP1/nsP2 and nsP2/nsP3 sites very efficiently, preventing accumulation of P123 and allowing the formation of the late replication complex (By similarity). Specific enzymatic cleavages in vivo yield mature proteins (By similarity). The processing of the polyprotein is temporally regulated (By similarity). In early stages (1.7 hpi), P123' is cleaved at the nsP1/nsP2 site with low efficiency (By similarity). After replication of the viral minus-strand RNAs (4 hpi), the polyproteins are cut at the nsP1/nsP2 and nsP2/nsP3 sites very efficiently, preventing accumulation of P123' and allowing the formation of the late replication complex (By similarity). Palmitoylated by host palmitoyltransferases ZDHHC2 and ZDHHC19. Phosphorylated by host on serines and threonines. Phosphorylated by host on serines and threonines. Ubiquitinated; targets the protein for rapid degradation via the ubiquitin system (By similarity). Nsp4 is present in extremely low quantities due to low frequency of translation through the amber stop-codon and the degradation by the ubiquitin pathway (By similarity). Viral replication produces dsRNA in the late phase of infection, resulting in a strong activation of host EIF2AK2/PKR, leading to almost complete phosphorylation of EIF2A (By similarity). This inactivates completely cellular translation initiation, resulting shutoff of host proteins synthesis (By similarity). However, phosphorylation of EIF2A is probably not the only mechanism responsible for the host translation shutoff (By similarity). The viral translation can still occur normally because it relies on a hairpin structure in the coding region of sgRNA and is EIF2A-, EIF2D-, EIF4G- EIF4A-independent (By similarity). The genome codes for P123, but readthrough of a terminator codon UGA occurs between the codons for Asn-1856 and Arg-1858 giving rise to P1234 (Probable). P1234 is cleaved quickly by nsP2 into P123' and nsP4 (By similarity). Further processing of p123' gives nsP1, nsP2 and nsP3' which is 6 amino acids longer than nsP3 since the cleavage site is after the readthrough (By similarity). This unusual molecular mechanism ensures that few nsP4 are produced compared to other non-structural proteins (By similarity). Mutant viruses with no alternative termination site grow significantly slower than wild-type virus (By similarity). The opal termination codon is frequently mutated to a sense codon on passage in cell culture (By similarity). The presence of the opal codon may be a requirement for viral maintenance in both vertebrate and invertebrate hosts and a selective advantage may be conferred in cell culture for the sense codon (By similarity). +Involved in the import of GDP-mannose from the cytoplasm into the Golgi lumen. Defective copy causes severe glycosylation defect and abnormal retention of soluble endoplasmic reticulum proteins. Involved in vanadate sensitivity. Homooligomer. Recycles between the Golgi apparatus and the endoplasmic reticulum. Present with 31900 molecules/cell in log phase SD medium. Belongs to the TPT transporter family. SLC35D subfamily. +Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system. ATP + H2O + phosphate(out) = ADP + H(+) + 2 phosphate(in) The complex is composed of two ATP-binding proteins (PstB), two transmembrane proteins (PstC and PstA) and a solute-binding protein (PstS). Belongs to the ABC transporter superfamily. Phosphate importer (TC 3.A.1.7) family. +Could be involved in detoxification of extraneous host-cell epoxides. Catalyzes the hydrolysis of small aromatic epoxide-containing substrates such as trans-1,3-diphenylpropene oxide, trans and cis-stilbene oxide, and terpenoid epoxide. an epoxide + H2O = an ethanediol Homodimer. Belongs to the AB hydrolase superfamily. Epoxide hydrolase family. +RNA-directed RNA polymerase that catalyzes the transcription of viral mRNAs, their capping and polyadenylation. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The viral polymerase binds to the genomic RNA at the 3' leader promoter, and transcribes subsequently all viral mRNAs with a decreasing efficiency. The first gene is the most transcribed, and the last the least transcribed. The viral phosphoprotein acts as a processivity factor. Capping is concommitant with initiation of mRNA transcription. Indeed, a GDP polyribonucleotidyl transferase (PRNTase) adds the cap structure when the nascent RNA chain length has reached few nucleotides. Ribose 2'-O methylation of viral mRNA cap precedes and facilitates subsequent guanine-N-7 methylation, both activities being carried by the viral polymerase. Polyadenylation of mRNAs occur by a stuttering mechanism at a slipery stop site present at the end viral genes. After finishing transcription of a mRNA, the polymerase can resume transcription of the downstream gene. RNA-directed RNA polymerase that catalyzes the replication of viral genomic RNA. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The replicase mode is dependent on intracellular N protein concentration. In this mode, the polymerase replicates the whole viral genome without recognizing transcriptional signals, and the replicated genome is not caped or polyadenylated. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + 2 S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + H(+) + 2 S-adenosyl-L-homocysteine a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-methionine = a 5'-end (5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + H(+) + S-adenosyl-L-homocysteine a 5'-end triphospho-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + GDP + H(+) = a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + diphosphate a 5'-end (5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-homocysteine GTP + H2O = GDP + H(+) + phosphate May form homodimer. Interacts with the P protein. L and P are packaged asymmetrically towards the blunt end of the virus. Belongs to the rhabdoviruses protein L family. +Belongs to the PPR family. PCMP-H subfamily. +Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides (By similarity). Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low. Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids. Binds 2 manganese ions per subunit. Belongs to the peptidase M17 family. +Might have a role in establishing the nucleoid structure of elementary bodies. Specific to the EB (elementary body) form in the life cycle of chlamydiae. Belongs to the histone H1/H5 family. HCT subfamily. +Component of the cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery required for the maturation of extramitochondrial Fe-S proteins. Part of an electron transfer chain functioning in an early step of cytosolic Fe-S biogenesis, facilitating the de novo assembly of a [4Fe-4S] cluster on the scaffold complex cfd1-nbp35. Electrons are transferred to dre2 from NADPH via the FAD- and FMN-containing protein tah18. Tah18-dre2 are also required for the assembly of the diferric tyrosyl radical cofactor of ribonucleotide reductase (RNR), probably by providing electrons for reduction during radical cofactor maturation in the catalytic small subunit rnr2. Monomer. Interacts with tah18. Interacts with mia40. The C-terminal domain binds 2 Fe-S clusters but is otherwise mostly in an intrinsically disordered conformation. The N-terminal domain has structural similarity with S-adenosyl-L-methionine-dependent methyltransferases, but does not bind S-adenosyl-L-methionine. It is required for correct assembly of the 2 Fe-S clusters. The twin Cx2C motifs are involved in the recognition by the mitochondrial mia40-erv1 disulfide relay system. The formation of 2 disulfide bonds in the Cx2C motifs through dithiol/disulfide exchange reactions effectively traps the protein in the mitochondrial intermembrane space. Belongs to the anamorsin family. +Venom dipeptidyl-peptidase which removes N-terminal dipeptides sequentially from polypeptides having unsubstituted N-termini provided that the penultimate residue is proline. May process promelittin into its active form and/or modulate the chemotactic activity of immune cells after the insect sting. Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, from a polypeptide, preferentially when Yaa is Pro, provided Zaa is neither Pro nor hydroxyproline. Inhibited by diprotin A. Expressed by the venom duct. Causes an allergic reaction in human. Belongs to the peptidase S9B family. DPPIV subfamily. +Stabilizer subunit of the dolichol-phosphate-mannose synthase complex. Protein modification; protein glycosylation. Belongs to the DPM3 family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Binds 1 zinc ion per subunit. Belongs to the peptidase M48B family. +Catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation. Cofactor biosynthesis; adenosylcobalamin biosynthesis. Belongs to the CobB/CobQ family. CobQ subfamily. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Transfers an acetyl group from acetyl-CoA to L-homoserine, forming acetyl-L-homoserine. acetyl-CoA + L-homoserine = CoA + O-acetyl-L-homoserine Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; O-acetyl-L-homoserine from L-homoserine: step 1/1. Homodimer. Belongs to the AB hydrolase superfamily. MetX family. +Non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA. Homodimer. The ends of the coiled-coil dimer bind to each other, forming polymers. Interacts with FtsZ. Localizes to the septum at mid-cell, in a FtsZ-like pattern. Belongs to the ZapB family. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. 2 D-sedoheptulose 7-phosphate = D-glycero-alpha-D-manno-heptose 7-phosphate + D-glycero-beta-D-manno-heptose 7-phosphate Binds 1 zinc ion per subunit. Carbohydrate biosynthesis; D-glycero-D-manno-heptose 7-phosphate biosynthesis; D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate from sedoheptulose 7-phosphate: step 1/1. Homotetramer. The reaction produces a racemic mixture of D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate. Belongs to the SIS family. GmhA subfamily. +Belongs to the eukaryotic ribosomal protein eL22 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Catalyzes the conversion of heme O to heme A by two successive hydroxylations of the methyl group at C8. The first hydroxylation forms heme I, the second hydroxylation results in an unstable dihydroxymethyl group, which spontaneously dehydrates, resulting in the formyl group of heme A. 2 A + Fe(II)-heme o + H2O = 2 AH2 + Fe(II)-heme a Porphyrin-containing compound metabolism; heme A biosynthesis; heme A from heme O: step 1/1. Interacts with CtaB. Belongs to the COX15/CtaA family. Type 2 subfamily. +Belongs to the ycf15 family. Could be the product of a pseudogene. +Probably involved in bacterial recognition. May be a lectin that function as part of a transmembrane signaling complex during phagocytosis. Also bound to inner membrane of certain cytoplasmic vesicles. Belongs to the tectonin family. +Epithelial ion channel that plays an important role in the regulation of epithelial ion and water transport and fluid homeostasis. Mediates the transport of chloride ions across the cell membrane (By similarity). Channel activity is coupled to ATP hydrolysis. The ion channel is also permeable to HCO(3)(-); selectivity depends on the extracellular chloride concentration. Exerts its function also by modulating the activity of other ion channels and transporters. Contributes to the regulation of the pH and the ion content of the epithelial fluid layer. Modulates the activity of the epithelial sodium channel (ENaC) complex, in part by regulating the cell surface expression of the ENaC complex. May regulate bicarbonate secretion and salvage in epithelial cells by regulating the transporter SLC4A7. Can inhibit the chloride channel activity of ANO1 (By similarity). Plays a role in the chloride and bicarbonate homeostasis during sperm epididymal maturation and capacitation (By similarity). ATP + H2O + closed Cl(-) channel = ADP + phosphate + open Cl(-) channel. Monomer; does not require oligomerization for channel activity. May form oligomers in the membrane (By similarity). Interacts with SLC26A3, SLC26A6 and SLC9A3R1 (By similarity). Interacts with SHANK2 (By similarity). Interacts with MYO6 (By similarity). Interacts (via C-terminus) with GOPC (via PDZ domain); this promotes CFTR internalization and thereby decreases channel activity. Interacts with SLC4A7 through SLC9A3R1. Found in a complex with MYO5B and RAB11A. Interacts with ANO1. Interacts with SLC26A8 (By similarity). Interacts with AHCYL1; the interaction increases CFTR activity (By similarity). Interacts with CSE1L (By similarity). The core-glycosylated form interacts with GORASP2 (via PDZ GRASP-type 1 domain) in respone to ER stress (By similarity). Interacts with MARCHF2; the interaction leads to CFTR ubiqtuitination and degradation (By similarity). The channel is internalized from the cell surface into an endosomal recycling compartment, from where it is recycled to the cell membrane. In the oviduct and bronchus, detected on the apical side of epithelial cells, but not associated with cilia. In Sertoli cells, a processed product is detected in the nucleus. ER stress induces GORASP2-mediated unconventional (ER/Golgi-independent) trafficking of core-glycosylated CFTR to cell membrane. Binds and hydrolyzes ATP via the two cytoplasmic ABC transporter nucleotide-binding domains. The two ATP-binding domains interact with each other, forming a head-to-tail dimer. Normal ATPase activity requires interaction between the two domains. The first ABC transporter nucleotide-binding domain has no ATPase activity by itself. The PDZ-binding motif mediates interactions with GOPC and with the SLC4A7, SLC9A3R1/EBP50 complex. The disordered R region mediates channel activation when it is phosphorylated, but not in the absence of phosphorylation. N-glycosylated. Phosphorylated; cAMP treatment promotes phosphorylation and activates the channel. Dephosphorylation decreases the ATPase activity (in vitro). Phosphorylation at PKA sites activates the channel. Phosphorylation at PKC sites enhances the response to phosphorylation by PKA. Phosphorylated by AMPK; this inhibits channel activity. Ubiquitinated, leading to its degradation in the lysosome. Deubiquitination by USP10 in early endosomes enhances its endocytic recycling to the cell membrane. Ubiquitinated by RNF185 during ER stress. Ubiquitinated by MARCHF2 (By similarity). Belongs to the ABC transporter superfamily. ABCC family. CFTR transporter (TC 3.A.1.202) subfamily. +Regulates ADAM17 protease, a sheddase of the epidermal growth factor (EGF) receptor ligands and TNF, thereby plays a role in sleep, cell survival, proliferation, migration and inflammation. Does not exhibit any protease activity on its own. Interacts with EGF (By similarity). Interacts (via cytoplasmic N-terminus) with FRMD8/iTAP; this interaction leads to mutual protein stabilization (PubMed:29897333, PubMed:29897336). Interacts with ADAM17/TACE (PubMed:29897333, PubMed:29897336). Found in the epidermis and esophageal epithelium. The disease is caused by variants affecting the gene represented in this entry. Belongs to the peptidase S54 family. Extended N-terminus. Truncated N-terminus. +Belongs to the UPF0758 family. +DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function. Has a putative N-terminal zinc-finger, a middle region with homology to RecA with ATPase motifs including the RadA KNRFG motif, while the C-terminus is homologous to Lon protease. Belongs to the RecA family. RadA subfamily. +Catalyzes the hydroxylation of L-kynurenine (L-Kyn) to form 3-hydroxy-L-kynurenine (L-3OHKyn). Required for synthesis of quinolinic acid. H(+) + L-kynurenine + NADPH + O2 = 3-hydroxy-L-kynurenine + H2O + NADP(+) Cofactor biosynthesis; NAD(+) biosynthesis; quinolinate from L-kynurenine: step 1/3. Belongs to the aromatic-ring hydroxylase family. KMO subfamily. +Activates hepatocyte growth factor (HGF) by converting it from a single chain to a heterodimeric form. Heterodimer of a short chain and a long chain linked by a disulfide bond. Secreted as an inactive single-chain precursor and is then activated to a heterodimeric form. Liver. Belongs to the peptidase S1 family. +Chemotactic-signal transducers respond to changes in the concentration of attractants and repellents in the environment, transduce a signal from the outside to the inside of the cell, and facilitate sensory adaptation through the variation of the level of methylation (Probable). Directly recognizes five C4-dicarboxylic acids: L-malic, citramalic, citraconic, bromosuccinic and methylsuccinic acids (PubMed:17933940, PubMed:29391435). Three of the identified ligands act as chemoattractants (L-malic, D,L-bromosuccinic and L-citramalic acids) whereas two of them (L-methylsuccinic and citraconic acids) behave as antagonists by inhibiting the downstream chemotaxis signaling cascade (PubMed:29391435). Antagonists compete with chemoattractants, thereby decreasing the affinity for chemoattractants and the subsequent chemotactic response (PubMed:29391435). Acts through the che chemosensory pathway (PubMed:29391435). Homodimer. The ligand-binding domain (LBD) is dimeric in the presence and the absence of ligands. Mutant shows a dramatic reduction in chemotaxis for all ligands, but it does not affect response to casamino acids (PubMed:29391435). Mutant showed no attraction to malate at any of the concentrations tested (PubMed:17933940). Mutation does not affect plant root colonization (PubMed:29391435). Belongs to the methyl-accepting chemotaxis (MCP) protein family. +Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF2. Belongs to the prokaryotic/mitochondrial release factor family. +Transcription regulator of hematopoietic cell differentiation. Binds gamma-satellite DNA. Binds with higher affinity to gamma satellite A. Plays a role in the development of lymphocytes, B- and T-cells. Binds and activates the enhancer (delta-A element) of the CD3-delta gene. Repressor of the TDT (terminal deoxynucleotidyltransferase) gene during thymocyte differentiation. Regulates transcription through association with both HDAC-dependent and HDAC-independent complexes. Targets the 2 chromatin-remodeling complexes, NuRD and BAF (SWI/SNF), in a single complex (PYR complex), to the beta-globin locus in adult erythrocytes. Increases normal apoptosis in adult erythroid cells (By similarity). Confers early temporal competence to retinal progenitor cells (RPCs). Function is isoform-specific and is modulated by dominant-negative inactive isoforms (By similarity). Heterodimer with other IKAROS family members. Interacts with IKZF4 AND IKZF5 (By similarity). Component of the chromatin-remodeling NuRD repressor complex which includes at least HDAC1, HDAC2, RBBP4, RBBP7, IKZF1, MTA2, MBD2, MBD3, MTA1L1, CHD3 and CHD4. Interacts directly with the CHD4 component of the NuRD complex. Interacts directly with SMARCA4; the interaction associates IKFZ1 with the BAF complex. Interacts with SUMO1; the interaction sumoylates IKAROS, promoted by PIAS2 and PIAS3. Interacts with PIAS2 (isoform alpha); the interaction promotes sumoylation and reduces transcription repression. Interacts, to a lesser extent, with PIAS3. Interacts with PPP1CC; the interaction targets PPP1CC to pericentromeric heterochromatin, dephosphorylates IKAROS, stabilizes it and prevents it from degradation. Interacts with IKZF3. In resting lymphocytes, distributed diffusely throughout the nucleus. Localizes to pericentromeric heterochromatin in proliferating cells. This localization requires DNA binding which is regulated by phosphorylation / dephosphorylation events. In resting lymphocytes, distributed diffusely throughout the nucleus. Localizes to pericentromeric heterochromatin in proliferating cells. This localization requires DNA binding which is regulated by phosphorylation / dephosphorylation events. Strongly expressed in T-cells and their progenitors,in B-cells, and in all early embryonic retinal progenitor cells (RPCs). Isoforms V and VI are the predominant isoforms in lymphocytes. First detected in fetal liver and embryonic thymus. The N-terminal zinc-fingers 2 and 3 are required for DNA binding as well as for targeting IKFZ1 to pericentromeric heterochromatin. The C-terminal zinc-finger domain is required for dimerization. Phosphorylation at Ser-357 and Ser-360 downstream of SYK induces nuclear translocation (By similarity). Phosphorylation controls cell-cycle progression from late G(1) stage to S stage. Hyperphosphorylated during G2/M phase. Dephosphorylated state during late G(1) phase. Phosphorylation on Thr-140 is required for DNA and pericentromeric location during mitosis. CK2 is the main kinase, in vitro. GSK3 and CDK may also contribute to phosphorylation of the C-terminal serine and threonine residues. Phosphorylation on these C-terminal residues reduces the DNA-binding ability. Phosphorylation/dephosphorylation events on Ser-13 and Ser-293 regulate TDT expression during thymocyte differentiation. Dephosphorylation by protein phosphatase 1 regulates stability and pericentromeric heterochromatin location. Phosphorylated in both lymphoid and non-lymphoid tissues. Sumoylated. Simultaneous sumoylation on the 2 sites results in a loss of both HDAC-dependent and HDAC-independent repression. Has no effect on pericentromeric heterochromatin location. Desumoylated by SENP1. Polyubiquitinated. Defects in hemopoietic stem cell activity. Progressive reduction in multipotent CFU-S(14) (colony-forming unit-spleen) progenitors and the earliest erythroid-restricted precursors (BFU-E). Belongs to the Ikaros C2H2-type zinc-finger protein family. +Catalyzes the hydrolysis of UDP-3-O-myristoyl-N-acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate, the committed step in lipid A biosynthesis. a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 2/6. Belongs to the LpxC family. +Iron-sulfur cluster scaffold protein which can assemble [4Fe-4S] clusters and deliver them to target proteins. Monomer and homohexamer; the apo-NFU1 is a monomer, while the holo-NFU1 is a hexamer composed of a trimer of dimer that is probably linked by some 4Fe-4S cluster. Interacts with HIRA and EPM2A/laforin. Interacts with BOLA3. Interacts with HSPA9. Belongs to the NifU family. +Histone methyltransferase that specifically methylates monomethylated 'Lys-20' (H4K20me1) and dimethylated 'Lys-20' (H4K20me2) of histone H4 to produce respectively dimethylated 'Lys-20' (H4K20me2) and trimethylated 'Lys-20' (H4K20me3) and thus regulates transcription and maintenance of genome integrity (PubMed:15145825, PubMed:28114273). In vitro also methylates unmodified 'Lys-20' (H4K20me0) of histone H4 and nucleosomes (By similarity). H4 'Lys-20' trimethylation represents a specific tag for epigenetic transcriptional repression (PubMed:15145825). Mainly functions in pericentric heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin in these regions (PubMed:15145825). KMT5B is targeted to histone H3 via its interaction with RB1 family proteins (RB1, RBL1 and RBL2) (PubMed:15750587, PubMed:16612004). Facilitates TP53BP1 foci formation upon DNA damage and proficient non-homologous end-joining (NHEJ)-directed DNA repair by catalyzing the di- and trimethylation of 'Lys-20' of histone H4 (By similarity). May play a role in class switch reconbination by catalyzing the di- and trimethylation of 'Lys-20' of histone H4 (PubMed:28114273). N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H(+) + N(6),N(6)-dimethyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine N(6),N(6)-dimethyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine Inhibited by 6,7-Dichloro-N-cyclopentyl-4-(pyridin-4-yl)phthalazin-1-amine (A-196). Homodimer (PubMed:24049080). Interacts with HP1 proteins CBX1, CBX3 and CBX5. Interacts with RB1 family proteins RB1, RBL1 and RBL2. Associated with pericentric heterochromatin. CBX1 and CBX5 are required for the localization to pericentric heterochromatin. Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar4-20 subfamily. +Sequence-specific endonuclease that cleaves unmethylated GATC sequences. It is involved in DNA mismatch repair. Belongs to the MutH family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +S-adenosyl-L-methionine-dependent methyltransferase responsible for the addition of the methyl group in the formation of N6-methyl-N6-threonylcarbamoyladenosine at position 37 (m(6)t(6)A37) of the tRNA anticodon loop of tRNA(Ser)(GCU). The methyl group of m(6)t(6)A37 may improve the efficiency of the tRNA decoding ability. May bind to tRNA. N(6)-L-threonylcarbamoyladenosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(6)-methyl,N(6)-L-threonylcarbamoyladenosine(37) in tRNA + S-adenosyl-L-homocysteine Belongs to the tRNA methyltransferase O family. +Component of the PAF1 complex which is a multifunctional complex involved in transcription initiation via genetic interactions with TATA-binding proteins, elongation and transcription-coupled histone modification. Component of the PAF1 complex which consists of at least cdc-73, ctr-9, leo-1, pafo-1 and rtfo-1. Nuclear localization depends on ctr-9, pafo-1 and cdc-73. Located in nuclei before mitosis. Located in the cytoplasm upon mitotic nuclear membrane breakdown. Located in nuclei when nuclear envelope is reassembled in telophase. Expressed in both somatic cells and germ cells from the one-cell stage onwards. RNAi-mediated knock-down is maternal effect embryonic lethal. Embryogenesis proceeds more slowly, with embryos displaying defects in the positioning and shape of epidermal cells. Belongs to the LEO1 family. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Component of SUN-protein-containing multivariate complexes also called LINC complexes which link the nucleoskeleton and cytoskeleton by providing versatile outer nuclear membrane attachment sites for cytoskeletal filaments (PubMed:24667841, PubMed:25759303). Required for the maintenance and/or formation of polarized nuclear shape in root hairs (PubMed:21294795, PubMed:25759303). Modulates the anchoring and mobility of WIP proteins and RANGAP1 in the nuclear envelope (NE) (PubMed:22270916). In association with SUN2, may be involved in telomere attachment to nuclear envelope in the prophase of meiosis (PubMed:25412930). As component of the SUN-WIP-WIT2-KAKU1 complex, mediates the transfer of cytoplasmic forces to the nuclear envelope (NE), leading to nuclear shape changes (PubMed:25759303). Forms homomers (e.g. dimers, trimers and tetramers) and heteromers with SUN2 (PubMed:19807882, PubMed:25217773). Interacts with SUN3, SUN4 and TIK (PubMed:25217773). Core component of the LINC complex which is composed of inner nuclear membrane SUN domain-containing proteins coupled to outer nuclear membrane WIP and WIT proteins. The LINC complex also involves nucleoskeletal proteins CRWN/LINC and possibly KAKU4 and the cytoskeletal myosin KAKU1 (PubMed:25759303). Interacts with LINC1, WIP1, WIP2 and WIP3 at the nuclear envelope (NE) (PubMed:22270916, PubMed:24667841). Interacts with SINE1, SINE2, SINE3 AND SINE4 (PubMed:24891605). Interacts with NEAP1, NEA2 and NEAP3 (PubMed:27630107). Dynamic localization during mitosis and meosis, tightly coupled with nuclear envelope (NE) dynamics. Localized with the nuclear envelope during meiotic prophase I. NE re-formation during metaphase is temporally and spatially coordinated with plant-specific microtubule structures such as phragmoplasts. During anaphase, after NE breakdown (NEBD), predominantly localized with the endoplasmic reticulum, in the outside of the segregated chromosomes and not in between segregated chromosomes. Expressed in roots, hypocotyls, cotyledons and leaves and inflorescences. The SUN domain may play a role in nuclear anchoring and/or migration (By similarity). The SUN domain is required for interactions with WIP proteins (PubMed:22270916). No visible phenotype. When associated with SUN2 disruption, abnormal nuclear shape, rounded instead of elongated, in some cells (e.g. mature root hairs) but also numerous meiotic defects namely a delay in the progression of meiosis, absence of full synapsis and a reduction in the mean cell chiasma frequency. +The exact function of MAP2 is unknown but MAPs may stabilize the microtubules against depolymerization. They also seem to have a stiffening effect on microtubules. Interacts with KNDC1 (via KIND2); the interaction enhances MAP2 phosphorylation and localizes KNDC1 to dendrites. Interacts with DPYSL5 (By similarity). Phosphorylated at serine residues in K-X-G-S motifs by causing MAP/microtubule affinity-regulating kinase (MARK1 or MARK2), detachment from microtubules, and their disassembly (By similarity). The interaction with KNDC1 enhances MAP2 threonine phosphorylation (PubMed:17984326). +Envelope protein part of the entry-fusion complex responsible for the virus membrane fusion with host cell membrane during virus entry. Also plays a role in cell-cell fusion (syncytium formation) (By similarity). Part of a stable entry-fusion complex (EFC) which is at least composed of proteins A16, A21, A28, G3, G9, H2, J5, and L5. Formation of the viral membrane is necessary for the assembly of the complex (By similarity). Component of the mature virion (MV) membrane. The mature virion is located in the cytoplasm of infected cells and is probably released by cell lysis (By similarity). Belongs to the poxviridae A16/G9/J5 family. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +Transcriptional repressor which coordinates circadian rhythm and metabolic pathways in a heme-dependent manner. Integral component of the complex transcription machinery that governs circadian rhythmicity and forms a critical negative limb of the circadian clock by directly repressing the expression of core clock components ARTNL/BMAL1, CLOCK and CRY1. Also regulates genes involved in metabolic functions, including lipid and bile acid metabolism, adipogenesis, gluconeogenesis and the macrophage inflammatory response. Acts as a receptor for heme which stimulates its interaction with the NCOR1/HDAC3 corepressor complex, enhancing transcriptional repression. Recognizes two classes of DNA response elements within the promoter of its target genes and can bind to DNA as either monomers or homodimers, depending on the nature of the response element. Binds as a monomer to a response element composed of the consensus half-site motif 5'-[A/G]GGTCA-3' preceded by an A/T-rich 5' sequence (RevRE), or as a homodimer to a direct repeat of the core motif spaced by two nucleotides (RevDR-2). Acts as a potent competitive repressor of ROR alpha (RORA) function and regulates the levels of its ligand heme by repressing the expression of PPARGC1A, a potent inducer of heme synthesis. Regulates lipid metabolism by repressing the expression of APOC3 and by influencing the activity of sterol response element binding proteins (SREBPs); represses INSIG2 which interferes with the proteolytic activation of SREBPs which in turn govern the rhythmic expression of enzymes with key functions in sterol and fatty acid synthesis. Regulates gluconeogenesis via repression of G6PC1 and PEPCK and adipocyte differentiation via repression of PPARG. Regulates glucagon release in pancreatic alpha-cells via the AMPK-NAMPT-SIRT1 pathway and the proliferation, glucose-induced insulin secretion and expression of key lipogenic genes in pancreatic-beta cells. Positively regulates bile acid synthesis by increasing hepatic expression of CYP7A1 via repression of NR0B2 and NFIL3 which are negative regulators of CYP7A1. Modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy; controls mitochondrial biogenesis and respiration by interfering with the STK11-PRKAA1/2-SIRT1-PPARGC1A signaling pathway. Represses the expression of SERPINE1/PAI1, an important modulator of cardiovascular disease and the expression of inflammatory cytokines and chemokines in macrophages. Represses gene expression at a distance in macrophages by inhibiting the transcription of enhancer-derived RNAs (eRNAs). Plays a role in the circadian regulation of body temperature and negatively regulates thermogenic transcriptional programs in brown adipose tissue (BAT); imposes a circadian oscillation in BAT activity, increasing body temperature when awake and depressing thermogenesis during sleep. In concert with NR2E3, regulates transcriptional networks critical for photoreceptor development and function. In addition to its activity as a repressor, can also act as a transcriptional activator. In the ovarian granulosa cells acts as a transcriptional activator of STAR which plays a role in steroid biosynthesis. In collaboration with SP1, activates GJA1 transcription in a heme-independent manner. Represses the transcription of CYP2B10, CYP4A10 and CYP4A14 (PubMed:30555544). Represses the transcription of CES2 (PubMed:29653076). Represses and regulates the circadian expression of TSHB in a NCOR1-dependent manner (PubMed:24794873). Negatively regulates the protein stability of NR3C1 and influences the time-dependent subcellular distribution of NR3C1, thereby affecting its transcriptional regulatory activity (PubMed:27686098). Plays a critical role in the circadian control of neutrophilic inflammation in the lung; under resting, non-stress conditions, acts as a rhythmic repressor to limit inflammatory activity whereas in the presence of inflammatory triggers undergoes ubiquitin-mediated degradation thereby relieving inhibition of the inflammatory response (PubMed:29533925). Plays a key role in the circadian regulation of microglial activation and neuroinflammation; suppresses microglial activation through the NF-kappaB pathway in the central nervous system (PubMed:30792350). Plays a role in the regulation of the diurnal rhythms of lipid and protein metabolism in the skeletal muscle via transcriptional repression of genes controlling lipid and amino acid metabolism in the muscle (PubMed:30096135). Binds DNA as a monomer or a homodimer (By similarity). Interacts with NR2E3 and ZNHIT1 (By similarity). Interacts with C1D (PubMed:9405624). Interacts with SP1 (PubMed:22549838). Interacts with OPHN1 (via C-terminus) (PubMed:21874017). Interacts with PER2; the interaction associates PER2 to ARNTL promoter region (PubMed:20159955, PubMed:22170608). Interacts with CRY1 (By similarity). Interacts with CCAR2 (PubMed:23398316). Interacts with SIAH2 (By similarity). Interacts with FBXW7 and CDK1 (PubMed:27238018). Interacts with HUWE1 (By similarity). Interacts with NR0B2 (PubMed:25212631, PubMed:30555544). Interacts with NFIL3 (PubMed:29653076). Interacts (via domain NR LBD) with HSP90AA1 and HSP90AB1 (PubMed:27686098). Localizes to the cytoplasm, dendrites and dendritic spine in the presence of OPHN1 (PubMed:21874017). Localizes predominantly to the nucleus at ZT8 whereas it is cytoplasmic at ZT20 (PubMed:27686098). Phosphorylation by CSNK1E enhances its cytoplasmic localization (PubMed:29508494). Expressed during adipocyte differentiation (at protein level). Expressed in skeletal muscle, bladder, lumbar spinal cord, pancreatic islets and hypothalamus. Expressed in developing and adult retina. In the adult retina, predominantly expressed in the outer nuclear layer, where rod and cone cells reside, and also localized to the ganglion cell layer. Expressed in a circadian manner in the liver (PubMed:27686098). Expressed in a circadian manner in the lung with a peak between ZT8 and ZT12 (PubMed:29533925). During development at embryonic day 18.5 dpc, expressed in the outer neuroblastic layer of the retina where developing postmitotic photoreceptors and retinal progenitors reside (at protein level). Expression oscillates diurnally in the suprachiasmatic nucleus (SCN) of the hypothalamus as well as in peripheral tissues. In bladder smooth muscle cells, pancreas and lumbar spinal cord, exhibits night/day variations with a peak time at circadian time (CT) 4-12 and a trough at CT16-24. Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain. Ubiquitinated, leading to its proteasomal degradation (PubMed:20534529). Ubiquitinated by the SCF(FBXW7) complex when phosphorylated by CDK1 leading to its proteasomal degradation (PubMed:27238018). Ubiquitinated by SIAH2; leading to its proteasomal degradation (By similarity). Rapidly ubiquitinated in response to inflammatory triggers and sumoylation is a prerequisite to its ubiquitination (PubMed:29533925). Sumoylated by UBE2I, desumoylated by SENP1, and sumoylation is a prerequisite to its ubiquitination. Phosphorylated by CSNK1E; phosphorylation enhances its cytoplasmic localization. Undergoes lysosome-mediated degradation in a time-dependent manner in the liver. Mice display increased cold tolerance, higher oxygen consumption rates, enhanced brown adipose tissue metabolic capacity, maintenance of higher body temperature throughout the light phase and increased glucose uptake only during the day. They also show retinal abnormalities such as pan-retinal spotting and decreased response to light and decreased bile acid accumulation. Double knockout for NR1D1 and PER2 show a significantly shorter period length compared with wild type or single knockouts for both genes. 50% of double knockouts animals show a stable circadian throughout at least 5 weeks in constant darkness. The other 50% of animals lose their circadian rhythmicity when held in constant darkness for an average of 21 days. Animals have blunted steady-state levels of glycogen in the liver in spite of normal patterns of food consumption. Mice show exaggerated pulmonary inflammatory responses (PubMed:29533925). Mice display enhanced spontaneous hippocampal microglial and astrocyte activation, increased microglial NF-kappaB signaling and exacerbated LPS-induced neuroinflammation in the hippocampus (PubMed:30792350). Conditional knockout of both NR1D1 and NR1D2 in bronchiolar epithelial cells abolished diurnal rhythmicity of PER2 in the bronchioles and increased inflammatory responses and chemokine activation (PubMed:29533925). Belongs to the nuclear hormone receptor family. NR1 subfamily. +DNA binding protein that function as transcriptional activator. May play a role in the determination and function of cell types in the brain. Belongs to the distal-less homeobox family. +Catalyzes the sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine. H2O + L-histidinol + 2 NAD(+) = 3 H(+) + L-histidine + 2 NADH Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 9/9. Belongs to the histidinol dehydrogenase family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette. Homodimer, forms a heterotetramer with a Cas2 homodimer. Belongs to the CRISPR-associated endonuclease Cas1 family. +GTP + H2O = GDP + H(+) + phosphate Alternates between an inactive form bound to GDP and an active form bound to GTP. Activated by a guanine nucleotide-exchange factor (GEF) and inactivated by a GTPase-activating protein (GAP). Inner surface of plasma membrane. This p21 transforming protein was generated by a transduction of rodent cellular H-ras-1 gene. Belongs to the small GTPase superfamily. Ras family. +Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. (2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 4/5. Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface. Belongs to the enolase family. +Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain. Dimer of alpha and beta chains. A typical microtubule is a hollow water-filled tube with an outer diameter of 25 nm and an inner diameter of 15 nM. Alpha-beta heterodimers associate head-to-tail to form protofilaments running lengthwise along the microtubule wall with the beta-tubulin subunit facing the microtubule plus end conferring a structural polarity. Microtubules usually have 13 protofilaments but different protofilament numbers can be found in some organisms and specialized cells. Undergoes a tyrosination/detyrosination cycle, the cyclic removal and re-addition of a C-terminal tyrosine residue by the enzymes tubulin tyrosine carboxypeptidase (TTCP) and tubulin tyrosine ligase (TTL), respectively. Acetylation of alpha chains at Lys-40 stabilizes microtubules and affects affinity and processivity of microtubule motors. This modification has a role in multiple cellular functions, ranging from cell motility, cell cycle progression or cell differentiation to intracellular trafficking and signaling (By similarity). Belongs to the tubulin family. +Involved in the biosynthesis of a moiety on the core of the lipopolysaccharide molecule. Assembles at the inner surface of the cytoplasmic membrane. Belongs to the glycosyltransferase 25 family. +Belongs to the HflD family. +Belongs to the hssA/B family. +Probably necessary for the cotranslation of trpF. It may also function as a subunit or stabilizer of phosphoribosylanthranilate isomerase (trpF). Amino-acid biosynthesis; L-tryptophan biosynthesis. +Contributes to protect fish blood from freezing at subzero sea water temperatures. Lowers the blood freezing point. Binds to nascent ice crystals and prevents further growth. Detected in blood serum (at protein level). Belongs to the type-III AFP family. +Belongs to the eukaryotic ribosomal protein eL40 family. +Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. ATP + meso-2,6-diaminoheptanedioate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate Cell wall biogenesis; peptidoglycan biosynthesis. Carboxylation is probably crucial for Mg(2+) binding and, consequently, for the gamma-phosphate positioning of ATP. Belongs to the MurCDEF family. MurE subfamily. +Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains (By similarity). Protein modification; protein ubiquitination. The APC/C is composed of at least 12 subunits. ANAPC16 associates with the rest of the complex independently of ANAPC2 and ANAPC11 (By similarity). Belongs to the APC16 family. Extended N-terminus. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo-MPT) cofactor (Moco or molybdenum cofactor) to form Mo-molybdopterin guanine dinucleotide (Mo-MGD) cofactor. GTP + H(+) + Mo-molybdopterin = diphosphate + Mo-molybdopterin guanine dinucleotide Monomer. The N-terminal domain determines nucleotide recognition and specific binding, while the C-terminal domain determines the specific binding to the target protein. Belongs to the MobA family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be a menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 2 family. +Belongs to the universal ribosomal protein uL29 family. +Catalyzes the degradation of compounds such as putrescine, histamine, spermine, and spermidine, substances involved in allergic and immune responses, cell proliferation, tissue differentiation, tumor formation, and possibly apoptosis. H2O + histamine + O2 = H2O2 + imidazole-4-acetaldehyde + NH4(+) Binds 1 copper ion per subunit. Binds 2 calcium ions per subunit. Contains 1 topaquinone per subunit. Inhibited by amiloride in a competitive manner. Homodimer; disulfide-linked. N-glycosylated; the glycans are primarily linear, di-, or tribranched fucosylated complex type. Topaquinone (TPQ) is generated by copper-dependent autoxidation of a specific tyrosyl residue. Belongs to the copper/topaquinone oxidase family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Involved in oxygen transport from the lung to the various peripheral tissues. Hemopressin acts as an antagonist peptide of the cannabinoid receptor CNR1. Hemopressin-binding efficiently blocks cannabinoid receptor CNR1 and subsequent signaling. Heterotetramer of two alpha chains and two beta chains. Red blood cells. In inbred mouse strains there are at least 6 alleles that can occur at the HBA locus: A, B, C, D, F, or G. Strains carrying the A and F alleles produce a single kind of alpha chain, whereas those carrying B, C, D, or G each produce 2 kinds of chains. The sequence shown is that of the B(1) and D(1) allele chains. Belongs to the globin family. +Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source. ATP + deamido-NAD(+) + NH4(+) = AMP + diphosphate + H(+) + NAD(+) Cofactor biosynthesis; NAD(+) biosynthesis; NAD(+) from deamido-NAD(+) (ammonia route): step 1/1. Homodimer. Belongs to the NAD synthetase family. +Peptidoglycan polymerase that is essential for cell division. [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H(+) Cell wall biogenesis; peptidoglycan biosynthesis. Localizes to the division septum. Belongs to the SEDS family. FtsW subfamily. +This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a 'molecular matchmaker', a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex. Belongs to the DNA mismatch repair MutL/HexB family. +Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). diphosphate + N-(5-phospho-beta-D-ribosyl)anthranilate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate Binds 2 magnesium ions per monomer. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 2/5. Homodimer. Belongs to the anthranilate phosphoribosyltransferase family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +Catalytic subunit of the TRAMP5 complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Polyadenylates RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. TRF5 is also required for proper nuclear division in mitosis and sister chromatid cohesion. Involved in the regulation of histone mRNA levels. May mediate mitotic chromosome condensation (By similarity). ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide Belongs to the DNA polymerase type-B-like family. +Belongs to the universal ribosomal protein uS9 family. +One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA. Homotetramer, a dimer of dimers. One homotetramer interacts with 1 SecA dimer. Belongs to the SecB family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 2 subfamily. +May play a role in photosystem I and II biogenesis. Belongs to the PsbN family. Originally thought to be a component of PSII; based on experiments in Synechocystis, N.tabacum and barley, and its absence from PSII in T.elongatus and T.vulcanus, this is probably not true. +Catalyzes the reduction of a wide range of aldehydes into their corresponding alcohols. Has a strong preference for NADPH over NADH as the electron donor. Cannot use a ketone as substrate. Is a major source of NADPH-dependent aldehyde reductase activity in E.coli. The in vivo functions of YahK has yet to be determined. a primary alcohol + NADP(+) = an aldehyde + H(+) + NADPH Binds 2 Zn(2+) ions per subunit. kcat is 11.2 sec(-1) for acetaldehyde reduction. kcat is 11.6 sec(-1) for propionaldehyde reduction. kcat is 12.3 sec(-1) for glyceraldehyde reduction. kcat is 41.6 sec(-1) for butyraldehyde reduction. kcat is 32.1 sec(-1) for isobutyraldehyde reduction. kcat is 32.6 sec(-1) for crotonaldehyde reduction. kcat is 13.4 sec(-1) for glutaraldehyde reduction. kcat is 0.18 sec(-1) for 5-hydroxyvalerate reduction. kcat is 18.3 sec(-1) for hexanaldehyde reduction. kcat is 7.75 sec(-1) for benzaldehyde reduction. kcat is 12.5 sec(-1) for furfural reduction. kcat is 4.7 sec(-1) for butanol oxidation. kcat is 6.7 sec(-1) for 1,4-butanediol oxidation. Shows a constant increase in activity until 60 degrees Celsius using butyraldehyde as substrate. Belongs to the zinc-containing alcohol dehydrogenase family. +Mediates both low-affinity uptake and efflux of sugar across the plasma membrane. Forms homooligomers and/or heterooligomers. Belongs to the SWEET sugar transporter family. +To E.coli YibQ. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + H2O + oxidized [flavodoxin] = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + reduced [flavodoxin] Binds 1 [4Fe-4S] cluster. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 5/6. Belongs to the IspG family. +Belongs to the UPF0758 family. +Forms oligomers. Belongs to the MraZ family. +Component of the elastin-associated microfibrils. Glycosylated. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the cyclophilin-type PPIase family. PPIL3 subfamily. +Essential protein. Putative transcription factor. Homo or heterodimer. Interacts with ZHD1, ZHD3, ZHD4, ZHD5, ZHD6, ZHD7, ZHD8, ZHD9, ZHD10 and ZHD11. Mostly expressed in flowers and, to a lower extent, in inflorescence, stems and leaves. The homeodomain differs form the typical one by having namely 4 instead of 3 extra amino acids inserted in the loop between helix 1 and helix 2. Arrested at early embryo stages. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +May modulate calcium-mediated postsynaptic signals. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation. Directly interacts with APBA2. Forms a tripartite complex with APBA2 and APP. Interacts with low affinity with KLC1 (By similarity). Most prominent in the postsynaptic specializations of asymmetric (type I) synapses with both axodendritic and axospinous localization. Binds synaptic Ca(2+) with its cytoplasmic domain. Proteolytically processed under normal cellular conditions. A primary zeta-cleavage generates a large extracellular (soluble) N-terminal domain (sAlc) and a short C-terminal transmembrane fragment (CTF1). A secondary cleavage catalyzed by gamma-secretase within the transmembrane domain releases the beta-Alc-beta chain in the extracellular milieu and produces an intracellular fragment (AlcICD). This processing is strongly suppressed in the tripartite complex formed with APBA2 and APP, which seems to prevent the association with gamma-secretase (By similarity). +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Belongs to the urease gamma subunit family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Feedback inhibited by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the natural substrates and inhibitors of the enzyme. Belongs to the ATP phosphoribosyltransferase family. Long subfamily. +Reversible hydration of carbon dioxide. H(+) + hydrogencarbonate = CO2 + H2O Inhibited by acetazolamide. Homodimer. Belongs to the alpha-carbonic anhydrase family. +Acts as a coactivator during transcriptional activation of nuclear genes related to mitochondrial biogenesis and cell growth. Involved in the transcription coactivation of CREB and NRF1 target genes (By similarity). Interacts with CREB1 and NRF1. Colocalizes with NRF1. Expressed in liver, heart, skeletal muscle, kidney and white and brown adipose tissues. Up-regulated by serum (at protein level). Up-regulated by serum. Up-regulated weakly in brown adipose tissue by exposure of animals to cold. +Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NAD(+) (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADPH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NADP(+) Belongs to the MnmG family. TrmFO subfamily. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] In the egg, expressed predominantly in the animal hemisphere. This pattern of expression persists throughout the cleavage and blastula stages. At the gastrula stage, expression is restricted to the ectoderm. In later-stage embryos, expressed over the entire embryonic surface including the open neural plate at stage 15 and the neural tube at stage 22. In tadpoles, strongly expressed in the neural tube, motor neurons, brain regions and sensory organs (otic vesicle and eye). Also expressed in the perisomitic mesoderm, brachial arches and embryonic epidermis of tadpoles. Expressed both maternally and zygotically. Expressed throughout development. Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. SNF1 subfamily. +Involved in serotonin biosynthesis. Catalyzes the conversion of tryptamine to serotonin (PubMed:21080162, PubMed:23053415, PubMed:20150424, PubMed:23521226). Accumulation of serotonin may play a role in innate immunity (PubMed:20150424). O2 + reduced [NADPH--hemoprotein reductase] + tryptamine = H(+) + H2O + oxidized [NADPH--hemoprotein reductase] + serotonin Expression increases in the panicle from 7 days before flowering to flowering stage, to become undetectable 7 days after flowering. Induced by N-acetylchitooligosaccharide elicitor and infection with a compatible race of the rice blast fungus Magnaporthe oryzae (PubMed:20150424). Induced by salt stress, methyl viologen, acifluorfen and cadmium (PubMed:23053415). Belongs to the cytochrome P450 family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Binds 2 divalent ions per subunit. Binds 1 potassium ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Homotetramer; dimer of dimers. Belongs to the AdoMet synthase family. +APOE is an apolipoprotein, a protein associating with lipid particles, that mainly functions in lipoprotein-mediated lipid transport between organs via the plasma and interstitial fluids. APOE is a core component of plasma lipoproteins and is involved in their production, conversion and clearance. Apoliproteins are amphipathic molecules that interact both with lipids of the lipoprotein particle core and the aqueous environment of the plasma. As such, APOE associates with chylomicrons, chylomicron remnants, very low density lipoproteins (VLDL) and intermediate density lipoproteins (IDL) but shows a preferential binding to high-density lipoproteins (HDL). It also binds a wide range of cellular receptors including the LDL receptor/LDLR and the very low-density lipoprotein receptor/VLDLR that mediate the cellular uptake of the APOE-containing lipoprotein particles. Finally, APOE has also a heparin-binding activity and binds heparan-sulfate proteoglycans on the surface of cells, a property that supports the capture and the receptor-mediated uptake of APOE-containing lipoproteins by cells. In the plasma, APOE is associated with chylomicrons, chylomicrons remnants, VLDL, LDL and HDL lipoproteins. Lipid poor oligomeric APOE is associated with the extracellular matrix in a calcium- and heparan-sulfate proteoglycans-dependent manner. Lipidation induces the release from the extracellular matrix. APOE exists as multiple glycosylated and sialylated glycoforms within cells and in plasma. The extent of glycosylation and sialylation are tissue and context specific. Glycated in plasma VLDL. Phosphorylated by FAM20C in the extracellular medium. Belongs to the apolipoprotein A1/A4/E family. +Belongs to the UPF0758 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS8 family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Belongs to the PPR family. P subfamily. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) Binds 1 zinc ion per subunit. Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. Belongs to the class-II aminoacyl-tRNA synthetase family. +Involved in early neuronal development; required for cell cycle exit and differentiation of primary neurons (By similarity). Cooperates synergistically with pak3 to promote primary neural differentiation within the neural plate (PubMed:24095902). May play a role in promoting megakaryocyte differentiation (By similarity). Maternally expressed. Expressed at the animal half during the blastula stage. Expressed in the central, posterior and anterior neural plate regions, including the eye field at stage 12.5. Expressed in the posterior neural plate at stage 15. Later on, expressed in the developing nervous system. Expressed through the eye vesicle at stage 20. Strongly expressed in differentiating primary neurons in the brain, spinal cord and retina from stages 24 to 31. Not detected in the lens at any developmental stages. Up-regulated by the proneural transcription factors Neurog2, Neurod1 and Ebf3. Morpholino knockdown of the protein causes an accumulation of neuronal progenitor cells resulting in the neural plate expansion. Belongs to the MTURN family. +Belongs to the RemA family. +Viroporin that forms a homopentameric ion channel displaying low ion selectivity (PubMed:18369195, PubMed:22621926, PubMed:25100835, PubMed:27817112). May play a role in virus morphogenesis and pathogenicity at various stages of the viral life cycle. Accumulates at the membrane of the Golgi apparatus in infected cells and may facilitate virus release by modifying the secretory pathway (PubMed:15105532, PubMed:23229815). May enhance host membrane permeability and disrupt cellular ion homeostasis, which can be sensed as damage-associated molecular patterns/danger signals, triggering NLRP3 inflammasome activation and inflammatory immune response (PubMed:23229815). Also inhibits host TNFA-mediated signaling pathway and may delay apoptosis, allowing time for the virus to replicate (PubMed:17494063). Channel activity is inhibited by copper (PubMed:22621926). Also inhibited by small-molecule pyronin B (PubMed:25100835). Homopentamer forming a funnel-like pore (PubMed:18036342, PubMed:18369195, PubMed:22621926). Interacts with glycoprotein G; this interaction occurs on the surface of virion particles and infected cells (PubMed:18036342). Interacts with host BCAP31 (via C-terminus); this interaction is direct (PubMed:25854864). Present in very small amount in the virion. Detected in lipid rafts of host Golgi apparatus membrane. Four species of SH have been detected in infected cell cytoplasm: a 7.5 kDa non-glycosylated form (SH0), a 13-15 kDa form that contains one or two N-linked carbohydrate side chains of the high-mannose type (SHg), a 21-30 kDa polylactosaminoglycan-modified form of the protein (SHp), and the isoform generated by alternative translational initiation (PubMed:2649692). Of these different forms, SH0 is by far the most abundant protein detected during virus infection (PubMed:2649692). Tyrosine phosphorylated. Produced by alternative initiation at Met-23 of isoform SH and gives rise to a 4.6 kDa truncated form of the non-glycosylated protein. Belongs to the orthopneumovirus small hydrophobic protein family. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +Oligomerizes in the host endoplasmic reticulum into predominantly trimers. In a second time, gp160 transits in the host Golgi, where glycosylation is completed. The precursor is then proteolytically cleaved in the trans-Golgi and thereby activated by cellular furin or furin-like proteases to produce gp120 and gp41. Attaches the virus to the host lymphoid cell by binding to the primary receptor CD4. This interaction induces a structural rearrangement creating a high affinity binding site for a chemokine coreceptor like CXCR4 and/or CCR5. Acts as a ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on dendritic cells (DCs), and on endothelial cells of liver sinusoids and lymph node sinuses. These interactions allow capture of viral particles at mucosal surfaces by these cells and subsequent transmission to permissive cells. HIV subverts the migration properties of dendritic cells to gain access to CD4+ T-cells in lymph nodes. Virus transmission to permissive T-cells occurs either in trans (without DCs infection, through viral capture and transmission), or in cis (following DCs productive infection, through the usual CD4-gp120 interaction), thereby inducing a robust infection. In trans infection, bound virions remain infectious over days and it is proposed that they are not degraded, but protected in non-lysosomal acidic organelles within the DCs close to the cell membrane thus contributing to the viral infectious potential during DCs' migration from the periphery to the lymphoid tissues. On arrival at lymphoid tissues, intact virions recycle back to DCs' cell surface allowing virus transmission to CD4+ T-cells. Acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During fusion of viral and target intracellular membranes, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Complete fusion occurs in host cell endosomes and is dynamin-dependent, however some lipid transfer might occur at the plasma membrane. The virus undergoes clathrin-dependent internalization long before endosomal fusion, thus minimizing the surface exposure of conserved viral epitopes during fusion and reducing the efficacy of inhibitors targeting these epitopes. Membranes fusion leads to delivery of the nucleocapsid into the cytoplasm. The mature envelope protein (Env) consists of a homotrimer of non-covalently associated gp120-gp41 heterodimers. The resulting complex protrudes from the virus surface as a spike. There seems to be as few as 10 spikes on the average virion. Interacts with host CD4, CCR5 and CXCR4. Gp120 also interacts with the C-type lectins CD209/DC-SIGN and CLEC4M/DC-SIGNR (collectively referred to as DC-SIGN(R)). Gp120 and gp41 interact with GalCer. Gp120 interacts with host ITGA4/ITGB7 complex; on CD4+ T-cells, this interaction results in rapid activation of integrin ITGAL/LFA-1, which facilitates efficient cell-to-cell spreading of HIV-1. Gp120 interacts with cell-associated heparan sulfate; this interaction increases virus infectivity on permissive cells and may be involved in infection of CD4- cells. The mature envelope protein (Env) consists of a homotrimer of non-covalently associated gp120-gp41 heterodimers. The resulting complex protrudes from the virus surface as a spike. There seems to be as few as 10 spikes on the average virion. The surface protein is not anchored to the viral envelope, but associates with the extravirion surface through its binding to TM. It is probably concentrated at the site of budding and incorporated into the virions possibly by contacts between the cytoplasmic tail of Env and the N-terminus of Gag. It is probably concentrated at the site of budding and incorporated into the virions possibly by contacts between the cytoplasmic tail of Env and the N-terminus of Gag. Some of the most genetically diverse regions of the viral genome are present in Env. They are called variable regions 1 through 5 (V1 through V5). Coreceptor usage of gp120 is determined mainly by the primary structure of the third variable region (V3) in the outer domain of gp120. The sequence of V3 determines which coreceptor, CCR5 and/or CXCR4 (corresponding to R5/macrophage, X4/T cell and R5X4/T cell and macrophage tropism), is used to trigger the fusion potential of the Env complex, and hence which cells the virus can infect. Binding to CCR5 involves a region adjacent in addition to V3. The membrane proximal external region (MPER) present in gp41 is a tryptophan-rich region recognized by the antibodies 2F5, Z13, and 4E10. MPER seems to play a role in fusion. The 17 amino acids long immunosuppressive region is present in many retroviral envelope proteins. Synthetic peptides derived from this relatively conserved sequence inhibit immune function in vitro and in vivo. The YXXL motif is involved in determining the exact site of viral release at the surface of infected mononuclear cells and promotes endocytosis. YXXL and di-leucine endocytosis motifs interact directly or indirectly with the clathrin adapter complexes, opperate independently, and their activities are not additive. The CD4-binding region is targeted by the antibody b12. Highly glycosylated by host. The high number of glycan on the protein is reffered to as 'glycan shield' because it contributes to hide protein sequence from adaptive immune system. Palmitoylation of the transmembrane protein and of Env polyprotein (prior to its proteolytic cleavage) is essential for their association with host cell membrane lipid rafts. Palmitoylation is therefore required for envelope trafficking to classical lipid rafts, but not for viral replication. Specific enzymatic cleavages in vivo yield mature proteins. Envelope glycoproteins are synthesized as an inactive precursor that is heavily N-glycosylated and processed likely by host cell furin in the Golgi to yield the mature SU and TM proteins. The cleavage site between SU and TM requires the minimal sequence [KR]-X-[KR]-R. About 2 of the 9 disulfide bonds of gp41 are reduced by P4HB/PDI, following binding to CD4 receptor. Inhibitors targeting HIV-1 viral envelope proteins are used as antiretroviral drugs. Attachment of virions to the cell surface via non-specific interactions and CD4 binding can be blocked by inhibitors that include cyanovirin-N, cyclotriazadisulfonamide analogs, PRO 2000, TNX 355 and PRO 542. In addition, BMS 806 can block CD4-induced conformational changes. Env interactions with the coreceptor molecules can be targeted by CCR5 antagonists including SCH-D, maraviroc (UK 427857) and aplaviroc (GW 873140), and the CXCR4 antagonist AMD 070. Fusion of viral and cellular membranes can be inhibited by peptides such as enfuvirtide and tifuvirtide (T 1249). Resistance to inhibitors associated with mutations in Env are observed. Most of the time, single mutations confer only a modest reduction in drug susceptibility. Combination of several mutations is usually required to develop a high-level drug resistance. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Belongs to the HIV-1 env protein family. HIV drug resistance database +Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate + tRNA(n) Homohexameric ring arranged as a trimer of dimers. Belongs to the RNase PH family. +Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP. Allosterically activated by GTP. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uracil: step 1/1. Belongs to the UPRTase family. +Possible disease resistance protein. Although strongly related to the NB-LRR family, it is shorter and lacks the LRR repeats that are present in other proteins of the family. Functional and comparative genomics of disease resistance gene homologs +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +The E.coli ykgEFG operon is a clear homolog of the B.subtilis lutABC operon, however it is not able of restoring L-lactate utilization to the B.subtilis mutant for lutABC operon. Thus, ykgEFG operon may contribute to lactate catabolism in E.coli, but under conditions other than those tested, or alternatively, the ykgEFG operon may be responsible for the catabolism of a metabolite other than (but perhaps related to) lactate in E.coli. Belongs to the LutB/YkgF family. +Belongs to the bacterial ribosomal protein bL27 family. +Belongs to the RANBP1 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Global transcriptional regulator that plays a key role in stress response and exerts either positive or negative regulation of genes. Acts by interacting with the C-terminal domain of the alpha subunit of the RNA polymerase (RNAP). This interaction can enhance binding of RNAP to the promoter region of target genes and stimulate their transcription, or block interaction of RNAP with activator. Interacts with the C-terminal domain of the alpha subunit of the RNAP. Belongs to the ArsC family. Spx subfamily. +Contributes to the maintenance of intracerebral BDNF levels within the normal range, which is necessary for the preservation of spatial learning and the resistance to neuronal cell death caused by ischemic stress (By similarity). May enhance growth factor-induced ERK1 and ERK2 phosphorylation, including that induced by PDGF and FGF. May attenuate NGF-promoted ELK1 phosphorylation in a microtubule-dependent manner. Expressed predominantly in brain and heart (at protein level). In the brain, detected in astrocytes. Isoform 1 and isoform 2 are only expressed in brain. Isoform 3 is expressed in both heart and brain. Up-regulated in glioblastoma multiforme cells. Expressed in a cell cycle-specific manner in glioblastoma multiple cells. Low levels in G2/M cells increase with progression through G1 phase and entry and progression through S phase. Phosphorylated in an aortic smooth muscle cell line, following PDGF treatment. Belongs to the NDRG family. Extended N-terminus. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase C chain family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase C chain family. +Catalyzes the hydrolysis of fructose 1,6-bisphosphate (Fru 1,6-P2) and sedoheptulose 1,7-bisphosphate (Sed 1,7-P2) to fructose 6-phosphate and sedoheptulose 7-phosphate, respectively. beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate D-sedoheptulose 1,7-bisphosphate + H2O = D-sedoheptulose 7-phosphate + phosphate Carbohydrate biosynthesis; Calvin cycle. Homotetramer. Belongs to the FBPase class 2 family. +Part of the ABC transporter complex NikABCDE involved in nickel import. Responsible for energy coupling to the transport system. ATP + H2O + Ni(2+)(out) = ADP + H(+) + Ni(2+)(in) + phosphate The complex is composed of two ATP-binding proteins (NikD and NikE), two transmembrane proteins (NikB and NikC) and a solute-binding protein (NikA). Belongs to the ABC transporter superfamily. Nickel importer (TC 3.A.1.5.3) family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Binds 1 [2Fe-2S] cluster. The F420-non-reducing hydrogenase vhc is composed of three subunits; VhcA, VhcD and VhcG. By selenium deprivation. Belongs to the MvhD/VhuD family. +Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate. ATP + L-glutamate = ADP + L-glutamyl 5-phosphate Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 1/2. Belongs to the glutamate 5-kinase family. +Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism. adenine + H(+) + H2O = hypoxanthine + NH4(+) Binds 1 zinc ion per subunit. Belongs to the metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. Adenine deaminase type 2 subfamily. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 3 family. +Promotes the exchange of Ras-bound GDP by GTP. Expressed during development. +Involved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. The regulation of gene expression in response to changes in cell density is called quorum sensing. Catalyzes the transformation of S-ribosylhomocysteine (RHC) to homocysteine (HC) and 4,5-dihydroxy-2,3-pentadione (DPD). S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine Binds 1 Fe cation per subunit. Homodimer. Belongs to the LuxS family. +Global transcriptional regulator that plays a key role in stress response and exerts either positive or negative regulation of genes (PubMed:12642660, PubMed:15659166, PubMed:16885442, PubMed:18662407, PubMed:18687074, PubMed:29271514). Acts by interacting with the C-terminal domain of the alpha subunit of the RNA polymerase (RNAP) (PubMed:12642660, PubMed:15659166, PubMed:18687074, PubMed:20084284). This interaction can enhance binding of RNAP to the promoter region of target genes and stimulate their transcription, or block interaction of RNAP with activator proteins and repress transcription (PubMed:12642660, PubMed:15659166, PubMed:18687074, PubMed:20084284). Exhibits no DNA-binding activity (PubMed:15659166, PubMed:18687074). Induces the expression of a large number of genes in response to a variety of stress conditions, such as disulfide, heat and cell wall stress, while concurrently repressing transcription of genes involved in various developmental and growth-related pathways during periods of extreme stress (PubMed:12642660, PubMed:14597697). Functions in the oxidative stress response via induction of the transcription of thioredoxin (trxA) and thioredoxin reductase (trxB) during thiol-specific oxidative (disulfide) stress (PubMed:14597697, PubMed:15659166, PubMed:18687074). Mediates response to oxidative stress caused by paraquat (PQ) via induction of the methionine sulfoxide reductase genes, msrA and msrB (PubMed:18662407). Also acts as a transcriptional activator of the bacillithiol (BSH) biosynthesis genes in response to oxidizing conditions and thio-reactive compounds (PubMed:23894131). Involved in heat stress response and thermotolerance development, which results in diminished cellular protein aggregates (PubMed:24417481). Plays an important adaptive role in the cell wall stress response (PubMed:29271514). Participates in sulfate-dependent control of organosulfur metabolism. Negatively controls, via CymR, the expression of the organosulfur utilization operons ytmI, yxeI and ssu, and directly activates yrrT operon expression during growth in medium containing methionine as sole sulfur source (PubMed:16885442). Negatively affects competence and sporulation (PubMed:11703662, PubMed:12028382). Inhibits biofilm formation in response to disulfide stress by repressing biofilm matrix genes (PubMed:30718304). Under non-stress conditions, Spx is degraded by ClpXP and, to a lesser extent, by ClpCP (PubMed:12057962, PubMed:12642660, PubMed:19074380). Efficient dedradation by ClpXP requires the adapter protein SpxH/YjbH (PubMed:17908206, PubMed:19074380). Binding to SpxH/YjbH reduces the overall conformational flexibility of Spx and stabilizes the C-terminal ClpX recognition region of Spx (PubMed:30982633). In addition, activity is modulated by the formation of a disulfide bound within the N-terminal Cys-X-X-Cys (CXXC) motif, which is required for the transcriptional activation of trxA and trxB, or for the activation of msrAB operon expression following paraquat oxidative stress (PubMed:15659166, PubMed:18662407). However, it seems that formation of the disulfide bound is not essential for induction of all Spx-controlled genes, as for example the case of BSH biosynthesis genes (PubMed:23894131). Similarly, induction of the Spx regulon during cell wall stress is not accompanied by oxidation of the disulfide switch, but requires Spx stabilization by the anti-adapter protein SpxO/YirB (PubMed:29271514, PubMed:30001325). Interacts with the C-terminal domain of the alpha subunit of the RNAP (PubMed:12642660, PubMed:16249335, PubMed:19580872, PubMed:20084284, PubMed:22307755). A single Spx monomer interacts with RNAP to form the transcription activation complex (PubMed:22307755). Interacts with the adapter protein SpxH/YjbH (PubMed:19074380, PubMed:24942655, PubMed:30982633). Transcribed from at least five promoters located in the yjbC regulatory region or in the yjbC-spx intergenic region (PubMed:17158660, PubMed:29271514). Induced by heat, salt, ethanol and disulfide stress and also by phosphate limitation (PubMed:11544224, PubMed:14597697, PubMed:24417481). Induced by cell wall stress but not by membrane stress (PubMed:29271514). Transcribed under partial control of SigM ECF sigma factor (PubMed:17434969, PubMed:29271514). Repressed by YodB and PerR. YodB protects a region that includes the P3 -10 and -35 regions, while PerR binds to a region downstream of the P3 transcriptional start site (PubMed:17158660). The C-terminal region is essential for structural folding and for interaction with SpxH/YjbH (PubMed:24942655). A conformational change during oxidation of Spx to the disulfide form likely alters the structure of Spx alpha helix alpha4, which contains residues that function in transcriptional activation and Spx/RNAP-promoter interaction (PubMed:20084284). Inactivation of the gene results in ClpP-independent competence development as well as partial suppression of the sporulation defect conferred by clpP mutation (PubMed:11703662). Null mutant shows hypersensitivity to disulfide stress and to paraquat (PubMed:14597697, PubMed:18662407). Mutants have increased sensitivity toward cell wall active antibiotics inhibiting both early and late steps in peptidoglycan synthesis (PubMed:29271514). Cells lacking the gene are defective in thermotolerance (PubMed:24417481). Belongs to the ArsC family. Spx subfamily. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, HCO(3)(-)/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate. ATP + hydrogencarbonate + L-threonine = diphosphate + H2O + L-threonylcarbamoyladenylate Belongs to the SUA5 family. TsaC subfamily. +Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes monoubiquitination. Involved in mitomycin-C (MMC)-induced DNA repair. Acts as a specific E2 ubiquitin-conjugating enzyme for the Fanconi anemia complex by associating with E3 ubiquitin-protein ligase FANCL and catalyzing monoubiquitination of FANCD2, a key step in the DNA damage pathway (PubMed:16916645, PubMed:17938197, PubMed:19111657, PubMed:19589784, PubMed:28437106). Also mediates monoubiquitination of FANCL and FANCI (PubMed:16916645, PubMed:17938197, PubMed:19111657, PubMed:19589784). May contribute to ubiquitination and degradation of BRCA1 (PubMed:19887602). In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11'-, 'Lys-27'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination (PubMed:20061386). S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine. Protein modification; protein ubiquitination. Directly interacts with FANCL (PubMed:16916645, PubMed:17938197, PubMed:19111657, PubMed:21775430, PubMed:24389026). Interacts with BRCA1 (PubMed:19887602). Accumulates to chromatin. Down-regulated following hypoxia. Up-regulated in breast cancers. Auto-ubiquitinated. Effects of auto-monoubiquitination at Lys-91 and Lys-182 are unclear: according to a report, monoubiquitination inactivates E2 enzyme activity (PubMed:16916645). In contrast, according to another report, autoubiquitination does not affect E2 enzyme activity (PubMed:19111657). The disease is caused by variants affecting the gene represented in this entry. Belongs to the ubiquitin-conjugating enzyme family. +Encapsidates the negative strand viral RNA, protecting it from nucleases. The encapsidated genomic RNA is termed the ribonucleoprotein (RNP) and serves as template for transcription and replication. The RNP needs to be localized in the host nucleus to start an infectious cycle, but is too large to diffuse through the nuclear pore complex. NP comprises at least 2 nuclear localization signals that are responsible for the active RNP import into the nucleus through cellular importin alpha/beta pathway. Later in the infection, nclear export of RNPs are mediated through viral proteins NEP interacting with M1 which binds nucleoproteins. It is possible that nucleoprotein binds directly host exportin-1/XPO1 and plays an active role in RNPs nuclear export. M1 interaction with RNP seems to hide nucleoprotein's nuclear localization signals. Soon after a virion infects a new cell, M1 dissociates from the RNP under acidification of the virion driven by M2 protein. Dissociation of M1 from RNP unmasks nucleoprotein's nuclear localization signals, targeting the RNP to the nucleus. Homomultimerizes to form the nucleocapsid. May bind host exportin-1/XPO1. Binds to viral genomic RNA. Protein-RNA contacts are mediated by a combination of electrostatic interactions between positively charged residues and the phosphate backbone and planar interactions between aromatic side chains and bases. Late in virus-infected cells, may be cleaved from a 56-kDa protein to a 53-kDa protein by a cellular caspase. This cleavage might be a marker for the onset of apoptosis in infected cells or have a specific function in virus host interaction. Belongs to the influenza viruses nucleoprotein family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Belongs to the polyribonucleotide nucleotidyltransferase family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 1 Zn(2+) ion per subunit. In plastids the minimal PEP RNA polymerase catalytic core is composed of four subunits: alpha, beta, beta', and beta''. When a (nuclear-encoded) sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. RpoC1 subfamily. Extended N-terminus. Extended N-terminus. +Acts as NAD-dependent protein lipoamidase, biotinylase, deacetylase and ADP-ribosyl transferase (PubMed:19220062). Catalyzes more efficiently removal of lipoyl- and biotinyl- than acetyl-lysine modifications. Inhibits the pyruvate dehydrogenase complex (PDH) activity via the enzymatic hydrolysis of the lipoamide cofactor from the E2 component, DLAT, in a phosphorylation-independent manner (PubMed:25525879). Catalyzes the transfer of ADP-ribosyl groups onto target proteins, including mitochondrial GLUD1, inhibiting GLUD1 enzyme activity. Acts as a negative regulator of mitochondrial glutamine metabolism by mediating mono ADP-ribosylation of GLUD1: expressed in response to DNA damage and negatively regulates anaplerosis by inhibiting GLUD1, leading to block metabolism of glutamine into tricarboxylic acid cycle and promoting cell cycle arrest (PubMed:16959573). In response to mTORC1 signal, SIRT4 expression is repressed, promoting anaplerosis and cell proliferation (PubMed:23663782). Acts as a tumor suppressor (PubMed:23562301, PubMed:23663782). Also acts as a NAD-dependent protein deacetylase: mediates deacetylation of 'Lys-471' of MLYCD, inhibiting its activity, thereby acting as a regulator of lipid homeostasis (PubMed:23746352). Does not seem to deacetylate PC (PubMed:23438705). Controls fatty acid oxidation by inhibiting PPARA transcriptional activation. Impairs SIRT1-PPARA interaction probably through the regulation of NAD(+) levels (PubMed:24043310, PubMed:20685656). Down-regulates insulin secretion (By similarity). (R)-N(6)-lipoyl-L-lysyl-[protein] + H2O + NAD(+) = 2''-O-lipoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide H2O + N(6)-biotinyl-L-lysyl-[protein] + NAD(+) = 2''-O-biotinyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide H2O + N(6)-acetyl-L-lysyl-[protein] + NAD(+) = 2''-O-acetyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide L-cysteinyl-[protein] + NAD(+) = H(+) + nicotinamide + S-(ADP-D-ribosyl)-L-cysteinyl-[protein] Binds 1 zinc ion per subunit. Interacts with IDE and SLC25A5 (By similarity). Interacts with GLUD1 (PubMed:16959573). Interacts with DLAT and PDHX (By similarity). Interacts with MCCC1 (via the biotin carboxylation domain) (PubMed:23438705). Interacts with PCCA and PC (PubMed:23438705). Detected in kidney, heart, brain, liver and pancreatic islets (at protein level). Expression is directly activated by ATF4/CREB2. In response to mTORC1 signal, expression is down-regulated due to degradation of ATF4/CREB2 (PubMed:23663782). Induced following DNA damage (PubMed:23562301). The expression is strongly inhibited by fasting (PubMed:24043310). No visible phenotype. Decreased mitochondrial protein ADP-ribosylation. Increased plasma insulin levels. Mice develop lung tumors more frequently. Defects in lipid metabolism, leading to increased protection against diet-induced obesity. Animals show higher levels of NAD(+) in liver (PubMed:24043310). In the hepatic periportal zone, decreased number of mitochondria with an increase in their length (PubMed:24043310). According to some authors, ADP-ribosyltransferase activity of sirtuins may be an inefficient side reaction of the deacetylase activity and may not be physiologically relevant. Belongs to the sirtuin family. Class II subfamily. Extended N-terminus. +Contributes to protect fish blood from freezing at subzero sea water temperatures. Lowers the blood freezing point. Binds to nascent ice crystals and prevents further growth (By similarity). Detected in blood serum (at protein level). Belongs to the type-III AFP family. +Catalyzes the reduction of Delta(1)-pyrroline-2-carboxylate (Pyr2C) to L-proline, using NADPH as the electron donor. May be involved in a degradation pathway that converts trans-3-hydroxy-L-proline (t3LHyp) to L-proline. L-proline + NAD(+) = 1-pyrroline-2-carboxylate + H(+) + NADH L-proline + NADP(+) = 1-pyrroline-2-carboxylate + H(+) + NADPH kcat is 54 sec(-1) for Pyr2C reduction using NADPH. Homodimer. Belongs to the LDH2/MDH2 oxidoreductase family. +NDH-1 shuttles electrons from an unknown electron donor, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH-1 can be composed of about 15 different subunits; different subcomplexes with different compositions have been identified which probably have different functions. Belongs to the complex I NdhO subunit family. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. adenosine + H(+) + H2O = inosine + NH4(+) 2'-deoxyadenosine + H(+) + H2O = 2'-deoxyinosine + NH4(+) Binds 1 zinc ion per subunit. Belongs to the metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. Adenosine deaminase subfamily. +Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+) Binds 1 dipyrromethane group covalently. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. Monomer. The porphobilinogen subunits are added to the dipyrromethane group. Belongs to the HMBS family. +Serine palmitoyltransferase (SPT). The heterodimer formed with LCB2 constitutes the catalytic core (By similarity). H(+) + hexadecanoyl-CoA + L-serine = 3-oxosphinganine + CO2 + CoA Lipid metabolism; sphingolipid metabolism. Heterodimer with LCB2. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2 (By similarity). Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Cell division protein that is part of the divisome complex and is recruited early to the Z-ring. Probably stimulates Z-ring formation, perhaps through the cross-linking of FtsZ protofilaments. Its function overlaps with FtsA. Homodimer. Interacts with FtsZ. Localizes to the division site, in a FtsZ-dependent manner. Belongs to the SepF family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway. D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = beta-D-fructose 6-phosphate + D-erythrose 4-phosphate Carbohydrate degradation; pentose phosphate pathway; D-glyceraldehyde 3-phosphate and beta-D-fructose 6-phosphate from D-ribose 5-phosphate and D-xylulose 5-phosphate (non-oxidative stage): step 2/3. Belongs to the transaldolase family. Type 2 subfamily. +Catalyzes the specific phosphorylation of 1,6-anhydro-N-acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. Is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling. 1,6-anhydro-N-acetyl-beta-muramate + ATP + H2O = ADP + H(+) + N-acetyl-D-muramate 6-phosphate Amino-sugar metabolism; 1,6-anhydro-N-acetylmuramate degradation. Cell wall biogenesis; peptidoglycan recycling. Belongs to the anhydro-N-acetylmuramic acid kinase family. +Transfers dimethylallyl groups to AMP as part of the biosynthesis of cytokinin phytohormones. AMP + dimethylallyl diphosphate = diphosphate + N(6)-(dimethylallyl)adenosine 5'-phosphate Belongs to the isopentenyl transferase family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Protects the bacterial cell from host peptidases. Belongs to the protease inhibitor I39 (alpha-2-macroglobulin) family. Bacterial alpha-2-macroglobulin subfamily. +Regulates cytotoxic granule exocytosis in effector lymphocytes, thus acting as a critical mediator of inflammation in a broad range of infectious and non-infectious diseases (By similarity). Essential for cytotoxic degranulation of natural killer (NK) cells and CD8(+) T-cells and for the activation of CD4(+) T-cells following infection (By similarity). Plays a critical role in CD8(+) T-cell and NK cell-mediated cytolysis of target cells and contributes to the cytolytic activity via the perforin/granzyme pathway by enhancing exocytosis of LAMP1-carrying lytic granules (By similarity). Contributes to NK cell-mediated control of cancer metastasis (By similarity). Belongs to the PMP-22/EMP/MP20 family. +ATP-binding RNA helicase involved in 40S ribosomal subunit biogenesis and is required for the normal formation of 18S rRNAs through pre-rRNA processing at A0, A1 and A2 sites. Required for vegetative growth (By similarity). ATP + H2O = ADP + H(+) + phosphate The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis. Belongs to the DEAD box helicase family. DDX49/DBP8 subfamily. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Catalyzes the excretion of spermidine. Forms a complex with MdtI. Belongs to the drug/metabolite transporter (DMT) superfamily. Small multidrug resistance (SMR) (TC 2.A.7.1) family. MdtJ subfamily. +Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Belongs to the Nudix hydrolase family. RppH subfamily. +Participates in the translocation of lipoproteins from the inner membrane to the outer membrane. Only forms a complex with a lipoprotein if the residue after the N-terminal Cys is not an aspartate (The Asp acts as a targeting signal to indicate that the lipoprotein should stay in the inner membrane). Monomer. Belongs to the LolA family. +Despite the protein kinase domain is proposed to act predominantly as an ATPase (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. RIO-type Ser/Thr kinase family. +May be involved in transcriptional regulation. Overexpression causes down-regulation of a number of genes involved in the immune response. Some genes are also up-regulated. Detected in spleen and thymus but not in liver, muscle, heart, kidney, brain, bone marrow or pancreas. Expressed in CD19+, CD4+ and CD8+ lymphocytes but not in CD11b+ lymphocytes or peritoneal macrophages (at protein level). Up-regulated during the transition from CD4-/CD8- to CD4+/CD8+ thymocytes. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS17 family. +alpha-D-xylose = alpha-D-xylulofuranose Binds 2 magnesium ions per subunit. Homotetramer. Belongs to the xylose isomerase family. +ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys) Binds 3 Mg(2+) ions per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Involved in the early processing steps of the pre-rRNA in the maturation pathway leading to the 18S rRNA. Belongs to the RRP36 family. +In the embryo, expressed in newly arisen somatic blastomeres. Expressed in the somatic lineage from the 4-cell to 60-cell stage. Belongs to the Pes-10 family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. Extended N-terminus. +Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore. Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization either through clathrin-dependent endocytosis or through clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore. Homotrimer of disulfide-linked HA1-HA2. Targeted to the apical plasma membrane in epithelial polarized cells through a signal present in the transmembrane domain. Associated with glycosphingolipid- and cholesterol-enriched detergent-resistant lipid rafts. Palmitoylated. In natural infection, inactive HA is matured into HA1 and HA2 outside the cell by one or more trypsin-like, arginine-specific endoprotease secreted by the bronchial epithelial cells. One identified protease that may be involved in this process is secreted in lungs by Clara cells. Major glycoprotein, comprises over 80% of the envelope proteins present in virus particle. The extent of infection into host organism is determined by HA. Influenza viruses bud from the apical surface of polarized epithelial cells (e.g. bronchial epithelial cells) into lumen of lungs and are therefore usually pneumotropic. The reason is that HA is cleaved by tryptase clara which is restricted to lungs. However, HAs of H5 and H7 pantropic avian viruses subtypes can be cleaved by furin and subtilisin-type enzymes, allowing the virus to grow in other organs than lungs. The influenza A genome consist of 8 RNA segments. Genetic variation of hemagglutinin and/or neuraminidase genes results in the emergence of new influenza strains. The mechanism of variation can be the result of point mutations or the result of genetic reassortment between segments of two different strains. Belongs to the influenza viruses hemagglutinin family. +Possibly involved in pGI2 replication mechanism. +Cytochromes P450 are a group of heme-thiolate monooxygenases. They oxidize a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Belongs to the cytochrome P450 family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity and assembly of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Interacts with TMEM242 (By similarity). Belongs to the complex I subunit 2 family. +Mitochondrial trifunctional enzyme catalyzes the last three of the four reactions of the mitochondrial beta-oxidation pathway. The mitochondrial beta-oxidation pathway is the major energy-producing process in tissues and is performed through four consecutive reactions breaking down fatty acids into acetyl-CoA. Among the enzymes involved in this pathway, the trifunctional enzyme exhibits specificity for long-chain fatty acids. Mitochondrial trifunctional enzyme is a heterotetrameric complex composed of two proteins, the trifunctional enzyme subunit alpha/HADHA carries the 2,3-enoyl-CoA hydratase and the 3-hydroxyacyl-CoA dehydrogenase activities, while the trifunctional enzyme subunit beta/HADHB described here bears the 3-ketoacyl-CoA thiolase activity. acetyl-CoA + an acyl-CoA = a 3-oxoacyl-CoA + CoA acetyl-CoA + butanoyl-CoA = 3-oxohexanoyl-CoA + CoA acetyl-CoA + hexanoyl-CoA = 3-oxooctanoyl-CoA + CoA acetyl-CoA + octanoyl-CoA = 3-oxodecanoyl-CoA + CoA acetyl-CoA + decanoyl-CoA = 3-oxododecanoyl-CoA + CoA acetyl-CoA + dodecanoyl-CoA = 3-oxotetradecanoyl-CoA + CoA acetyl-CoA + tetradecanoyl-CoA = 3-oxohexadecanoyl-CoA + CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of 2 alpha/HADHA and 2 beta/HADHB subunits; forms the mitochondrial trifunctional enzyme. Also purified as higher order heterooligomers including a 4 alpha/HADHA and 4 beta/HADHB heterooligomer which physiological significance remains unclear. The mitochondrial trifunctional enzyme interacts with MTLN. Interacts with RSAD2/viperin. Protein stability and association with membranes require HADHA. Belongs to the thiolase-like superfamily. Thiolase family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +Adapter protein that plays essential roles in both innate and adaptive immunity. Plays a crucial role in the regulation of thymocyte development (PubMed:26195727). Mechanistically, mediates TCR-stimulated activation through recruiting MAP2K1/MEK1 to the Golgi and, thereby, facilitating the interaction of MAP2K1/MEK1 with its activator BRAF (PubMed:26195727). Also plays an essential role in regulatory T-cell stability and function by recruiting the serine-threonine phosphatase catalytic subunit (PPP2CA) to the lysosome, thereby facilitating the interaction of PP2Ac with the mTORC1 component RPTOR and restricting glycolytic metabolism (PubMed:30115741). Positively regulates TLR4 signaling activity in macrophage-mediated inflammation by acting as a molecular clamp to facilitate LPS-induced translocation of TLR4 to lipid rafts (PubMed:30115741). In response to viral infection, facilitates the recruitment of TRAF3 to MAVS within mitochondria leading to IRF3 activation and interferon production (PubMed:30115741). However, participates in the maintenance of immune homeostasis and the prevention of overzealous innate immunity by promoting 'Lys-48'-dependent ubiquitination of TBK1 (By similarity). Interacts (via its coiled-coil domain) with TRAF3 (via isoleucine zipper). Interacts with MAP2K1 (By similarity). Interacts with PPP2CA; this interaction targets PPP2CA to the lysosomes (By similarity). Interacts with MAVS (By similarity). Interacts with TBK1 (By similarity). Accumulates on the mitochondria after virus infection. Expressed in bone marrow, spleen and thymus. Not detected in heart, kidney and liver. Knockout mice have considerably lower frequencies of CD4(+) and CD8(+) single positive thymocytes, and concomitantly higher frequencies of double positive thymocytes (PubMed:26195727). TRAF3IP3 deletion also affects regulatory T-cell transcriptional programs and stability (PubMed:30115741). In addition, mice show a severely compromised potential to induce interferon production and are vulnerable to RNA virus infection (PubMed:31390091). Sequencing errors. +Belongs to the UPF0391 family. +Repressor involved in the biosynthesis of the osmoprotectant glycine betaine. It represses transcription of the choline transporter BetT and the genes of BetAB involved in the synthesis of glycine betaine (By similarity). Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway [regulation]. +Involved in allosteric regulation of aspartate carbamoyltransferase. Binds 1 zinc ion per subunit. Contains catalytic and regulatory chains. Belongs to the PyrI family. +Catalyzes the dye-linked oxidation of primary alcohols to the corresponding aldehydes and the (subsequent) oxidation of the aldehydes to carboxylic acids. Active with primary alcohols, glycerol, 1,2-propanediol, 1,3-propanediol but not with methanol or sugar alcohols such as D-sorbitol. a primary alcohol + 2 oxidized [azurin] = an aldehyde + 2 H(+) + 2 reduced [azurin] Binds 1 PQQ group per subunit. PQQ is inserted between disulfide Cys-138-Cys-139 and the plane of Trp-266. Binds 1 Ca(2+) ion per subunit. Binds 1 heme c group per subunit. Exhibits higher affinity for 1-butanol compared to 1,2-propanediol but inhibited by 10 mM 1-butanol. Optimum pH is 8.0. Monomer. (S+)-propane-1,2-diol is the most effective whereas (R-)-propane-1,2-diol, ethanediol and glycerol are weaker inducers. Belongs to the bacterial PQQ dehydrogenase family. +Selectively hydrolyzes arachidonyl phospholipids in the sn-2 position releasing arachidonic acid. Together with its lysophospholipid activity, it is implicated in the initiation of the inflammatory response. a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) a 1-acyl-sn-glycero-3-phosphocholine + H2O = a fatty acid + H(+) + sn-glycerol 3-phosphocholine Stimulated by agonists such as ATP, EGF, thrombin and bradykinin as well as by cytosolic Ca(2+). Translocates to membrane vesicles in a calcium-dependent fashion. The N-terminal C2 domain associates with lipid membranes upon calcium binding. It modulates enzyme activity by presenting the active site to its substrate in response to elevations of cytosolic Ca(2+) (By similarity). Activated by phosphorylation on a serine residue. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Catalyzes the oxidation of erythronate-4-phosphate to 3-hydroxy-2-oxo-4-phosphonooxybutanoate. 4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + H(+) + NADH Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 2/5. Homodimer. Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Transports acetate. Belongs to the sodium:solute symporter (SSF) (TC 2.A.21) family. +Directly regulates filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localization and the establishment of cell polarity. Homodimer. Binds actin monomers (By similarity). Belongs to the CAP family. +Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily. +Antibacterial peptide, that adopts an alpha helical conformation which can disrupt bacterial membranes. Each caerin displays a different antimicrobial specificity. Expressed by the skin parotoid and/or rostral glands. Contains two amphipathic alpha helix regions separated by a region of less-defined helicity and greater flexibility. Belongs to the frog skin active peptide (FSAP) family. Caerin subfamily. +Bifunctional serine/threonine kinase and phosphorylase involved in the regulation of the pyruvate, phosphate dikinase (PPDK) by catalyzing its phosphorylation/dephosphorylation. ADP + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] = AMP + H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] + phosphate = diphosphate + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] Belongs to the pyruvate, phosphate/water dikinase regulatory protein family. PDRP subfamily. +Belongs to the UPF0316 family. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +The poly-Gly region is polymorphic and the number of Gly varies in the population (from 9 to 12). +Belongs to the eukaryotic ribosomal protein eS17 family. +Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins. Probable core component of the endosomal sorting required for transport complex III (ESCRT-III). ESCRT-III components are thought to multimerize to form a flat lattice on the perimeter membrane of the endosome (By similarity). Membrane-associated. Colocalizes to large vesicle-like structures with PDCD6IP/Alix. Belongs to the SNF7 family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds a dinuclear copper A center per subunit. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Found in a complex with TMEM177, COA6, COX18, COX20, SCO1 and SCO2. Interacts with TMEM177 in a COX20-dependent manner. Interacts with COX20. Interacts with COX16 (By similarity). Belongs to the cytochrome c oxidase subunit 2 family. +Catalyzes the O-sulfation of tyrosine residues within acidic motifs of polypeptides. 3'-phosphoadenylyl sulfate + L-tyrosyl-[protein] = adenosine 3',5'-bisphosphate + H(+) + O-sulfo-L-tyrosine-[protein] Expressed throughout the plant body, highest levels of expression are in the root apical meristem. Sequencing errors. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit. Contacts the 5S and 23S rRNAs (By similarity). Belongs to the universal ribosomal protein uL18 family. +Transcriptional regulator involved in developmental processes. Can activate POMC gene expression and repress the alpha glycoprotein subunit and thyroid-stimulating hormone beta promoters. The disease is caused by variants affecting the gene represented in this entry. +Catalyzes the formation of the isocyclic ring in chlorophyll biosynthesis. Mediates the cyclase reaction, which results in the formation of divinylprotochlorophyllide (Pchlide) characteristic of all chlorophylls from magnesium-protoporphyrin IX 13-monomethyl ester (MgPMME). 2 H(+) + Mg-protoporphyrin IX 13-monomethyl ester + 3 NADPH + 3 O2 = 3,8-divinyl protochlorophyllide a + 5 H2O + 3 NADP(+) Porphyrin-containing compound metabolism; chlorophyll biosynthesis (light-independent). Belongs to the AcsF family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +EF-1-beta and EF-1-beta' stimulate the exchange of GDP bound to EF-1-alpha to GTP. EF-1 is composed of 4 subunits: alpha, beta (1B-alpha=beta'), delta (1B-beta), and gamma (1B-gamma). Belongs to the EF-1-beta/EF-1-delta family. +Belongs to the UPF0282 family. +Key regulator of RAB11-dependent vesicular trafficking during neurite extension through polarized membrane transport. Promotes axonal elongation and contributes to the establishment of neuronal cell polarity. Involved in nerve growth factor-induced neurite formation in VAPA-dependent manner. Contributes to both the formation and stabilization of the tubular ER network. Involved in ER morphogenesis by regulating the sheet-to-tubule balance and possibly the density of tubule interconnections. Can form homooligomers (monomers, dimers and tetramers). Localizes to endoplasmic reticulum tubular network. +Involved in control of the biosynthesis of leucine. +Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA and the activity is stimulated by poly(A)-binding protein pab1. PAN deadenylation is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping and subsequent 5'-3' exonucleolytic degradation by xrn1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails. Exonucleolytic cleavage of poly(A) to 5'-AMP. Binds 2 metal cations per subunit in the catalytic exonuclease domain. Positively regulated by the regulatory subunit pan3. Forms a heterotrimer with an asymmetric homodimer of the regulatory subunit pan3 to form the poly(A)-nuclease (PAN) deadenylation complex. Contains a pseudo-UCH domain. This ubiquitin C-terminal hydrolase (UCH)-like or ubiquitin specific protease (USP)-like domain is predicted to be catalytically inactive because it lacks the active site catalytic triad characteristic of thiol proteases, with residues at the equivalent structural positions that are incompatible with catalysis, and it cannot bind ubiquitin. It functions as a structural scaffold for intra- and intermolecular interactions in the complex. The linker, or PAN3 interaction domain (PID), between the WD40 repeats and the pseudo-UCH domain mediates interaction with pan3. Belongs to the peptidase C19 family. PAN2 subfamily. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Belongs to the UPF0735 family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +Encapsidates the genome, protecting it from nucleases. If expressed without protein P it binds non-specifically RNA and therefore can bind it's own mRNA. Interaction with protein P abolishes any non-specific RNA binding, and prevents phosphorylation. The soluble N-P complex encapsidates specifically the genomic RNA, with protein N protecting the genome like a pearl necklace. The encapsidated genomic RNA is termed the nucleocapsid (NC) and serves as template for viral transcription and replication. Protein N binds protein P in the NC through a different interaction, and can be phosphorylated. Subsequent viral replication is dependent on intracellular concentration of newly synthesized protein N. During replication, encapsidation by protein N is coupled to RNA synthesis and all replicative products are resistant to nucleases (By similarity). Homomultimerizes to form the nucleocapsid. Binds to viral genomic RNA (By similarity). Phosphorylated by host. Belongs to the lyssavirus nucleocapsid protein family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Antitoxin component of a type II toxin-antitoxin (TA) system that counteracts the effect of the HigB toxin (PubMed:19423702, PubMed:8645296, PubMed:24257752). Binds to its own promoter and regulates transcription of the higB/higA operon (PubMed:24257752). Forms a complex with the mRNA interferase HigB which inhibits the mRNA interferase activity (PubMed:19423702). The heterodimer dimerizes to form a HigB-(HigA)2-HigB tetramer that is able to bind to the DNA (PubMed:24257752). +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. 2-oxoglutarate + O-phospho-L-serine = 3-phosphooxypyruvate + L-glutamate 2-oxoglutarate + 4-(phosphooxy)-L-threonine = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate Binds 1 pyridoxal phosphate per subunit. Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 2/3. Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 3/5. Homodimer. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. SerC subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 13 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 1 family. +GTPase that recruits MYO1E to MHC class II-containing vesicles via the effector protein ARL14EP and hence controls the movement of these vesicles along the actin cytoskeleton in dendritic cells. Interacts with ARL14EP. Colocalizes with MHC II-containing cytoplasmic vesicles. Expressed in immature dendritic cells. Belongs to the small GTPase superfamily. Arf family. +Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine Purine metabolism; AMP biosynthesis via salvage pathway; AMP from adenine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Methylated by PrmB. Belongs to the universal ribosomal protein uL3 family. +Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Belongs to the Nudix hydrolase family. RppH subfamily. +Catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 2/4. Belongs to the GPI family. +Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate. ATP + L-glutamate = ADP + L-glutamyl 5-phosphate Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 1/2. Belongs to the glutamate 5-kinase family. +Transcriptional repressor of the nikABCDE operon. Is active in the presence of excessive concentrations of intracellular nickel. Binds 1 nickel ion per subunit. Homotetramer. Belongs to the transcriptional regulatory CopG/NikR family. +Plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag-Pol, or to Gag-Pol binding host factors. Interaction with HECT ubiquitin ligases probably links the viral protein to the host ESCRT pathway and facilitates release. Targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the pre-integration complex. Constituent of the pre-integration complex (PIC) which tethers the latter to mitotic chromosomes. This allows the integration of the viral genome into the host DNA. Forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex. Involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization. Acts as a nucleic acid chaperone which is involved in rearrangement of nucleic acid secondary structures during gRNA retrotranscription. The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell (Potential). Cleaves the translation initiation factor eIF4G leading to the inhibition of host cap-dependent translation (By similarity). RT is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends. Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step that requires cell division, the PIC enters cell nucleus. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The last step is viral DNA integration into host chromosome. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Endonucleolytic cleavage to 5'-phosphomonoester. The RT polymerase active site binds 2 magnesium ions. Binds 1 magnesium ion for ribonuclease H (RNase H) activity. Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions. Most efficiently inhibited by Amprenavir, which is able to block Gag-Pol processing in infected cells. Homohexamer; further associates as homomultimer (By similarity). The virus core is composed of a lattice formed from hexagonal rings, each containing six capsid monomers (By similarity). Interacts with mouse UBE2I and mouse PIAS4 (By similarity). Interacts (via PPXY motif) with host NEDD4 (By similarity). Interacts (via PSAP motif) with host TSG101 (By similarity). Interacts (via LYPX(n)L motif) with host PDCD6IP (By similarity). The reverse transcriptase is a monomer (Potential). Interacts (via RNase domains) with host release factor ETF1; this interaction is essential for translational readthrough of amber codon between viral gag and pol genes, as well as for viral replication (By similarity). Homodimer (By similarity). These locations are probably linked to virus assembly sites. Localizes to the host cytoplasm early in infection and binds to the mitotic chromosomes later on. Late-budding domains (L domains) are short sequence motifs essential for viral particle release. They can occur individually or in close proximity within structural proteins. They interacts with sorting cellular proteins of the multivesicular body (MVB) pathway. Most of these proteins are class E vacuolar protein sorting factors belonging to ESCRT-I, ESCRT-II or ESCRT-III complexes. RNA-binding phosphoprotein p12 contains one L domain: a PPXY motif which potentially interacts with the WW domain 3 of NEDD4 E3 ubiquitin ligase. PPXY motif is essential for virus egress. Matrix protein p15 contains one L domain: a PTAP/PSAP motif, which potentially interacts with the UEV domain of TSG101. The junction between the matrix protein p15 and RNA-binding phosphoprotein p12 also contains one L domain: a LYPX(n)L motif which potentially interacts with PDCD6IP. Both PSAP and LYPX(n)L domains might play little to no role in budding and possibly drive residual virus release. contains. Ubiquitinated by ITCH. Gag can recruit the ubiquitin ligase Itch in an L domain-independent manner to facilitate virus release via a mechanism that involves Gag ubiquitination. Specific enzymatic cleavages by the viral protease yield mature proteins. The protease is released by autocatalytic cleavage. The polyprotein is cleaved during and after budding, this process is termed maturation. Sumoylated; which is required for virus replication. Phosphorylated on serine residues. This protein is translated as a gag-pol fusion protein by episodic readthrough of the gag protein termination codon. Readthrough of the terminator codon TAG occurs between the codons for 538-Asp and 540-Gly. Nucleocapsid protein p10-Pol released from Pol polyprotein (NC-pol) is a few amino acids shorter than the nucleocapsid protein p10 released from Gag polyprotein (NC-gag). The reverse transcriptase is an error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template swiching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs. Belongs to the retroviral Pol polyprotein family. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +Integrin alpha-V:beta-8 (ITGAV:ITGB8) is a receptor for fibronectin (PubMed:1918072). It recognizes the sequence R-G-D in its ligands (PubMed:1918072). Integrin alpha-V:beta-6 (ITGAV:ITGB6) mediates R-G-D-dependent release of transforming growth factor beta-1 (TGF-beta-1) from regulatory Latency-associated peptide (LAP), thereby playing a key role in TGF-beta-1 activation on the surface of activated regulatory T-cells (Tregs) (Probable). Required during vasculogenesis (By similarity). Heterodimer of an alpha and a beta subunit (PubMed:1918072). Beta-8 (ITGB8) associates with alpha-V (ITGAV) to form ITGAV:ITGB8 (PubMed:1918072, PubMed:22278742). ITGAV:ITGB8 interacts with TGFB1 (PubMed:22278742). Placenta, kidney, brain, ovary, uterus and in several transformed cells. Transiently expressed in 293 human embryonic kidney cells. Belongs to the integrin beta chain family. +Catalyzes the NAD(P)-dependent oxidation of 4-(phosphooxy)-L-threonine (HTP) into 2-amino-3-oxo-4-(phosphooxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP). 4-(phosphooxy)-L-threonine + NAD(+) = 3-amino-2-oxopropyl phosphate + CO2 + NADH Binds 1 divalent metal cation per subunit. Can use ions such as Zn(2+), Mg(2+) or Co(2+). Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 4/5. Homodimer. The active site is located at the dimer interface. Belongs to the PdxA family. +Involved in cell wall metabolism and required for the separation of the mother and daughter cells. Belongs to the WD repeat DSE1 family. +Insecticidal neurotoxin. Shows competition for site 3 of insect voltage-gated sodium channels (Nav). Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Has no effect on lepidopteran larvae when injected at 20 pmol/g, or on mice when injected intracranially at 32.8 nmol/g. Belongs to the neurotoxin 14 (magi-1) family. 09 (magi-1) subfamily. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Processively dephosphorylates Ser-5 of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit (rpb-1). Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Ssu-72 is required for 3'-end formation of snoRNAs (By similarity). H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Component of the cleavage and polyadenylation factor (CPF) complex. Belongs to the SSU72 phosphatase family. +Catalyzes the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine, resulting in the formation of riboflavin and 5-amino-6-(D-ribitylamino)uracil. 2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) = 5-amino-6-(D-ribitylamino)uracil + riboflavin Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 2/2. Homotrimer. +Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains. Part of the 30S ribosomal subunit. Belongs to the bacterial ribosomal protein bS16 family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Catalyzes the formation of sulfite from adenosine 5'-phosphosulfate (APS) using thioredoxin as an electron donor. [thioredoxin]-disulfide + AMP + 2 H(+) + sulfite = [thioredoxin]-dithiol + adenosine 5'-phosphosulfate Binds 1 [4Fe-4S] cluster per subunit. Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate. Belongs to the PAPS reductase family. CysH subfamily. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Self assembles to form an icosahedral capsid. Most capsids appear to be large particles with an icosahedral symmetry of T=4 and consist of 240 copies of capsid protein, though a fraction forms smaller T=3 particles consisting of 180 capsid proteins. Entering capsids are transported along microtubules to the nucleus. Phosphorylation of the capsid is thought to induce exposure of nuclear localization signal in the C-terminal portion of the capsid protein that allows binding to the nuclear pore complex via the importin (karyopherin-) alpha and beta. Capsids are imported in intact form through the nuclear pore into the nuclear basket, where it probably binds NUP153. Only capsids that contain the mature viral genome can release the viral DNA and capsid protein into the nucleoplasm. Immature capsids get stuck in the basket. Capsids encapsulate the pre-genomic RNA and the P protein. Pre-genomic RNA is reverse-transcribed into DNA while the capsid is still in the cytoplasm. The capsid can then either be directed to the nucleus, providing more genomes for transcription, or bud through the endoplasmic reticulum to provide new virions. Homodimerizes, then multimerizes. Interacts with cytosol exposed regions of viral L glycoprotein present in the reticulum-to-Golgi compartment. Interacts with human FLNB. Phosphorylated form interacts with host importin alpha; this interaction depends on the exposure of the NLS, which itself depends upon genome maturation and/or phosphorylation of the capsid protein. Interacts with host NUP153. Phosphorylated by host SRPK1, SRPK2, and maybe protein kinase C or GAPDH. Phosphorylation is critical for pregenomic RNA packaging. Protein kinase C phosphorylation is stimulated by HBx protein and may play a role in transport of the viral genome to the nucleus at the late step during the viral replication cycle. Belongs to the orthohepadnavirus core antigen family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +Essential protein required for ovules fertilization (PubMed:15634699, PubMed:19171893). Component of the origin recognition complex (ORC) that binds origins of replication. It has a role in both chromosomal replication and mating type transcriptional silencing. Binds to the ARS consensus sequence (ACS) of origins of replication (By similarity). H3K4me3 effector that regulates positively the transcription of a subset of genes (PubMed:19171893). Component of the origin recognition complex (ORC) composed of at least ORC1 (ORC1A or ORC1B), ORC2, ORC3, ORC4, ORC5 and ORC6. ORC is regulated in a cell-cycle and development dependent manner. It is sequentially assembled at the exit from anaphase of mitosis and disassembled as cells enter S phase. Interacts directly with ORC2 and ORC5 (PubMed:15358564, PubMed:16179646). Binds mostly unmodified histone H3, and, with lower efficiency, H3K4me1 H3K4me2 and H3K4me3 (PubMed:19171893, PubMed:26876097). Follow a cell-cycle regulation with a peak at the G1/S-phase (PubMed:16179646). Mostly expressed in flower buds, and, to a lower exent, in roots, leaves and stems (PubMed:16179646, PubMed:15358564). Restricted to proliferating cells. First active during embryogenesis, but inactive in mature embryos. Expressed in shoot and root apical meristems. Later observed in lateral root primordia and meristems. Detected in young flower buds, developing anthers and mature pollen. Regulated by E2F (PubMed:16179646, PubMed:16126853). Accumulates rapidly after cell cycle reactivation by sucrose addition following cell cycle arrest mediated by sucrose deprivation (PubMed:16179646, PubMed:15358564). Lethal (PubMed:19171893). Unfertilized ovules but normal pollen tube attraction (PubMed:15634699). Belongs to the ORC1 family. +Blocks small conductance calcium-activated potassium channels (KCNN, SK). Low toxicity by intracerebroventricular injection into mice. Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to a beta-sheet by disulfide bonds (CSalpha/beta). Belongs to the short scorpion toxin superfamily. Potassium channel inhibitor family. Alpha-KTx 09 subfamily. +Belongs to the UPF0178 family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Belongs to the prespore-cell-inducing factor family. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate. S-adenosyl-L-methionine + trans-aconitate = (E)-3-(methoxycarbonyl)pent-2-enedioate + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. Tam family. +Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate. (2R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (2S)-2-acetolactate + H(+) + NADPH (2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP(+) = (S)-2-ethyl-2-hydroxy-3-oxobutanoate + H(+) + NADPH Binds 2 magnesium ions per subunit. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 2/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 2/4. Belongs to the ketol-acid reductoisomerase family. +Forms an icosahedral capsid with a T=7 symmetry and a 50 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. Binds to heparan sulfate proteoglycans on cell surface of basal layer keratinocytes to provide initial virion attachment. This binding mediates a conformational change in the virus capsid that facilitates efficient infection. The virion enters the host cell via endocytosis. During virus trafficking, L1 protein dissociates from the viral DNA and the genomic DNA is released to the host nucleus. The virion assembly takes place within the cell nucleus. Encapsulates the genomic DNA together with protein L2. Self-assembles into homopentamers. The capsid has an icosahedral symmetry and consists of 72 capsomers, with each capsomer being a pentamer of L1. Interacts with the minor capsid protein L2; this interaction is necessary for viral genome encapsidation. Interacts with protein E2; this interaction enhances E2-dependent replication and transcription activation. Belongs to the papillomaviridae L1 protein family. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +6-beta-testosterone hydroxylase. an organic molecule + O2 + reduced [NADPH--hemoprotein reductase] = an alcohol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] By phenobarbital. Belongs to the cytochrome P450 family. +TFIIIC mediates tRNA and 5S RNA gene activation by binding to intragenic promoter elements. Upstream of the transcription start site, TFIIIC assembles the initiation complex TFIIIB-TFIIIC-tDNA, which is sufficient for RNA polymerase III recruitment and function. Part of the tauA domain of TFIIIC that binds boxA DNA promoter sites of tRNA and similar genes. Component of the TFIIIC complex composed of TFC1, TFC3, TFC4, TFC6, TFC7 and TFC8. The subunits are organized in two globular domains, tauA and tauB, connected by a proteolysis-sensitive and flexible linker. Present with 2660 molecules/cell in log phase SD medium. +RNA-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. This subunit can bind 18S rRNA. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The eIF-3 complex interacts with pix. Belongs to the eIF-3 subunit G family. +Catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation. Cofactor biosynthesis; adenosylcobalamin biosynthesis. Belongs to the CobB/CobQ family. CobQ subfamily. +Belongs to the bacterial ribosomal protein bL32 family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +Could be involved in insertion of integral membrane proteins into the membrane. Belongs to the UPF0161 family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Catalyzes the conversion of AMP and phosphate to adenine and ribose 1,5-bisphosphate (R15P). Exhibits phosphorylase activity toward CMP and UMP in addition to AMP. Functions in an archaeal AMP degradation pathway, together with R15P isomerase and RubisCO. AMP + phosphate = adenine + alpha-D-ribose 1,5-bisphosphate CMP + phosphate = alpha-D-ribose 1,5-bisphosphate + cytosine phosphate + UMP = alpha-D-ribose 1,5-bisphosphate + uracil Belongs to the thymidine/pyrimidine-nucleoside phosphorylase family. Type 2 subfamily. +Endonuclease that cleaves only one strand of asymmetric DNA substrates threrby introducing interruptions into the template or coding strand. Expressed in the early phase of the viral replicative cycle. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Transports adenine, hypoxanthine, xanthine and uracil. Transport is probably proton-dependent. Inhibited by the proton gradient disruptor carbonyl cyanide m-chlorophenylhydrazone (CCCP), but not by the sodium gradient disruptor ouabain. Belongs to the nucleobase:cation symporter-2 (NCS2) (TC 2.A.40) family. Azg-like subfamily. +Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF2 stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA upstream of exon-exon junctions. In vitro, stimulates translation; the function is independent of association with UPF2 and components of the EJC core. Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Core component of the mRNA splicing-dependent exon junction complex (EJC); the core complex contains CASC3, EIF4A3, MAGOH or MAGOHB, and RBM8A. The EJC core components EIF4A3 and the MAGOH-RBM8A dimer form a composite binding site for UPF3B which overlaps with the EJC binding site for WIBG (PubMed:16601204, PubMed:18066079, PubMed:23917022, PubMed:20479275). Interacts with EST1A, UPF2 and RBM8A (PubMed:12554878, PubMed:18066079, PubMed:15004547). Interacts with CPSF6 (PubMed:19864460). Interacts with DHX34; the interaction is RNA-independent. Shuttling between the nucleus and the cytoplasm. Expressed in testis, uterus, prostate, heart, muscle, brain, spinal cord and placenta. The disease is caused by variants affecting the gene represented in this entry. Belongs to the RENT3 family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Short-chain specific acyl-CoA dehydrogenase is one of the acyl-CoA dehydrogenases that catalyze the first step of mitochondrial fatty acid beta-oxidation, an aerobic process breaking down fatty acids into acetyl-CoA and allowing the production of energy from fats. The first step of fatty acid beta-oxidation consists in the removal of one hydrogen from C-2 and C-3 of the straight-chain fatty acyl-CoA thioester, resulting in the formation of trans-2-enoyl-CoA. Among the different mitochondrial acyl-CoA dehydrogenases, short-chain specific acyl-CoA dehydrogenase acts specifically on acyl-CoAs with saturated 4 to 6 carbons long primary chains. a short-chain 2,3-saturated fatty acyl-CoA + H(+) + oxidized [electron-transfer flavoprotein] = a short-chain (2E)-enoyl-CoA + reduced [electron-transfer flavoprotein] butanoyl-CoA + H(+) + oxidized [electron-transfer flavoprotein] = (2E)-butenoyl-CoA + reduced [electron-transfer flavoprotein] H(+) + oxidized [electron-transfer flavoprotein] + pentanoyl-CoA = (2E)-pentenoyl-CoA + reduced [electron-transfer flavoprotein] H(+) + hexanoyl-CoA + oxidized [electron-transfer flavoprotein] = (2E)-hexenoyl-CoA + reduced [electron-transfer flavoprotein] Binds 1 FAD per subunit. Lipid metabolism; mitochondrial fatty acid beta-oxidation. Homotetramer. Belongs to the acyl-CoA dehydrogenase family. +Essential for cardiac morphogenesis. Binds DNA on E-box consensus sequence 5'-CANNTG-3' (By similarity). Plays an important role in limb development, particularly in the establishment of anterior-posterior polarization of the limb bud. Efficient DNA binding requires dimerization with another bHLH protein. At stages 8 to 9, expressed in the whole lateral plate mesoderm and precardiogenic mesoderm. At stage 10, expressed throughout the cardiac tube and the sinus venosus. By stage 15, expressed homogeneously in the various region of the heart, including the atria, future left ventricle, bulbus cordis and truncus arteriosus, and in the forming branchial arches. Expression persists through stage 20, but decreases thereafter. In the developing limbs, from the initiation of the buds (stages 16 to 17), expression is down-regulated at the anterior of the limb buds so that a gradient expression along the anterior-posterior axis of the bud is established with higher expression at the posterior border. At later stages, expression is restricted to the posterior border of the zeugopod and to the posterior autopod. In the autopod, dynamic expression of HAND2 affects the interdigital regions, the lateral borders of the digits and eventually the developing ventral tendons. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair. Hydrolysis of Ala-|-Gly bond in repressor LexA. Homodimer. Belongs to the peptidase S24 family. +Its primary physiological function is unclear. May play a role in neuronal development and synaptic plasticity. May be required for neuronal myelin sheath maintenance. May promote myelin homeostasis through acting as an agonist for ADGRG6 receptor. May play a role in iron uptake and iron homeostasis. Soluble oligomers are toxic to cultured neuroblastoma cells and induce apoptosis (in vitro) (By similarity). Association with GPC1 (via its heparan sulfate chains) targets PRNP to lipid rafts. Also provides Cu(2+) or Zn(2+) for the ascorbate-mediated GPC1 deaminase degradation of its heparan sulfate side chains (PubMed:12732622, PubMed:16492732, PubMed:19242475, PubMed:19568430). Monomer and homodimer. Has a tendency to aggregate into amyloid fibrils containing a cross-beta spine, formed by a steric zipper of superposed beta-strands. Soluble oligomers may represent an intermediate stage on the path to fibril formation. Copper binding may promote oligomerization. Interacts with GRB2, APP, ERI3/PRNPIP and SYN1 (PubMed:11571277). Mislocalized cytosolically exposed PrP interacts with MGRN1; this interaction alters MGRN1 subcellular location and causes lysosomal enlargement (By similarity). Interacts with APP. Interacts with KIAA1191 (By similarity). Interacts with ADGRG6 (PubMed:27501152). Targeted to lipid rafts via association with the heparan sulfate chains of GPC1. Colocates, in the presence of Cu(2+), to. vesicles in para- and perinuclear regions, where both proteins undergo internalization. Heparin displaces PRNP from lipid rafts and promotes endocytosis. Highly expressed in the brain, lung, kidney and heart. Expressed at low levels in the liver and spleen. The normal, monomeric form has a mainly alpha-helical structure. The disease-associated, protease-resistant form forms amyloid fibrils containing a cross-beta spine, formed by a steric zipper of superposed beta-strands. Disease mutations may favor intermolecular contacts via short beta strands, and may thereby trigger oligomerization. Contains an N-terminal region composed of octamer repeats. At low copper concentrations, the sidechains of His residues from three or four repeats contribute to the binding of a single copper ion. Alternatively, a copper ion can be bound by interaction with the sidechain and backbone amide nitrogen of a single His residue. The observed copper binding stoichiometry suggests that two repeat regions cooperate to stabilize the binding of a single copper ion. At higher copper concentrations, each octamer can bind one copper ion by interactions with the His sidechain and Gly backbone atoms. A mixture of binding types may occur, especially in the case of octamer repeat expansion. Copper binding may stabilize the conformation of this region and may promote oligomerization. N-glycosylated. Found in high quantity in the brain of humans and animals infected with degenerative neurological diseases such as kuru, Creutzfeldt-Jakob disease (CJD), Gerstmann-Straussler syndrome (GSS), scrapie, bovine spongiform encephalopathy (BSE), transmissible mink encephalopathy (TME), etc. No visible phenotype. Mice develop chronic demyelinating polyneuropathy after 60 weeks. Mice show abnormally low iron levels throughout the body, and are mildly anemic. Iron accumulates in duodenum enterocytes, suggesting impaired transport from the intestine to the blood. Mice deficient for both Prnd and Prnp have the same phenotype as mice lacking Prnd; they are born at the expected Mendelian rate and appear grossly normal and healthy (PubMed:15161660, PubMed:15007175). Females are fertile, but males deficient for both Prnd and Prnp are sterile, in spite of normal mating behavior (PubMed:15161660, PubMed:15007175). Male sterility is due to impaired acrosome reaction (PubMed:15161660). Mutant sperm are able to fertilize oocytes in vitro, but many of the resulting embryos die before the morula stage (PubMed:15161660). Mutant sperm cells have elevated levels of DNA damage and DNA strand breaks, and this may be the cause for embryonic lethality (PubMed:15161660). Aging mice deficient for both Prnd and Prnp do not display loss of cerebellar Purkinje cells or develop ataxia, and do not develop neurological defects (PubMed:15007175). Belongs to the prion family. +Involved in chemotaxis. Part of a chemotaxis signal transduction system that modulates chemotaxis in response to various stimuli. Catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins or MCP) by CheR. Also mediates the irreversible deamidation of specific glutamine residues to glutamic acid. [protein]-L-glutamate 5-O-methyl ester + H2O = H(+) + L-glutamyl-[protein] + methanol H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Contains a C-terminal catalytic domain, and an N-terminal region which modulates catalytic activity. Phosphorylated by CheA. Phosphorylation of the N-terminal regulatory domain activates the methylesterase activity. Belongs to the CheB family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 2 family. +Found in functional membrane microdomains (FMM) that may be equivalent to eukaryotic membrane rafts. FMMs are highly dynamic and increase in number as cells age. Flotillins are thought to be important factors in membrane fluidity. Homooligomerizes. Belongs to the flotillin-like FloA family. +Forms a channel through the cell membrane that allows diffusion of small hydrophilic molecules. The channel adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective (By similarity). Consists mainly of membrane-spanning sided beta-sheets. Belongs to the eukaryotic mitochondrial porin (TC 1.B.8.1) family. +Required for replication-independent chromatin assembly and for the periodic repression of histone gene transcription during the cell cycle. Belongs to the WD repeat HIR1 family. +alpha-D-xylose = alpha-D-xylulofuranose Binds 2 magnesium ions per subunit. Homotetramer. Belongs to the xylose isomerase family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Deiminated on Arg-4 in granulocytes upon calcium entry. Monoubiquitination of Lys-120 (H2AK119Ub) by RING1, TRIM37 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. It is involved in the initiation of both imprinted and random X inactivation. Ubiquitinated H2A is enriched in inactive X chromosome chromatin. Ubiquitination of H2A functions downstream of methylation of 'Lys-27' of histone H3 (H3K27me). H2AK119Ub by RNF2/RING2 can also be induced by ultraviolet and may be involved in DNA repair. Monoubiquitination of Lys-120 (H2AK119Ub) by TRIM37 may promote transformation of cells in a number of breast cancers (PubMed:25470042). Following DNA double-strand breaks (DSBs), it is ubiquitinated through 'Lys-63' linkage of ubiquitin moieties by the E2 ligase UBE2N and the E3 ligases RNF8 and RNF168, leading to the recruitment of repair proteins to sites of DNA damage. Ubiquitination at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) in response to DNA damage is initiated by RNF168 that mediates monoubiquitination at these 2 sites, and 'Lys-63'-linked ubiquitin are then conjugated to monoubiquitin; RNF8 is able to extend 'Lys-63'-linked ubiquitin chains in vitro. Deubiquitinated by USP51 at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) after damaged DNA is repaired (PubMed:27083998). H2AK119Ub and ionizing radiation-induced 'Lys-63'-linked ubiquitination (H2AK13Ub and H2AK15Ub) are distinct events. Phosphorylation on Ser-2 (H2AS1ph) is enhanced during mitosis. Phosphorylation on Ser-2 by RPS6KA5/MSK1 directly represses transcription. Acetylation of H3 inhibits Ser-2 phosphorylation by RPS6KA5/MSK1. Phosphorylation at Thr-121 (H2AT120ph) by DCAF1 is present in the regulatory region of many tumor suppresor genes and down-regulates their transcription. Glutamine methylation at Gln-105 (H2AQ104me) by FBL is specifically dedicated to polymerase I. It is present at 35S ribosomal DNA locus and impairs binding of the FACT complex (PubMed:24352239). Symmetric dimethylation on Arg-4 by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage. Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes. Lactylated in macrophages by EP300/P300 by using lactoyl-CoA directly derived from endogenous or exogenous lactate, leading to stimulates gene transcription. Monoisotopic with N-acetylserine. Belongs to the histone H2A family. +Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit. S-adenosyl-L-methionine + uridine(2552) in 23S rRNA = 2'-O-methyluridine(2552) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase RlmE family. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +Belongs to the WHI2 family. +Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Strictly DNA-template-directed DNA polymerase, preferentially acting on DNA structures containing gaps from one to a few nucleotides and bearing a phosphate group at the 5' end of the downstream DNA. The fact that PolX is able to conduct filling of a single-nucleotide gap, allowing further sealing of the resulting nick by a DNA ligase, points to a putative role in base excision repair (BER) during the B.subtilis life cycle. Moreover, also possesses a 3'-5' exonuclease activity able to edit unpaired 3'-termini in a gapped DNA substrate and likely involved in resecting unannealed 3'-termini during DNA repair. The same PolX molecule could perform the subsequent gap-filling step. Does not display 5'-deoxyribose 5'-phosphate (dRP) lyase activity, as predicted by the lack of the lysine and tyrosine residues responsible for the dRP lyase activity in some other PolX members. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. Probably binds 2 divalent metal cations per N-terminal polymerase domain. Mn(2+) is more effective than Mg(2+) for DNA polymerase activity. Probably binds 3 Mn(2+) ions per C-terminal exonuclease domain. Mg(2+) cannot replace Mn(2+) for 3'-5' exonuclease activity. The polymerization activity is inhibited in the presence of 2'-3'-dideoxynucleoside 5'-triphosphate (ddNTP). Monomer. The 3'-5' exonuclease activity resides in the C-terminal PHP domain. In the N-terminal section; belongs to the DNA polymerase type-X family. In the C-terminal section; belongs to the PHP family. +Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Belongs to the thiamine-phosphate synthase family. +A P subtype restriction enzyme that recognizes the double-stranded sequence 5'-GRCGYC-3' and cleaves after R-2. Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. +The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel (By similarity). Belongs to the peptidase T1A family. +Potential apoptotic regulator. Belongs to the BI1 family. LFG subfamily. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +ATP + D-glucose = ADP + D-glucose 6-phosphate + H(+) Belongs to the bacterial glucokinase family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +Could be involved in tyrosine phosphatase signalling pathways, having MAP-kinases as substrates. H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Non-dividing gametes did not express the VH-PTP13 gene whereas synchronously dividing vegetative cells only expressed VH-PTP13 in the early G1-phase of the cycle. By oxidative stress. Belongs to the protein-tyrosine phosphatase family. Non-receptor class dual specificity subfamily. +Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. (2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 4/5. Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface. Belongs to the enolase family. +Tachykinins are active peptides which excite neurons, evoke behavioral responses, are potent vasodilators and secretagogues, and contract (directly or indirectly) many smooth muscles. Expressed by the skin glands. Belongs to the tachykinin family. +Part of the DNA-dependent RNA polymerase which catalyzes the transcription of viral DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of early, intermediate and late genes. DNA-dependent RNA polymerase associates with the early transcription factor (ETF), itself composed of D6 and A7, thereby allowing the early genes transcription. Late transcription, and probably also intermediate transcription, require newly synthesized RNA polymerase. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The DNA-dependent RNA polymerase used for intermediate and late genes expression consists of eight subunits 147 kDa, 133 kDa, 35 kDa, 30 kDa, 22 kDa, 19 kDa, 18 kDa and 7 kDa totalling more than 500 kDa in mass. The same holoenzyme, with the addition of the transcription-specificity factor RAP94, is used for early gene expression. All the enzymes and other proteins required to synthesize early mRNAs are packaged within the virion core along with the DNA genome. This is necessary because viral early mRNAs are synthesized within minutes after virus entry into the cell and are extruded through pores in the core particle. Belongs to the poxviridae DNA-directed RNA polymerase 35 kDa subunit family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Required for maturation of urease via the functional incorporation of the urease nickel metallocenter. UreD, UreF and UreG form a complex that acts as a GTP-hydrolysis-dependent molecular chaperone, activating the urease apoprotein by helping to assemble the nickel containing metallocenter of UreC. The UreE protein probably delivers the nickel. Belongs to the UreF family. +Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate. S-adenosyl-L-methionine + trans-aconitate = (E)-3-(methoxycarbonyl)pent-2-enedioate + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. Tam family. +Part of the Tol-Pal system, which plays a role in outer membrane invagination during cell division and is important for maintaining outer membrane integrity. The Tol-Pal system is composed of five core proteins: the inner membrane proteins TolA, TolQ and TolR, the periplasmic protein TolB and the outer membrane protein Pal. They form a network linking the inner and outer membranes and the peptidoglycan layer. Belongs to the TolB family. +SASP are bound to spore DNA. They are double-stranded DNA-binding proteins that cause DNA to change to an a-like conformation. They protect the DNA backbone from chemical and enzymatic cleavage and are thus involved in dormant spore's high resistance to UV light. SASP are degraded in the first minutes of spore germination and provide amino acids for both new protein synthesis and metabolism. Belongs to the alpha/beta-type SASP family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds a dinuclear copper A center per subunit. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of a catalytic core of 3 subunits and several supernumerary subunits. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII). Belongs to the cytochrome c oxidase subunit 2 family. +Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides. Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low. Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids. Binds 2 manganese ions per subunit. Belongs to the peptidase M17 family. +Could be involved in insertion of integral membrane proteins into the membrane. Belongs to the UPF0161 family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily. +SUMO-specific isopeptidase involved in protein desumoylation. Specifically binds SUMO proteins with a higher affinity for SUMO2 and SUMO3 which it cleaves more efficiently. Also able to process full-length SUMO proteins to their mature forms (By similarity). Plays a key role in RNA polymerase-II-mediated snRNA transcription in the Cajal bodies (By similarity). Is a component of complexes that can bind to U snRNA genes (By similarity). Interacts with ELL. Belongs to the peptidase C19 family. Probably inactive as a hydrolase due to lack of catalytic Cys and His. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Catalyzes the dephosphorylation of 2-phosphoglycolate. 2-phosphoglycolate + H2O = glycolate + phosphate Belongs to the archaeal SPP-like hydrolase family. +Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids (By similarity). Forms a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD. During infection by the bacteriophage CTX-phi, it is required by the bacteriophage, which uses host XerC and XerD proteins to integrate the bacterial genome. Belongs to the 'phage' integrase family. XerD subfamily. +Acts as a metalloprotease. Penetrates intact tissue and specifically cleaves the vesicle-associated membrane protein 2 (VAMP2) (part of the SNARE complex) involved in pancreatic secretion, thus disrupting the normal vesicular traffic (By similarity). Binds 1 zinc ion per subunit. Inhibited by EDTA. Expressed by the venom gland. Contains several disulfide bonds. Belongs to the venom metalloproteinase (M12B) family. +Involved in the control of cell movement by regulating actin cytoskeleton homeostasis and filopodium and lamellipodium formation (PubMed:22751924). When unphosphorylated, induces cell migration (PubMed:22751924). When phosphorylated by MAPK8, induces actin bundles formation and stabilization, thereby reducing actin plasticity, hence restricting cell movement, including neuronal migration (PubMed:22751924). May be involved in coupling the protein kinase C and calmodulin signal transduction systems (Probable). Binds to filamentous actin (F-actin), but not to monomeric G-actin, independently of its phosphorylation status (PubMed:22751924). Interacts with calmodulin (PubMed:1618855). Associates with the membrane via the insertion of the N-terminal N-myristoyl chain and the partial insertion of the effector domain (Probable). Association of the effector domain with membranes may be regulated by Ca(2+)/calmodulin (By similarity). Colocalizes with F-actin at the leading edge of migrating cells (PubMed:22751924). Expressed at high levels in brain cortex and hippocampus, including dentate gyrus, anterior olfactory nucleus, primary olfactory cortex, entorhinal cortex, medial preoptic area and dorsomedial hypothalamic nucleus (at protein level) (PubMed:1864362, PubMed:8406449, PubMed:9598313, PubMed:22751924). Expressed in neuronal cells (at protein level) (PubMed:22751924). Detected in the retina (PubMed:9598313). Strongly expressed in testis and uterus; expressed at lower levels in cerebellum, cerebrum, adipose tissue, spleen, kidney, thyroid, liver, lung, skeletal muscle and heart (PubMed:8406449). Detected in T-cells and B-cells (PubMed:8406449). Expressed in the developing neural tube as early as 8.5 dpc. Remains most highly expressed in the developing brain and spinal cord during later development at least until 14.5 dpc. Also detected in the lung, adrenal gland, gut and kidney, particularly the kidney cortex. Undetectable in the liver. Up-regulated in peritoneal macrophages in response to bacterial lipopolysaccharide (LPS). Phosphorylated (PubMed:1618855, PubMed:22751924). Phosphorylation at Ser-120 and Thr-183 is non-redundantly catalyzed by MAPK8 in vivo (PubMed:22751924). Phosphorylation at Thr-148 is preferentially catalyzed by MAPK8 in vivo, but this modification can also be catalyzed by other kinases in the absence of MAPK8 (PubMed:22751924). May be phosphorylated by protein kinase C, which disrupts the interaction with calmodulin (PubMed:1618855). Belongs to the MARCKS family. +Probably mediates the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Involved in the modulation of abscisic acid and stress-responsive genes. Interacts with DNMT2. Expressed in leaves, roots, stems, young plantlets, flowers and siliques. Highest levels in ovules, embryos, shoot apical meristems and first leaves. Also expressed in somatic embryos. Repressed by abscisic acid. Belongs to the histone deacetylase HD2 family. +Plays a highly specific role in the last step of keratinocyte differentiation. May have an essential function in lipid metabolism of the most differentiated epidermal layers. Exclusively expressed in the epidermis within the granular keratinocytes. Belongs to the AB hydrolase superfamily. Lipase family. +Expressed by the venom gland. Contains 7 disulfide bonds. Belongs to the CRISP family. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Multifunctional protein which displays endonuclease and helicase activities required for initiating and directing viral DNA replication. Also plays a role in viral packaging and transactivation of several promoters. Binds site-specifically to 2-3 approximate tandem copies within the origins of replication (Ori), unwinds this hairpin region and nicks one DNA strand thereby initiating the rolling circle replication (RCR). Cooperatively binds Ori with host PIF and probably other host factors, which activate the nickase function of NS1. Becomes covalently attached to the 5' end of the nick and provides a 3'OH for priming DNA synthesis. The helicase activity unwinds DNA in a 3'-5' direction on the longer strand. Inhibits the host cell cycle during the G1/S transition, the S-phase, and the G2/M transition. These arrests may provide essential cellular factors for viral DNA replication. Promotes apoptosis in host cell. ATP + H2O = ADP + H(+) + phosphate The endonuclease active site can probably bind other divalent cations. Homooligomer; when bound to DNA. In the N-terminus, the endonuclease region is involved in binding to the origin of replication. In the middle, there are the ATPase and helicase activities (By similarity). The C-terminus probably contains a transactivation domain (By similarity). Phosphorylated. Belongs to the parvoviruses initiator protein NS1 family. +Bifunctional serine/threonine kinase and phosphorylase involved in the regulation of the phosphoenolpyruvate synthase (PEPS) by catalyzing its phosphorylation/dephosphorylation. [pyruvate, water dikinase] + ADP = [pyruvate, water dikinase]-phosphate + AMP + H(+) [pyruvate, water dikinase]-phosphate + H(+) + phosphate = [pyruvate, water dikinase] + diphosphate Belongs to the pyruvate, phosphate/water dikinase regulatory protein family. PSRP subfamily. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Involved in the anomeric conversion of L-rhamnose. alpha-L-rhamnose = beta-L-rhamnose Carbohydrate metabolism; L-rhamnose metabolism. Homodimer. Belongs to the rhamnose mutarotase family. +Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). 5,6-dimethylbenzimidazole + nicotinate beta-D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate Nucleoside biosynthesis; alpha-ribazole biosynthesis; alpha-ribazole from 5,6-dimethylbenzimidazole: step 1/2. Belongs to the CobT family. +Catalyzes the NAD-dependent oxidation of the highly active 17beta-hydroxysteroids, such as estradiol (E2), testosterone (T), and dihydrotestosterone (DHT), to their less active forms and thus regulates the biological potency of these steroids. Oxidizes estradiol to estrone, testosterone to androstenedione, and dihydrotestosterone to 5alpha-androstan-3,17-dione. Also has 20-alpha-HSD activity. 17beta-estradiol + NAD(+) = estrone + H(+) + NADH NAD(+) + testosterone = androst-4-ene-3,17-dione + H(+) + NADH 17beta-hydroxy-5alpha-androstan-3-one + NAD(+) = 5alpha-androstan-3,17-dione + H(+) + NADH (20S)-hydroxypregn-4-en-3-one + NAD(+) = H(+) + NADH + progesterone Optimum pH is 9 with testosterone and estradiol as substrates and 5.5 with androstenedione and estrone as substrates. Homodimer. Expressed in placenta. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. This subunit is found at the monomer-monomer interface and is required for correct PSII assembly and/or dimerization. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbL family. +Beta-glucosidase highly specific for the cleavage of C-26-bound glucose moiety of furostanol glycosides torvosides A and H. Hydrolyzes only p-nitrophenyl-beta-glucoside, but not p-nitrophenyl-beta-D-fucoside, p-nitrophenyl-beta-L-fucoside, p-nitrophenyl-beta-D-xyloside, p-nitrophenyl-beta-D-galactoside, p-nitrophenyl-beta-D-NAc-glucosamine, p-nitrophenyl-beta-D-mannoside or any of the p-nitrophenyl-alpha-glycosides tested. H2O + protodioscin = 26-deglucoprotodioscin + D-glucose Inhibited by Hg(2+) and D-glucono-1,5-lactone. kcat is 8.6 sec(-1) for torvoside A. kcat is 7.7 sec(-1) for torvoside B. kcat is 9.1 sec(-1) for p-nitrophenyl-beta-glucoside. kcat is 8.3 sec(-1) for 4-methylumbelliferyl-beta-glucoside. Optimum pH is 5.0. Monomer. Expressed in petioles and leaves, but not in fruits. Glycosylated. Belongs to the glycosyl hydrolase 3 family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity). Involved in the regulation of basal defense responses against pathogens, and may be implicated in the cross-talk between the SA- and JA-dependent signaling pathways. Protein modification; protein ubiquitination. Interacts with TGA2, TGA3, TGA5, TGA6 and TGA7. Up-regulated following pathogen challenge or salicylic acid (SA) treatment, and down-regulated by methyl jasmonic acid (MeJA) treatment. The BTB/POZ domain mediates the interaction with some component of ubiquitin ligase complexes. Enhanced susceptibility to the virulent bacterial pathogen Pseudomonas syringe and to the fungal pathogen Erysiphe cichoracearum (powdery mildew). +Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity. adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue. Belongs to the radical SAM superfamily. RlmN family. +Belongs to the FliE family. +Belongs to the chlamydial CPn_0705/CT_671/TC_0042 family. +Prenyltransferase that catalyzes in vivo the transfer of the heptaprenyl moiety of heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP). This reaction is an ether-bond-formation step in the biosynthesis of archaea-type G1P-based membrane lipids found in Bacillales. all-trans-heptaprenyl diphosphate + sn-glycerol 1-phosphate = 3-heptaprenyl-sn-glycero-1-phosphate + diphosphate Membrane lipid metabolism; glycerophospholipid metabolism. Homodimer. Belongs to the GGGP/HepGP synthase family. Group I subfamily. +Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that regulates the response to oxidative stress by targeting nfe2l2/nrf2 for ubiquitination (PubMed:18057000). Keap1 acts as a key sensor of oxidative and electrophilic stress: in normal conditions, the BCR(KEAP1) complex mediates ubiquitination and degradation of nfe2l2/nrf2, a transcription factor regulating expression of many cytoprotective genes (PubMed:18057000). In response to oxidative stress, different electrophile metabolites trigger non-enzymatic covalent modifications of highly reactive cysteine residues in KEAP1, leading to inactivate the ubiquitin ligase activity of the BCR(KEAP1) complex, promoting nfe2l2/nrf2 nuclear accumulation and expression of phase II detoxifying enzymes (By similarity). Ubiquitin ligase activity of the BCR(KEAP1) complex is inhibited by oxidative stress and electrophile metabolites such as sulforaphane. Electrophile metabolites react with reactive cysteine residues in keap1 and trigger non-enzymatic covalent modifications of these cysteine residues, leading to inactivate the ubiquitin ligase activity of the BCR(KEAP1) complex. Protein modification; protein ubiquitination. Homodimer and heterodimer; heterodimerizes with keap1a (PubMed:18057000). Component of the BCR(KEAP1) E3 ubiquitin ligase complex, at least composed of 2 molecules of cul3, 2 molecules of keap1 (keap1a and/or keap1b), and rbx1 (By similarity). Interacts with nfe2l2/nrf2; the interaction is direct (By similarity). Mainly cytoplasmic. Widely expressed. Keap1 contains reactive cysteine residues that act as sensors for endogenously produced and exogenously encountered small molecules, which react with sulfhydryl groups and modify the cysteine sensors, leading to impair ability of the BCR(KEAP1) complex to ubiquitinate target proteins. Non-enzymatic covalent modifications of reactive cysteines by electrophile metabolites inactivate the BCR(KEAP1) complex. Belongs to the KEAP1 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Belongs to the UPF0301 (AlgH) family. +Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Is involved in the demethylation of trimethylated 'Lys-9' on histone H3 (H3K9me3), leading to an increase in ribosomal RNA expression. Also catalyzes the hydroxylation of 60S ribosomal protein L27a on 'His-39' (By similarity). May play an important role in cell growth and survival. May be involved in ribosome biogenesis, most likely during the assembly process of pre-ribosomal particles. 2-oxoglutarate + L-histidyl-[ribosomal protein uL15] + O2 = (3S)-3-hydroxy-L-histidyl-[ribosomal protein uL15] + CO2 + succinate Binds 1 Fe(2+) ion per subunit. Belongs to the ROX family. MINA53 subfamily. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseB family. +Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor. (S)-dihydroorotate + a quinone = a quinol + orotate Binds 1 FMN per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (quinone route): step 1/1. Monomer. Belongs to the dihydroorotate dehydrogenase family. Type 2 subfamily. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain. TUBB3 plays a role in dorsal root ganglion axon projection towards the spinal cord (PubMed:28483977). Dimer of alpha and beta chains. A typical microtubule is a hollow water-filled tube with an outer diameter of 25 nm and an inner diameter of 15 nM. Alpha-beta heterodimers associate head-to-tail to form protofilaments running lengthwise along the microtubule wall with the beta-tubulin subunit facing the microtubule plus end conferring a structural polarity. Microtubules usually have 13 protofilaments but different protofilament numbers can be found in some organisms and specialized cells. Highly expressed in testis. The MREI motif is common among all beta-tubulin isoforms and may be critical for tubulin autoregulation. Some glutamate residues at the C-terminus are polyglycylated, resulting in polyglycine chains on the gamma-carboxyl group. Glycylation is mainly limited to tubulin incorporated into axonemes (cilia and flagella) whereas glutamylation is prevalent in neuronal cells, centrioles, axonemes, and the mitotic spindle. Both modifications can coexist on the same protein on adjacent residues, and lowering polyglycylation levels increases polyglutamylation, and reciprocally. The precise function of polyglycylation is still unclear. Some glutamate residues at the C-terminus are polyglutamylated, resulting in polyglutamate chains on the gamma-carboxyl group (By similarity). Polyglutamylation plays a key role in microtubule severing by spastin (SPAST). SPAST preferentially recognizes and acts on microtubules decorated with short polyglutamate tails: severing activity by SPAST increases as the number of glutamates per tubulin rises from one to eight, but decreases beyond this glutamylation threshold (By similarity). Belongs to the tubulin family. +Catalyzes the formation of methylglyoxal from dihydroxyacetone phosphate. dihydroxyacetone phosphate = methylglyoxal + phosphate Belongs to the methylglyoxal synthase family. +Protamines substitute for histones in the chromatin of sperm during the haploid phase of spermatogenesis. They compact sperm DNA into a highly condensed, stable and inactive complex (By similarity). Belongs to the protamine P1 family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP). (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate Cofactor biosynthesis; molybdopterin biosynthesis. In the N-terminal section; belongs to the MoaC family. In the C-terminal section; belongs to the MoaB/Mog family. +Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P). D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate kcat is 6348 sec(-1) for isomerase activity. Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate from glycerone phosphate: step 1/1. Homodimer. Belongs to the triosephosphate isomerase family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Has flap endonuclease activity. During DNA replication, flap endonucleases cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds 2 Mg(2+) per subunit. Only one magnesium ion has a direct interaction with the protein, the other interactions are indirect. Binds 1 K(+) per subunit. The potassium ion strongly increases the affinity for DNA. Belongs to the Xni family. +CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). The type III-A Csm effector complex binds crRNA and acts as a crRNA-guided RNase, DNase and cyclic oligoadenylate synthase; binding of target RNA cognate to the crRNA is required for all activities. A single-strand deoxyribonuclease (ssDNase) which digests linear and circular ssDNA; has 5'-3' and 3'-5' exonuclease activity as well as a less efficient endonuclease activity. Has a minimal size requirement; 100 nucleotide ssDNA (nt) is more efficiently digested than 50 or 25 nt ssDNA, while 14 nt ssDNA is not cleaved at all. It has no activity on dsDNA or ssRNA. ssDNase activity is stimulated in the ternary Csm effector complex; binding of cognate target RNA activates the ssDNase, as the target RNA is degraded ssDNA activity decreases. When associated with the ternary Csm effector complex (the crRNA, Cas proteins and a cognate target ssRNA) synthesizes cyclic oligoadenylates (cOA) from ATP. cOAs are second messengers that stimulate the ssRNase activity of Csm6, inducing an antiviral state important for defense against invading nucleic acids. Ni(2+) and Mn(2+), but not Mg(2+), Ca(2+), Zn(2+), Co(2+), or Cu(2+), is required for ssDNase activity. ssDNase activity is inhibited by EDTA. Probably part of the Csm effector complex, that includes Cas10, Csm2, Csm3, Csm4, Csm5 and mature crRNA (By similarity). Will form a homodimer in solution, interacts with Csm4, which is a tighter, better association than the homodimeric Cas10 and uses the same interface for interaction (PubMed:25773141). The N-terminal HD domain has ssDNase activity (PubMed:25773141). The C-terminal GGDEF domain has the cOA synthesis activity (By similarity). Encoded in a type III-A CRISPR locus. Belongs to the CRISPR-associated Cas10/Csm1 family. +(6S)-10-formyltetrahydrofolate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide = (6S)-5,6,7,8-tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide H2O + IMP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide Purine metabolism; IMP biosynthesis via de novo pathway; 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide (10-formyl THF route): step 1/1. Purine metabolism; IMP biosynthesis via de novo pathway; IMP from 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide: step 1/1. The IMP cyclohydrolase activity resides in the N-terminal region. Belongs to the PurH family. +Belongs to the bacterial ribosomal protein bS21 family. +During nodulation in legume roots after Rhizobium infection. Belongs to the nodulin 20 family. It is uncertain whether Met-1 or Met-4 is the initiator. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Belongs to the major facilitator superfamily. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Apoprotein for the two 4Fe-4S centers FA and FB of photosystem I (PSI); essential for photochemical activity. FB is the terminal electron acceptor of PSI, donating electrons to ferredoxin. The C-terminus interacts with PsaA/B/D and helps assemble the protein into the PSI complex. Required for binding of PsaD and PsaE to PSI. PSI is a plastocyanin-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. hnu + oxidized [2Fe-2S]-[ferredoxin] + reduced [plastocyanin] = oxidized [plastocyanin] + reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters. Cluster 2 is most probably the spectroscopically characterized electron acceptor FA and cluster 1 is most probably FB. The eukaryotic PSI reaction center is composed of at least 11 subunits. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +H2O + L-arginine = L-citrulline + NH4(+) Amino-acid degradation; L-arginine degradation via ADI pathway; carbamoyl phosphate from L-arginine: step 1/2. Belongs to the arginine deiminase family. +Catalyzes the formation of S-adenosylmethionine from methionine and ATP. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Belongs to the AdoMet synthase 2 family. +Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose. beta-D-ribopyranose = beta-D-ribofuranose Carbohydrate metabolism; D-ribose degradation; D-ribose 5-phosphate from beta-D-ribopyranose: step 1/2. Homodecamer. Belongs to the RbsD / FucU family. RbsD subfamily. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. Homodimer. Belongs to the transketolase family. DXPS subfamily. +Attaches the virus to the host lymphoid cell by binding to the primary receptor CD4. This interaction induces a structural rearrangement creating a high affinity binding site for a chemokine coreceptor like CXCR4 and/or CCR5. Acts as a ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on dendritic cells (DCs), and on endothelial cells of liver sinusoids and lymph node sinuses. These interactions allow capture of viral particles at mucosal surfaces by these cells and subsequent transmission to permissive cells. HIV subverts the migration properties of dendritic cells to gain access to CD4+ T-cells in lymph nodes. Virus transmission to permissive T-cells occurs either in trans (without DCs infection, through viral capture and transmission), or in cis (following DCs productive infection, through the usual CD4-gp120 interaction), thereby inducing a robust infection. In trans infection, bound virions remain infectious over days and it is proposed that they are not degraded, but protected in non-lysosomal acidic organelles within the DCs close to the cell membrane thus contributing to the viral infectious potential during DCs' migration from the periphery to the lymphoid tissues. On arrival at lymphoid tissues, intact virions recycle back to DCs' cell surface allowing virus transmission to CD4+ T-cells. Acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During fusion of viral and target intracellular membranes, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Complete fusion occurs in host cell endosomes and is dynamin-dependent, however some lipid transfer might occur at the plasma membrane. The virus undergoes clathrin-dependent internalization long before endosomal fusion, thus minimizing the surface exposure of conserved viral epitopes during fusion and reducing the efficacy of inhibitors targeting these epitopes. Membranes fusion leads to delivery of the nucleocapsid into the cytoplasm. Oligomerizes in the host endoplasmic reticulum into predominantly trimers. In a second time, gp160 transits in the host Golgi, where glycosylation is completed. The precursor is then proteolytically cleaved in the trans-Golgi and thereby activated by cellular furin or furin-like proteases to produce gp120 and gp41. The mature envelope protein (Env) consists of a homotrimer of non-covalently associated gp120-gp41 heterodimers. The resulting complex protrudes from the virus surface as a spike. There seems to be as few as 10 spikes on the average virion. Interacts with host CD4, CCR5 and CXCR4. Gp120 also interacts with the C-type lectins CD209/DC-SIGN and CLEC4M/DC-SIGNR (collectively referred to as DC-SIGN(R)). Gp120 and gp41 interact with GalCer. Gp120 interacts with host ITGA4/ITGB7 complex; on CD4+ T-cells, this interaction results in rapid activation of integrin ITGAL/LFA-1, which facilitates efficient cell-to-cell spreading of HIV-1. Gp120 interacts with cell-associated heparan sulfate; this interaction increases virus infectivity on permissive cells and may be involved in infection of CD4- cells. The mature envelope protein (Env) consists of a homotrimer of non-covalently associated gp120-gp41 heterodimers. The resulting complex protrudes from the virus surface as a spike. There seems to be as few as 10 spikes on the average virion. The surface protein is not anchored to the viral envelope, but associates with the extravirion surface through its binding to TM. It is probably concentrated at the site of budding and incorporated into the virions possibly by contacts between the cytoplasmic tail of Env and the N-terminus of Gag. It is probably concentrated at the site of budding and incorporated into the virions possibly by contacts between the cytoplasmic tail of Env and the N-terminus of Gag. Some of the most genetically diverse regions of the viral genome are present in Env. They are called variable regions 1 through 5 (V1 through V5). Coreceptor usage of gp120 is determined mainly by the primary structure of the third variable region (V3) in the outer domain of gp120. The sequence of V3 determines which coreceptor, CCR5 and/or CXCR4 (corresponding to R5/macrophage, X4/T cell and R5X4/T cell and macrophage tropism), is used to trigger the fusion potential of the Env complex, and hence which cells the virus can infect. Binding to CCR5 involves a region adjacent in addition to V3. The membrane proximal external region (MPER) present in gp41 is a tryptophan-rich region recognized by the antibodies 2F5, Z13, and 4E10. MPER seems to play a role in fusion. The 17 amino acids long immunosuppressive region is present in many retroviral envelope proteins. Synthetic peptides derived from this relatively conserved sequence inhibit immune function in vitro and in vivo. The YXXL motif is involved in determining the exact site of viral release at the surface of infected mononuclear cells and promotes endocytosis. YXXL and di-leucine endocytosis motifs interact directly or indirectly with the clathrin adapter complexes, opperate independently, and their activities are not additive. The CD4-binding region is targeted by the antibody b12. Highly glycosylated by host. The high number of glycan on the protein is reffered to as 'glycan shield' because it contributes to hide protein sequence from adaptive immune system. Palmitoylation of the transmembrane protein and of Env polyprotein (prior to its proteolytic cleavage) is essential for their association with host cell membrane lipid rafts. Palmitoylation is therefore required for envelope trafficking to classical lipid rafts, but not for viral replication. Specific enzymatic cleavages in vivo yield mature proteins. Envelope glycoproteins are synthesized as an inactive precursor that is heavily N-glycosylated and processed likely by host cell furin in the Golgi to yield the mature SU and TM proteins. The cleavage site between SU and TM requires the minimal sequence [KR]-X-[KR]-R. About 2 of the 9 disulfide bonds of gp41 are reduced by P4HB/PDI, following binding to CD4 receptor. Inhibitors targeting HIV-1 viral envelope proteins are used as antiretroviral drugs. Attachment of virions to the cell surface via non-specific interactions and CD4 binding can be blocked by inhibitors that include cyanovirin-N, cyclotriazadisulfonamide analogs, PRO 2000, TNX 355 and PRO 542. In addition, BMS 806 can block CD4-induced conformational changes. Env interactions with the coreceptor molecules can be targeted by CCR5 antagonists including SCH-D, maraviroc (UK 427857) and aplaviroc (GW 873140), and the CXCR4 antagonist AMD 070. Fusion of viral and cellular membranes can be inhibited by peptides such as enfuvirtide and tifuvirtide (T 1249). Resistance to inhibitors associated with mutations in Env are observed. Most of the time, single mutations confer only a modest reduction in drug susceptibility. Combination of several mutations is usually required to develop a high-level drug resistance. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Belongs to the HIV-1 env protein family. +Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP). diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 1/2. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrE subfamily. +Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P). an N-acyl-D-glucosamine 6-phosphate = an N-acyl-D-mannosamine 6-phosphate Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 3/5. Belongs to the NanE family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Involved in the maturation of Asn-linked oligosaccharides. Progressively trim alpha-1,2-linked mannose residues from Man(9)GlcNAc(2) to produce Man(5)GlcNAc(2). 4 H2O + N(4)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 9A1,2,3B1,2,3) = 4 beta-D-mannose + N(4)-(alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 5A1,2) 3 H2O + N(4)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 8A1,2,3B1,3) = 3 beta-D-mannose + N(4)-(alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 5A1,2) Protein modification; protein glycosylation. Complex spatial distribution during embryogenesis, including expression in lobula plate giant neurons. Also expressed in adult wing and eyes. Expressed both maternally and zygotically during embryonic stages. Belongs to the glycosyl hydrolase 47 family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. a ubiquinone + H(+) + n Na(+)(in) + NADH = a ubiquinol + n Na(+)(out) + NAD(+) Composed of six subunits; NqrA, NqrB, NqrC, NqrD, NqrE and NqrF. Belongs to the NqrDE/RnfAE family. +Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor. (S)-dihydroorotate + NAD(+) = H(+) + NADH + orotate Binds 1 FMN per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (NAD(+) route): step 1/1. Heterotetramer of 2 PyrK and 2 PyrD type B subunits. Belongs to the dihydroorotate dehydrogenase family. Type 1 subfamily. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 4 family. +The glycine cleavage system catalyzes the degradation of glycine. (6S)-5,6,7,8-tetrahydrofolate + (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[protein] = (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + NH4(+) The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvT family. +Probably involved in a salvage pathway for GDP-D-mannose biosynthesis (PubMed:25500577). Catalyzes the reversible phosphorolysis of 1,2-beta-oligomannan. In phosphorolytic reactions, prefers beta-1,2-mannobiose (beta-1,2-Man2) as substrate. Produces alpha-D-mannose 1-phosphate, which is the precursor of GDP-D-mannose (PubMed:25500577). beta-D-mannopyranosyl-(1->2)-D-mannopyranose + phosphate = alpha-D-mannose 1-phosphate + D-mannose kcat is 10 sec(-1) with D-mannose as substrate (for the synthetic reaction). kcat is 11 sec(-1) with D-fructose as substrate (for the synthetic reaction). kcat is 7.0 sec(-1) with beta-1,2-Man2 as substrate (for the synthetic reaction). kcat is 12 sec(-1) with alpha-D-mannose 1-phosphate as substrate (for the synthetic reaction). Optimum pH is 6.0 for phosphorolytic activity. Optimum pH is 5.5 for the synthetic reaction. Nucleotide-sugar biosynthesis; GDP-alpha-D-mannose biosynthesis. Monomer. Belongs to the glycosyl hydrolase 130 family. +ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 2/3. Homotetramer. Belongs to the argininosuccinate synthase family. Type 1 subfamily. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-terminal L-methionyl-[peptide] Binds 1 Fe(2+) ion. Belongs to the polypeptide deformylase family. +Involved in 1,2-propanediol (1,2-PD) utilization within the bacterial microcompartment (BMC) dedicated to 1,2-PD degradation by catalyzing the conversion of propanoyl-CoA to propanoyl-phosphate. phosphate + propanoyl-CoA = CoA + propanoyl phosphate There are 2 Zn(2+) ions per monomer; Zn(2+) and CoA bind inbetween the 2 domains in each monomer. Polyol metabolism; 1,2-propanediol degradation. Formed by 2 beta-barrels, each is capped on both ends by short alpha-helices. Belongs to the PduL family. +Omega-conotoxins act at presynaptic membranes, they bind and block voltage-gated calcium channels (Cav). Expressed by the venom duct. The cysteine framework is VI/VII (C-C-CC-C-C). The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Is not hydroxylated. Belongs to the conotoxin O1 family. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +Belongs to the jacalin lectin family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Allosterically activated by GTP. Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Catalyzes a proton abstraction reaction that results in 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) and the formation of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC). 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate = (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate + pyruvate Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 3/7. Quinol/quinone metabolism; menaquinone biosynthesis. Monomer. Belongs to the AB hydrolase superfamily. MenH family. +Belongs to the universal ribosomal protein uS9 family. +IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. Monomer. Belongs to the IF-3 family. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +Belongs to the bacterial ribosomal protein bL34 family. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is composed of 13 subunits: eif3a, eif3b, eif3c, eif3d, eif3e, eif3f, eif3g, eif3h, eif3i, eif3j, eif3k, eif3l and eif3m. Belongs to the eIF-3 subunit E family. +Belongs to the bacterial ribosomal protein bS21 family. +Has high formaldehyde dehydrogenase activity in the presence of glutathione and catalyzes the oxidation of normal alcohols in a reaction that is not GSH-dependent. NADP(+) + S-(hydroxymethyl)glutathione = H(+) + NADPH + S-formylglutathione NAD(+) + S-(hydroxymethyl)glutathione = H(+) + NADH + S-formylglutathione a primary alcohol + NAD(+) = an aldehyde + H(+) + NADH a secondary alcohol + NAD(+) = a ketone + H(+) + NADH Binds 2 Zn(2+) ions per subunit. Homodimer. Belongs to the zinc-containing alcohol dehydrogenase family. Class-III subfamily. +Glucose-responsive transcription factor that regulates expression of several glucose transporter (HXT) genes in response to glucose. In the absence of glucose, it functions as a transcriptional repressor, whereas high concentrations of glucose cause it to function as a transcriptional activator. In cells growing on low levels of glucose, has a neutral role, neither repressing nor activating transcription. Binds the consensus binding site sequence 5'-CGGANNA-3', of which multiple copies are present in all HXT promoters regulated by RGT1 (By similarity). Glucose-induced phosphorylation regulates the DNA-binding activity. Hyperphosphorylation in cells growing on high levels of glucose does prevents DNA-binding and dephosphorylation restores DNA-binding ability (By similarity). Belongs to the EDS1/RGT1 family. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +D-arabinose 5-phosphate + H2O + phosphoenolpyruvate = 3-deoxy-alpha-D-manno-2-octulosonate-8-phosphate + phosphate Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate: step 2/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsA family. +Required for N-linked oligosaccharide assembly. Has a role in the last step of the synthesis of the Man(5)GlcNAc(2)-PP-dolichol core oligosaccharide on the cytoplasmic face of the endoplasmic reticulum. alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphosphodolichol + 2 GDP-alpha-D-mannose = alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphosphodolichol + 2 GDP + 2 H(+) Protein modification; protein glycosylation. Interacts with ALG1. Present with 3140 molecules/cell in log phase SD medium. Belongs to the glycosyltransferase group 1 family. Glycosyltransferase 4 subfamily. +Belongs to the BMP lipoprotein family. +Is able to cleave peptidoglycan. Belongs to the transglycosylase family. IsaA subfamily. +Represses transcription of the icaADBC operon necessary for biofilm production. Homodimer. Binding to the ica operator DNA involves two IcaR dimers and is highly cooperative. +Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol, an intermediate step in ubiquinone biosynthesis. a 4-hydroxy-3-all-trans-polyprenylbenzoate + H(+) = a 2-all-trans-polyprenylphenol + CO2 Binds 1 prenylated FMN (prenyl-FMN) per subunit. Cofactor biosynthesis; ubiquinone biosynthesis. Homohexamer. Belongs to the UbiD family. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Protein modifier that is covalently attached to lysine residues of substrate proteins, thereby targeting them for proteasomal degradation. The tagging system is termed pupylation. Protein degradation; proteasomal Pup-dependent pathway. Strongly interacts with the proteasome-associated ATPase ARC through a hydrophobic interface; the interacting region of Pup lies in its C-terminal half. There is one Pup binding site per ARC hexamer ring. The N-terminal unstructured half of Pup provides a signal required to initiate unfolding and degradation by the proteasome but is not needed for pupylation, while the C-terminal helical half of Pup interacts with ARC to target proteins to the proteasome. Is modified by deamidation of its C-terminal glutamine to glutamate by the deamidase Dop, a prerequisite to the subsequent pupylation process. Belongs to the prokaryotic ubiquitin-like protein family. +Belongs to the PPR family. P subfamily. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 1 family. +Involved in developmentally regulated synthesis of a compound biosynthetically related to polyketide antibiotics which is essential for spore color in Streptomyces halstedii. 4'-phosphopantetheine is transferred from CoA to a specific serine of the apo-ACP-like protein. +Belongs to the LysR transcriptional regulatory family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a(1), b(1), b'(1) and c(9-12). Belongs to the ATPase alpha/beta chains family. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. Binds 1 lipoyl cofactor covalently. The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvH family. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +A non-essential component of RNA polymerase (RNAP). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) RNAP is composed of a core of 2 alpha, a beta and a beta' subunit. The core is associated with a delta subunit, and at least one of epsilon or omega. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit epsilon family. +Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetyl-glucosamine (UDP-GlcNAc). Responsible for the acetylation of GlcN-1-P to GlcNAc-1-P, and for the uridyl transfer from UTP to GlcNAc-1-P, to produce UDP-GlcNAc and pyrophosphate (By similarity). H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; N-acetyl-alpha-D-glucosamine 1-phosphate from alpha-D-glucosamine 6-phosphate (route II): step 2/2. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; UDP-N-acetyl-alpha-D-glucosamine from N-acetyl-alpha-D-glucosamine 1-phosphate: step 1/1. In the N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family. In the C-terminal section; belongs to the transferase hexapeptide repeat family. +Belongs to the UPF0234 family. +Purine salvage pathway enzyme that catalyzes the transfer of the ribosyl-5-phosphate group from 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to the N9 position of the 6-oxopurines guanine and xanthine to form the corresponding ribonucleotides GMP (guanosine 5'-monophosphate) and XMP (xanthosine 5'-monophosphate), with the release of PPi. To a lesser extent, also acts on hypoxanthine. diphosphate + GMP = 5-phospho-alpha-D-ribose 1-diphosphate + guanine diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine diphosphate + IMP = 5-phospho-alpha-D-ribose 1-diphosphate + hypoxanthine Purine metabolism; GMP biosynthesis via salvage pathway; GMP from guanine: step 1/1. Purine metabolism; XMP biosynthesis via salvage pathway; XMP from xanthine: step 1/1. Homotetramer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. XGPT subfamily. +Component of the spindle-assembly checkpoint that prevents the onset of anaphase until all chromosomes are properly aligned at the metaphase plate. Required for the execution of the mitotic checkpoint which monitors the process of kinetochore-spindle attachment and inhibits the activity of the anaphase promoting complex until all chromosomes are aligned at the metaphase plate (By similarity). Interacts with cdc20. The protein has two highly different native conformations, an inactive open conformation that cannot bind cdc20 and that predominates in cytosolic monomers, and an active closed conformation. Belongs to the MAD2 family. The gene for this protein is duplicated in strains AX3 and AX4. These strains contain a duplication of a segment of 750 kb of chromosome 2 compared to the corresponding sequence in strain AX2. +Positively regulates the transcription of the maltose regulon whose gene products are responsible for uptake and catabolism of malto-oligosaccharides. Specifically binds to the promoter region of its target genes, recognizing a short DNA motif called the MalT box. Activated by ATP and maltotriose, which are both required for DNA binding. Monomer in solution. Oligomerizes to an active state in the presence of the positive effectors ATP and maltotriose. Belongs to the MalT family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +This regulatory protein, when combined with SAM (S-adenosylmethionine) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated (By similarity). Homodimer. Does not bind DNA by a helix-turn-helix motif. Belongs to the MetJ family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Zn(2+) ion per subunit. In plastids the minimal PEP RNA polymerase catalytic core is composed of four subunits: alpha, beta, beta', and beta''. When a (nuclear-encoded) sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. RpoC2 subfamily. +APOE is an apolipoprotein, a protein associating with lipid particles, that mainly functions in lipoprotein-mediated lipid transport between organs via the plasma and interstitial fluids. APOE is a core component of plasma lipoproteins and is involved in their production, conversion and clearance. Apoliproteins are amphipathic molecules that interact both with lipids of the lipoprotein particle core and the aqueous environment of the plasma. As such, APOE associates with chylomicrons, chylomicron remnants, very low density lipoproteins (VLDL) and intermediate density lipoproteins (IDL) but shows a preferential binding to high-density lipoproteins (HDL). It also binds a wide range of cellular receptors including the LDL receptor/LDLR, the LDL receptor-related proteins LRP1, LRP2 and LRP8 and the very low-density lipoprotein receptor/VLDLR that mediate the cellular uptake of the APOE-containing lipoprotein particles. Finally, APOE has also a heparin-binding activity and binds heparan-sulfate proteoglycans on the surface of cells, a property that supports the capture and the receptor-mediated uptake of APOE-containing lipoproteins by cells. A main function of APOE is to mediate lipoprotein clearance through the uptake of chylomicrons, VLDLs, and HDLs by hepatocytes. APOE is also involved in the biosynthesis by the liver of VLDLs as well as their uptake by peripheral tissues ensuring the delivery of triglycerides and energy storage in muscle, heart and adipose tissues. By participating in the lipoprotein-mediated distribution of lipids among tissues, APOE plays a critical role in plasma and tissues lipid homeostasis. APOE is also involved in two steps of reverse cholesterol transport, the HDLs-mediated transport of cholesterol from peripheral tissues to the liver, and thereby plays an important role in cholesterol homeostasis. First, it is functionally associated with ABCA1 in the biogenesis of HDLs in tissues. Second, it is enriched in circulating HDLs and mediates their uptake by hepatocytes. APOE also plays an important role in lipid transport in the central nervous system, regulating neuron survival and sprouting. Homotetramer. May interact with ABCA1; functionally associated with ABCA1 in the biogenesis of HDLs. May interact with APP/A4 amyloid-beta peptide; the interaction is extremely stable in vitro but its physiological significance is unclear. May interact with MAPT. May interact with MAP2. In the cerebrospinal fluid, interacts with secreted SORL1. In the plasma, APOE is associated with chylomicrons, chylomicrons remnants, VLDL, LDL and HDL lipoproteins. Lipid poor oligomeric APOE is associated with the extracellular matrix in a calcium- and heparan-sulfate proteoglycans-dependent manner. Lipidation induces the release from the extracellular matrix. APOE exists as multiple glycosylated and sialylated glycoforms within cells and in plasma. The extent of glycosylation and sialylation are tissue and context specific. Glycated in plasma VLDL. Phosphorylated by FAM20C in the extracellular medium. Belongs to the apolipoprotein A1/A4/E family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins serve in intracellular movements. Their highly divergent tails are presumed to bind to membranous compartments, which would be moved relative to actin filaments. May be involved in targeting of the catalytic subunit of protein phosphatase 1 during brain development (By similarity). Activates PI3K and concomitantly recruits the WAVE1 complex to the close vicinity of PI3K and regulates neuronal morphogenesis. Binds PPP1CA and/or PPP1CC. Binds F-actin in an ATP-sensitive manner (By similarity). Interacts with ACOT9, ARHGAP26 and PIK3R2. Interacts with components of the WAVE1 complex, CYFIP1 and NCKAP1; this interaction mediates PI3K-WAVE1 association and actin cytoskeleton remodeling (PubMed:21946561). Interacts with KIRREL3 (By similarity). Found in puncta in soma and processes of astrocytes and dissociated cerebellar cells with the morphology of migrating granule cells. Expressed predominantly in brain where it is present in the neurons, but not in astrocytes or oligodendrites. At postnatal day 1, highly expressed in upper neocortex and also detected in the olfactory bulb, but not in the striatum. Phosphorylated on tyrosine residues by FYN upon stimulation with CNTN5. Phosphorylation begins at 14 dpc, reaches a peak during perinatal days in brain, then gradually decreases. Triple knockout mice NYAP1/NYAP2/MYO16 are fertile and appear healthy. However, compared to wild-type mice they show a clear reduction in brain size, exhibiting a reduction in the size of the cortex and striatum, but not the olfactory bulb or corpus callosum. The total neurite length of neurons in these mice is also significantly shorter. In the N-terminal section; belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Myosin family. In the C-terminal section; belongs to the NYAP family. +H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 magnesium or manganese ions per subunit. Belongs to the PP2C family. +Belongs to the YejK family. +Galactose-binding protein which recognizes specific carbohydrate structures and agglutinates a variety of animal cells by binding to cell-surface glycoproteins and glycolipids. Calcium-dependent lectin. Shows high hemagglutinating activity in the presence of human erythrocytes, which are agglutinated with a minimum hemagglutination concentration (MHC) of 2.5-0.35 ug/ml. Causes indirect nephrotoxicity. Causes reductions in perfusion pressures, renal vascular resistance, urinary flow, glomerular filtration rate, sodium, potassium and chloride tubular transport. Its effects may be caused by the release of inflammatory mediators. Homodimer; disulfide-linked. Expressed by the venom gland. Hemagglutination activity is inhibited by D-lactose (MIC=1.75 mM), D-galactose (MIC=0.75 mM) and D-raphinose (MIC=3.5 mM). Is not inhibited by D-glucose, D-sucrose, D-maltose, D-mannose, D-fructose, D-threalose, and methyl-manopyrosonide (PubMed:15381156). Does not induce direct vasoactive effects in perfused arteriolar mesenteric bed, and does not potentiate bradykinin contraction in the ileum. Belongs to the true venom lectin family. The same name has been given to a lectin from Bothropoides pauloensis (AC P86970). +Belongs to the bacterial ribosomal protein bS16 family. +The BBSome complex is thought to function as a coat complex required for sorting of specific membrane proteins to the primary cilia. The BBSome complex is required for ciliogenesis but is dispensable for centriolar satellite function. This ciliogenic function is mediated in part by the Rab8 GDP/GTP exchange factor, which localizes to the basal body and contacts the BBSome. Rab8(GTP) enters the primary cilium and promotes extension of the ciliary membrane. Firstly the BBSome associates with the ciliary membrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor (GEF) for Rab8 and then the Rab8-GTP localizes to the cilium and promotes docking and fusion of carrier vesicles to the base of the ciliary membrane. The BBSome complex, together with the LTZL1, controls SMO ciliary trafficking and contributes to the sonic hedgehog (SHH) pathway regulation. Required for BBSome complex ciliary localization but not for the proper complex assembly (By similarity). Part of BBSome complex, that contains BBS1, BBS2, BBS4, BBS5, BBS7, BBS8/TTC8, BBS9 and BBIP10. Interacts with BBS2 (via C-terminus). Interacts with CCDC28B. Interacts with SMO; the interaction is indicative for the association of SMO with the BBsome complex to facilitate ciliary localization of SMO. May be due to a competing donor splice site. Due to intron retention. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the LeuD family. LeuD type 1 subfamily. +Belongs to the UPF0235 family. +The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The enzyme II UlaABC PTS system is involved in ascorbate transport. Homodimer. Induced by L-ascorbate. Repressed by UlaR. In classical PTS systems, the PTS EIIC type-2 domain forms the translocation channel and contains the specific substrate-binding site. UlaA does not exhibit the topological features of any recognized enzyme IIC. Belongs to the UlaA family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Catalyzes the hydroxylation of 2-nonaprenyl-3-methyl-6-methoxy-1,4-benzoquinol during ubiquinone biosynthesis. a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + AH2 + O2 = A + a 3-demethylubiquinol + H2O Binds 2 iron ions per subunit. Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the COQ7 family. +Acts as a negative regulator of the GCN2 kinase activity by disrupting the GCN1-GCN2 interaction in amino acid-starved cells (PubMed:19448108). Interacts with GCN1; this interaction prevents the interaction of GCN1 with GCN2 protein kinase and GCN2 activation in amino acid-starved cells (PubMed:19448108). Interacts with RBG1 (PubMed:19448108). Associates with ribosomes; the association occurs in a GCN1-dependent manner (PubMed:19448108). Present with 10300 molecules/cell in log phase SD medium. Belongs to the RWDD1/GIR2 family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Participates in both the initiation and recycling phases of transcription. In the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling. RNAP is composed of a core of 2 alpha, a beta and a beta' subunits. The core is associated with a delta subunit and one of several sigma factors. Belongs to the RpoE family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 2 [4Fe-4S] clusters per subunit. NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I 23 kDa subunit family. +G-protein coupled receptor for tyramine, a known neurotransmitter and neuromodulator and direct precursor of octopamine. Belongs to the G-protein coupled receptor 1 family. +Molecular chaperone; binds unfolded polypeptides in vitro, and has a weak ATPase activity. Forms a Heterooligomeric complex of two stacked eight-membered rings. Belongs to the TCP-1 chaperonin family. +Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishment of the nucleosome following the passage of RNA polymerase II (By similarity). Forms a stable heterodimer with POB3. The SPT16-POB3 dimer weakly associates with multiple molecules of NHP6 to form the FACT complex (By similarity). Belongs to the peptidase M24 family. SPT16 subfamily. Although related to the peptidase M24 family, this protein lacks conserved active site residues suggesting that it may lack peptidase activity. +ATPase subunit of a proteasome-like degradation complex; this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the ClpX chaperone family. HslU subfamily. +Induces the formation of specific membrane adhesion sites between the inner and outer membranes, apparently leading to host cell lysis. Lysis may be performed via activation of host murein hydrolases. +Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NAD(+) (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADPH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NADP(+) Belongs to the MnmG family. TrmFO subfamily. +Non-catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5' and 3' splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-OH termini. There are no conserved sequences at the splice sites, but the intron is invariably located at the same site in the gene, placing the splice sites an invariant distance from the constant structural features of the tRNA body. The tRNA splicing endonuclease is also involved in mRNA processing via its association with pre-mRNA 3'-end processing factors, establishing a link between pre-tRNA splicing and pre-mRNA 3'-end formation, suggesting that the endonuclease subunits function in multiple RNA-processing events (By similarity). tRNA splicing endonuclease is a heterotetramer composed of TSEN2, TSEN15, TSEN34/LENG5 and TSEN54. tRNA splicing endonuclease complex also contains proteins of the pre-mRNA 3'-end processing machinery such as CLP1, CPSF1, CPSF4 and CSTF2 (By similarity). May be transiently localized in the nucleolus. Belongs to the SEN54 family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Hydrolyzes GTP to GMP in 2 consecutive cleavage reactions, but the major reaction product is GDP (PubMed:8706832). Exhibits antiviral activity against influenza virus. Promotes oxidative killing and delivers antimicrobial peptides to autophagolysosomes, providing broad host protection against different pathogen classes (By similarity). Confers protection to the protozoan pathogen Toxoplasma gondii (By similarity). GTP + H2O = GDP + H(+) + phosphate Homodimer; homodimerization occurs upon GTP-binding and is required for the association with membranous structures. Heterodimer with other family members, including GBP1, GBP3, GBP4 and GBP5. GBP2-GBP5 dimers localize to the Golgi apparatus. By IFNG/IFN-gamma during macrophage activation, and by TNF and IL1B. Isoprenylation is required for proper subcellular location. Belongs to the TRAFAC class dynamin-like GTPase superfamily. GB1/RHD3 GTPase family. GB1 subfamily. +Belongs to the CDP-alcohol phosphatidyltransferase class-I family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +Belongs to the methyltransferase superfamily. +It is involved in synaptogenesis and promotes synapse differentiation (By similarity). Suppresses neurite outgrowth (PubMed:14550773). Interacts (via LRR 1 and 2 repeats) with PTPRD (via extracellular domain). In the adult, significant expression is detected only in the brain. Broadly expressed in embryonic brain with highest expression in subventricular zone, subplate, cortical plate, pyramidal cell layer of hippocampus, thalamus and hypothalamus. In the embryo, expressed from day 10-12 and continues through later gestational development and into adulthood. Belongs to the SLITRK family. +Probably plays an important role in intracellular peptide degradation. Release of an N-terminal amino acid, Xaa, from a peptide or arylamide. Xaa is preferably Glu or Asp but may be other amino acids, including Leu, Met, His, Cys and Gln. Binds 2 manganese ions per subunit. Homohexamer. Belongs to the peptidase M17 family. +Postsynaptic density membrane protein that indirectly regulates glutamatergic synaptic transmission through lysophosphatidic acid (LPA)-mediated signaling pathways (PubMed:19766573). Binds lysophosphatidic acid (LPA) and mediates its internalization into cells (PubMed:26671989). Could act as receptor or a transporter of this lipid at the post-synaptic membrane (PubMed:19766573, PubMed:26671989). Modulates lysophosphatidic acid (LPA) activity in neuron axonal outgrowth during development by attenuating phospholipid-induced axon collapse (By similarity). Brain-specific, it is exclusively expressed in neurons (at protein level). O-glycosylated. Probably at Ser-347. Knockout mice lacking Plppr4 are viable but show a severe alteration of synaptic transmission leading to juvenile epileptic seizures (PubMed:19766573). Excitatory transmission in CA1 pyramidal neurons is significantly increased (PubMed:19766573). It is associated with transiently reduced weight during development, a reduction in brain size and higher mortality 3 to 4 weeks after birth (PubMed:19766573). Heterozygous knockout mice, show loss of somatosensory filter function and altered resilience during stress-related behaviors (PubMed:26671989). Belongs to the PA-phosphatase related phosphoesterase family. Originally described as a 2-lysophosphatidate/LPA phosphatase (PubMed:12730698). However, following studies suggested it does not have such activity or only a residual one (PubMed:19766573). This is further supported by the fact that the phosphatase sequence motifs as well as the His residue acting as a nucleophile in active phosphatases of the PA-phosphatase related phosphoesterase family are not conserved (PubMed:19766573). +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +General amino acid control transactivator. Binds to the AP-1 consensus DNA binding element 5'-[AG]TGACTCAT-3'. Binds DNA as a dimer. Belongs to the bZIP family. GCN4 subfamily. +Required for cytochrome c synthesis and stage V of sporulation. Might transfer reducing equivalents across the cytoplasmic membrane, promoting efficient disulfide bond isomerization of proteins localized on the outer surface of the membrane or in the spore coat. Cytochrome c oxidase activity is partially restored by mutations in bdbC or bdbD that are defective in the synthesis of disulfide bond containing proteins. The same mutations abrogate the need for CcdA in sporulation. Belongs to the DsbD family. +Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones. Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines. 2 a quinone + H(+) + NADH = 2 a 1,4-benzosemiquinone + NAD(+) anthranilate + N,N-dimethyl-1,4-phenylenediamine + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 H(+) + 2 NADH Binds 1 FMN per subunit. Homodimer. Belongs to the azoreductase type 1 family. +May help in the organization of the PsaE and PsaF subunits. Belongs to the PsaJ family. +Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL27 family. +RNA-binding protein that specifically bind the 3'-UTR of VegT transcripts, leading to maintain their stability and stimulate their translation, thereby playing a role in germ layer formation. VegT is a localized maternal determinant essentially required for endoderm formation. Also has some proneural function in the open neural plate and in the context of retinogenesis. May also act as a mRNA splicing factor. May play a role in myogenic differentiation. Strongly expressed in the nervous system. Expressed at early neurula stages of development. Belongs to the RBM38 family. +Transcriptional corepressor. Functions with ripply2.2/bowline to down regulate transcription of tbx6-dependent gene expression. Represses transcription of siamois and nodal3. Interacts with tcf7, tcf7l1, ripply2.2/bowline, dscr6/ripply3 and foxd3. Associates with tbx6 in the presence of ripply2.2/bowline. Interacts with EFNB1 through the SP domain. Expressed at high levels in the spleen and ovary. Expressed maternally. At end of gastrulation, expressed in the prospective neural plate region. In neurula stages, shows highest expression in the sensorial layer of the neurectoderm, decreasing from anterior to posterior. Shows localized expression within the anterior neural plate, including the floor of the neural groove. Expressed in the cement gland anlage at stage 14. At stage 16, expressed in the neural groove, rhombomeres, forebrain and branchial arches. At stage 22, abundant in the eye vesicles, ear placodes, prospective branchial arches, pronephric anlage, prospective pronephric duct, presomitic mesoderm and the somites. In the developing brain, expression is dynamic, being most abundant in the mesencephalon and posterior rhombencephalon. At stage 30, expressed in cephalic ganglia V and VII and in stage 35, also IX and X. Also expressed in the future endocardium and pericardium. At stage 32, expressed in the neural groove, rhombomeres, forebrain and branchial arches. At stage 35, expressed in the future choroid plexus of the telencephalon and in the ependymal layer. Throughout the neural tube, expressed in a dorsal to ventral gradient. In the developing eye, expressed in the prospective ganglion cell layer, the ciliary marginal zone and the lens. WD repeat Groucho/TLE family members are characterized by 5 regions, a glutamine-rich Q domain, a glycine/proline-rich GP domain, a central CcN domain, containing a nuclear localization signal, and a serine/proline-rich SP domain. The most highly conserved are the N-terminal Q domain and the C-terminal WD-repeat domain. The SP domain is involved in EFNB1-binding. Ubiquitinated by XIAP/BIRC4. Belongs to the WD repeat Groucho/TLE family. It is uncertain whether Met-1 or Met-8 is the initiator. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Part of the Tol-Pal system, which plays a role in outer membrane invagination during cell division and is important for maintaining outer membrane integrity. The Tol-Pal system is composed of five core proteins: the inner membrane proteins TolA, TolQ and TolR, the periplasmic protein TolB and the outer membrane protein Pal. They form a network linking the inner and outer membranes and the peptidoglycan layer. Belongs to the TolB family. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Catalyzes the transfer of adenosine 5'-monophosphate (AMP) to Ser, Thr or Tyr residues of target proteins (AMPylation). ATP + L-tyrosyl-[protein] = diphosphate + O-(5'-adenylyl)-L-tyrosyl-[protein] ATP + L-threonyl-[protein] = 3-O-(5'-adenylyl)-L-threonyl-[protein] + diphosphate ATP + L-seryl-[protein] = 3-O-(5'-adenylyl)-L-seryl-[protein] + diphosphate Belongs to the SELO family. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +Inhibitor of cysteine proteinases. Inhibits host immune responses via its inhibition of host cathepsins (PubMed:19494265). Contributes to the suppression of the host's immune response to tick salivary proteins and is important for successful feeding on hosts (PubMed:17698852). Inhibits differentiation of host dendritic cells (PubMed:19494265, PubMed:25975355). Inhibits proliferation of host T-cells in response to antigen stimulus (PubMed:19494265). Down-regulates TLR2-mediated host responses to infection by B.burgdorferi and the production of the chemokine CCL3 by host dendritic cells (PubMed:25975355). Down-regulates host responses to infection by B.burgdorferi and the production of IFNB1 by host dendritic cells (PubMed:25975355). Down-regulates IL1B production by host mast cells, and this then leads to impaired activation of IL1R1, resulting in decreased IL9 production (PubMed:26078269). Inhibits host inflammatory reactions and recruitment of host neutrophils (PubMed:16772304). Inhibits papain and cathepsin-L (CTSL) (in vitro) (PubMed:16772304, PubMed:17698852, PubMed:20545851). Inhibits cathepsin-S (CTSS) (in vitro) (PubMed:17698852, PubMed:20545851). Inhibits CTSV and CTSC, but to a lesser degree (in vitro) (PubMed:16772304, PubMed:17698852). Monomer. Can form homodimers in vitro, but probably not in vivo. Homodimers are predicted to be inactive; dimerization disrupts the interaction with target proteases. Detected in saliva (at protein level) (PubMed:16772304). Detected in salivary gland and midgut (PubMed:17698852). Combined, RNAi-mediated down-regulation of Salivary cystatin-L and Salivary cystatin-L2 in salivary glands strongly impairs the tick's ability to feed on hosts. About 40% of the ticks cannot feed and die. The remainder show much reduced blood intake, appear unhealthy and display strongly reduced egg laying. RNAi-treated ticks show an impaired ability to suppress the host's immune response to tick salivary proteins. Belongs to the cystatin family. +Phospholipid scramblase involved in autophagy and cytoplasm to vacuole transport (Cvt) vesicle formation. Cycles between the preautophagosomal structure/phagophore assembly site (PAS) and the cytoplasmic vesicle pool and supplies membrane for the growing autophagosome. Lipid scramblase activity plays a key role in preautophagosomal structure/phagophore assembly by distributing the phospholipids that arrive through ATG2 from the cytoplasmic to the luminal leaflet of the bilayer, thereby driving autophagosomal membrane expansion. Required for mitophagy. Also involved in endoplasmic reticulum-specific autophagic process and is essential for the survival of cells subjected to severe ER stress. Different machineries are required for anterograde trafficking to the PAS during either the Cvt pathway or bulk autophagy and for retrograde trafficking. a 1,2-diacyl-sn-glycero-3-phosphocholine(in) = a 1,2-diacyl-sn-glycero-3-phosphocholine(out) a 1,2-diacyl-sn-glycero-3-phospho-L-serine(in) = a 1,2-diacyl-sn-glycero-3-phospho-L-serine(out) a 1,2-diacyl-sn-glycero-3-phosphoethanolamine(in) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine(out) a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate)(in) = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate)(out) Homotrimer; forms a homotrimer with a central pore that forms a path between the two membrane leaflets. Forms a homotrimer with a solvated central pore, which is connected laterally to the cytosol through the cavity within each protomer. Acts as a lipid scramblase that uses its central pore to function: the central pore opens laterally to accommodate lipid headgroups, thereby enabling lipid flipping and redistribution of lipids added to the outer leaflet of ATG9-containing vesicles, thereby enabling growth into autophagosomes. Phosphorylated by ATG1. ATG1 phosphorylation is required for preautophagosome elongation. Belongs to the ATG9 family. +Cytokinin receptor related to bacterial two-component regulators. Functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. Expressed in roots, leaf blades, leaf sheaths, shoot apex, flowers and panicles. Histidine-containing phosphotransfer domain (HPt) contains an active histidine that mediates the phosphotransfer. Activation probably requires a transfer of a phosphate group between a His in the transmitter domain and an Asp of the receiver domain. Sterility. +Plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons. Its association with pi-bodies suggests a participation in the primary piRNAs metabolic process. Required prior to the pachytene stage to facilitate the production of multiple types of piRNAs, including those associated with repeats involved in the regulation of retrotransposons. May act by mediating protein-protein interactions during germ cell maturation (By similarity). Interacts with DDX4, PIWIL1, RANBP9 and TDRD1. Component of the meiotic nuage, also named P granule, a germ-cell-specific organelle required to repress transposon activity during meiosis. Specifically localizes to pi-bodies, a subset of the nuage which contains primary piRNAs (By similarity). +Kills Lactococci. +Has aromatic amino acid transaminase activity. 2-oxoglutarate + an aromatic L-alpha-amino acid = an aromatic oxo-acid + L-glutamate Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. +May bind long-chain fatty acids, such as palmitate, and may play a role in lipid transport or fatty acid metabolism. Truncated N-terminus. +Component of the ubiquinol-cytochrome c oxidoreductase, a multisubunit transmembrane complex that is part of the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. The cytochrome b-c1 complex catalyzes electron transfer from ubiquinol to cytochrome c, linking this redox reaction to translocation of protons across the mitochondrial inner membrane, with protons being carried across the membrane as hydrogens on the quinol. In the process called Q cycle, 2 protons are consumed from the matrix, 4 protons are released into the intermembrane space and 2 electrons are passed to cytochrome c (By similarity). The 2 core subunits UQCRC1/QCR1 and UQCRC2/QCR2 are homologous to the 2 mitochondrial-processing peptidase (MPP) subunits beta-MPP and alpha-MPP respectively, and they seem to have preserved their MPP processing properties (By similarity). May be involved in the in situ processing of UQCRFS1 into the mature Rieske protein and its mitochondrial targeting sequence (MTS)/subunit 9 when incorporated into complex III (Probable). Seems to play an important role in the maintenance of proper mitochondrial function in nigral dopaminergic neurons (PubMed:33141179). Component of the ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), a multisubunit enzyme composed of 11 subunits. The complex is composed of 3 respiratory subunits cytochrome b, cytochrome c1 and Rieske protein UQCRFS1, 2 core protein subunits UQCRC1/QCR1 and UQCRC2/QCR2, and 6 low-molecular weight protein subunits UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and subunit 9, the cleavage product of Rieske protein UQCRFS1 (By similarity). The complex exists as an obligatory dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and cytochrome c oxidase (complex IV, CIV), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (PubMed:28844695). Interacts with BRAWNIN (PubMed:32161263). Interacts with STMP1 (By similarity). Expressed in brain, including substantia nigra, striatum, cortex and cerebellum, and in spinal cord, heart, kidney, liver and muscle. The protein represented in this entry is involved in disease pathogenesis. Belongs to the peptidase M16 family. UQCRC1/QCR1 subfamily. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Phosphorylated. Phosphorylation increases protein degradation. Belongs to the BZR/LAT61 family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +Located on the platform of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS11 family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 magnesium ions per subunit. Monomer. Belongs to the DNA polymerase type-Y family. +Belongs to the ycf45 family. +Catalyzes the NADPH-dependent reduction of N-acetyl-5-glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde. N-acetyl-L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + N-acetyl-L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 3/4. Belongs to the NAGSA dehydrogenase family. Type 2 subfamily. +Regulates endothelial chemotaxis and tube formation. Has a role in angiogenesis and apoptosis via modulation of the actin cytoskeleton and facilitation of proteasomal degradation of the apoptosis inhibitors BIRC3/IAP1 and BIRC2/IAP2 (By similarity). Interacts with FLNA. Interacts with the 20S proteasome subunit PSMA7. May be heavily O-glycosylated. Belongs to the ECSCR family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]CCGAC-3'. Binding to the C-repeat/DRE element mediates cold-inducible transcription. CBF/DREB1 factors play a key role in freezing tolerance and cold acclimation. Expressed in leaves and roots. By cold stress. Belongs to the AP2/ERF transcription factor family. ERF subfamily. +Receptor for SLIT2, and probably SLIT1, which are thought to act as molecular guidance cue in cellular migration, including axonal navigation at the ventral midline of the neural tube and projection of axons to different regions during neuronal development. Interacts with SLIT2. The disease is caused by variants affecting the gene represented in this entry. A chromosomal aberration involving ROBO2 is a cause of multiple congenital abnormalities, including severe bilateral VUR with ureterovesical junction defects. Translocation t(Y;3)(p11;p12) with PCDH11Y. This translocation disrupts ROBO2 and produces dominant-negative ROBO2 proteins that abrogate SLIT-ROBO signaling in vitro. Belongs to the immunoglobulin superfamily. ROBO family. +Expressed only in the forespore compartment of sporulating cells. Belongs to the SspN family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. RnhC subfamily. +The protein is truncated in this strain and presumably inactive. It has similarities with variola virus CrmB, but the product is inactivated due to several premature stop codon. +Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins. Interacts with the Sec translocase complex via SecD. Specifically interacts with transmembrane segments of nascent integral membrane proteins during membrane integration. Belongs to the OXA1/ALB3/YidC family. Type 1 subfamily. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine. [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(S)-S-oxide-[protein] [thioredoxin]-disulfide + H2O + L-methionine = [thioredoxin]-dithiol + L-methionine (S)-S-oxide Belongs to the MsrA Met sulfoxide reductase family. +Integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, functions primarily as a coreceptor for MHC class II molecule:peptide complex. The antigens presented by class II peptides are derived from extracellular proteins while class I peptides are derived from cytosolic proteins. Interacts simultaneously with the T-cell receptor (TCR) and the MHC class II presented by antigen presenting cells (APCs). In turn, recruits the Src kinase LCK to the vicinity of the TCR-CD3 complex. LCK then initiates different intracellular signaling pathways by phosphorylating various substrates ultimately leading to lymphokine production, motility, adhesion and activation of T-helper cells. In other cells such as macrophages or NK cells, plays a role in differentiation/activation, cytokine expression and cell migration in a TCR/LCK-independent pathway. Participates in the development of T-helper cells in the thymus and triggers the differentiation of monocytes into functional mature macrophages. (Microbial infection) Primary receptor for human immunodeficiency virus-1 (HIV-1) (PubMed:2214026, PubMed:16331979, PubMed:9641677, PubMed:12089508). Down-regulated by HIV-1 Vpu (PubMed:17346169). Acts as a receptor for Human Herpes virus 7/HHV-7 (PubMed:7909607). Forms disulfide-linked homodimers at the cell surface. Interacts with LCK (PubMed:16888650). Interacts with PTK2/FAK1 (PubMed:18078954). Binds to P4HB/PDI. Interacts with IL16; this interaction induces a CD4-dependent signaling in lymphocytes (PubMed:1673145). Interacts (via Ig-like V-type domain) with MHCII alpha chain (via alpha-2 domain) and beta chain (via beta-2 domain); this interaction increases the affinity of TCR for peptide-MHCII. CD4 oligomerization via Ig-like C2-type 2 and 3 domains appears to be required for stable binding to MHCII and adhesion between T cells and APCs (PubMed:27114505, PubMed:21900604, PubMed:7604010). (Microbial infection) Interacts with HIV-1 Envelope polyprotein gp160 and protein Vpu (PubMed:2214026, PubMed:16331979, PubMed:9641677, PubMed:7604010). (Microbial infection) Interacts with Human Herpes virus 7 surface proteins. Localizes to lipid rafts (PubMed:12517957, PubMed:9168119). Removed from plasma membrane by HIV-1 Nef protein that increases clathrin-dependent endocytosis of this antigen to target it to lysosomal degradation. Cell surface expression is also down-modulated by HIV-1 Envelope polyprotein gp160 that interacts with, and sequesters CD4 in the endoplasmic reticulum. Highly expressed in T-helper cells. The presence of CD4 is a hallmark of T-helper cells which are specialized in the activation and growth of cytotoxic T-cells, regulation of B cells, or activation of phagocytes. CD4 is also present in other immune cells such as macrophages, dendritic cells or NK cells. The Ig-like V-type domain mediates the interaction with MHCII. Palmitoylation and association with LCK contribute to the enrichment of CD4 in lipid rafts. Phosphorylated by PKC; phosphorylation at Ser-433 plays an important role for CD4 internalization. The OKT monoclonal antibodies are widely used for the analysis of human peripheral blood T-lymphocytes. OKT4 reacts with T-helper/inducer lymphocytes. The OKT4 epitope of the CD4 cell-surface protein is polymorphic in white, black, and Japanese populations. The variable phenotypic expression is due a CD4 polymorphism. OKT4 positive individuals carry Arg-265 and OKT4 negative individuals carry Trp-265 [MIM:613949]. The disease is caused by variants affecting the gene represented in this entry. CD4 entry +Component of the SOS system and an inhibitor of cell division. Accumulation of SulA causes rapid cessation of cell division and the appearance of long, non-septate filaments. In the presence of GTP, binds a polymerization-competent form of FtsZ in a 1:1 ratio, thus inhibiting FtsZ polymerization and therefore preventing it from participating in the assembly of the Z ring. This mechanism prevents the premature segregation of damaged DNA to daughter cells during cell division. Interacts with FtsZ. By DNA damage, as part of the SOS response. Is rapidly cleaved and degraded by the Lon protease once DNA damage is repaired. Belongs to the SulA family. +Acts as a co-agonist with PNU (an alpha-7 nAChR-selective allosteric modulator) at the endogenous alpha-7/CHRNA7 nicotinic acetylcholine receptors (nAChR) when tested in human SH-SY5Y neuroblastoma cells. Is the third alpha-conotoxin that acts as an agonist (after alpha-conotoxin SrIA/SrIB). Also acts as an antagonist at human alpha-7 nAChRs heterologously expressed in Xenopus oocytes (PubMed:24351107). Has possibly a distinct nAChR binding mode from other alpha-conotoxins, due to a different three residue motif (lacks the Ser-Xaa-Pro motif) (By similarity). Acts as a weak partial agonist at alpha-7/CHRNA7 nicotinic acetylcholine receptors (nAChR) when tested in human SH-SY5Y neuroblastoma cells (PubMed:24351107). Has possibly a distinct nAChR binding mode from other alpha-conotoxins, due to a different three residue motif (lacks the Ser-Xaa-Pro motif) (By similarity). Expressed by the venom duct. The cysteine framework is I (CC-C-C). Alpha4/7 pattern. Two 4-hydroxyprolines have been detected by MS but the assignment of which of the three prolines is modified is uncertain (PubMed:23152539, and PubMed:24351107). Neither MrIC, Mr1.7b, nor Mr1.7a inhibit alpha-7/CHRNA7, alpha-3-beta-2/CHRNA3-CHRNB2 and alpha-3-beta-4/CHRNA3-CHRNB4 nAChRs endogenously expressed in human SH-SY5Y neuroblastoma cells. MrIC does not activate alpha-3-beta-2/CHRNA3-CHRNB2 and alpha-3-beta-4/CHRNA3-CHRNB4 endogenously expressed in human SH-SY5Y neuroblastoma cells. Mr1.7b does not activate alpha-7 endogenously expressed in human SH-SY5Y neuroblastoma cells (PubMed:24351107). Belongs to the conotoxin A superfamily. The cDNA sequence of this peptide has been submitted (EMBL entry JF460791) and described in PubMed:22781954 under the name Mr1.8. +The JNK-interacting protein (JIP) group of scaffold proteins selectively mediates JNK signaling by aggregating specific components of the MAPK cascade to form a functional JNK signaling module (PubMed:14743216). Regulates lysosomal positioning by acting as an adapter protein which links PIP4P1-positive lysosomes to the dynein-dynactin complex (PubMed:29146937). Assists PIKFYVE selective functionality in microtubule-based endosome-to-TGN trafficking (By similarity). May play a role in spermatozoa-egg-interaction. Homodimer (PubMed:19644450). The homodimer interacts with ARF6, forming a heterotetramer (PubMed:19644450). Homooligomer (PubMed:19644450). Interacts with MAX, MAPK14, MAP3K3, MYC, KNS2 and MAP2K4 (By similarity). Interaction with KNS2 is important in the formation of ternary complex with MAPK8 (By similarity). Interacts with NFKB1 (PubMed:14743216). Interacts with PIP4P1 (PubMed:29146937). Interacts with PIKFYVE (By similarity). Interacts with MAPK8, MAPK9, MAPK10. Perinuclear distribution in response to stress signals such as UV radiation. Associated with the plasma membrane of the acrosomal compartment and also localizes in the acrosome matrix. Expressed only in testis on the round spermatids of stage I, II and II. Absent in spermatogonia and spermatocyte. Expressed in testis and in acute myeloid leukemia (AML) patients. Expressed in testis. Increased in systemic sclerosis fibroblasts. Phosphorylated by MAPK8 and MAPK14. Due to intron retention. Belongs to the JIP scaffold family. Probable cloning artifact. Probable cloning artifact. Contaminating sequence. Sequence of unknown origin in the C-terminal part. Truncated N-terminus. Extended N-terminus. Unlikely isoform. Aberrant splicing. Truncated N-terminus. +Required for normal beta-1,6-glucan synthesis. Belongs to the BIG1 family. +Belongs to the bacterial ribosomal protein bL32 family. +Anti-apoptotic protein which can regulate cell death by controlling caspases and by acting as an E3 ubiquitin-protein ligase. Has an unusual ubiquitin conjugation system in that it could combine in a single polypeptide, ubiquitin conjugating (E2) with ubiquitin ligase (E3) activity, forming a chimeric E2/E3 ubiquitin ligase. Its targets include CASP9 and DIABLO/SMAC. Acts as an inhibitor of CASP3, CASP7 and CASP9. Important regulator for the final stages of cytokinesis. Crucial for normal vesicle targeting to the site of abscission, but also for the integrity of the midbody and the midbody ring, and its striking ubiquitin modification. Required for normal placenta development. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Inhibited by DIABLO/SMAC, HTRA2, CASP3, CASP6, CASP7 and CASP9. Homodimer. Binds the activated, processed forms of CASP3, CASP6 and CASP7. Interacts with RNF41, KIF23/MKLP1, USP8/UBPY, BIRC5/survivin, MAP2K1/MEK1, RAB8A/RAB8, RAB11A/RAB11, PLK1, EXOC3/SEC6 and EXOC4/SEC8 (By similarity). Interacts with CASP9, DIABLO/SMAC and HTRA2. Exhibits cell cycle-dependent localization. Concentrates in a pericentriolar compartment in interphase, moves partially to spindle poles in metaphase, and finally localizes to the spindle midzone and the midbody in telophase and during cytokinesis. On the midbody, localizes to the midbody ring, also called Flemming body. In interphase cells, localizes to the trans-Golgi network membrane and endosomes. During cytokinesis, a fraction moves to the midzone where it specifically arrives at the midbody ring. After abscission completion, travels with the midbody remnant into one daughter cell, and remains bound to it until a new midbody ring is formed during the next cell division. Widely expressed. Highly expressed in the brain and kidney. The BIR domain is essential for its antiapoptotic function and is important for binding to DIABLO/SMAC and CASP9. Ubiquitinated. Ubiquitination is mediated by the RNF41 E3 ligase and leads to proteasomal degradation, impairing inhibition of apoptosis. Deubiquitinated by USP8/UBPY (By similarity). Mice exhibit perinatal lethality and growth deficiencies, which are linked to a defect in proper placental development. In the C-terminal section; belongs to the ubiquitin-conjugating enzyme family. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Binds 2 manganese ions per subunit. Belongs to the peptidase M24B family. +ATPase required for the post-translational delivery of tail-anchored (TA) proteins to the endoplasmic reticulum. Recognizes and selectively binds the transmembrane domain of TA proteins in the cytosol. This complex then targets to the endoplasmic reticulum by membrane-bound receptors, where the tail-anchored protein is released for insertion. This process is regulated by ATP binding and hydrolysis. ATP binding drives the homodimer towards the closed dimer state, facilitating recognition of newly synthesized TA membrane proteins. ATP hydrolysis is required for insertion. Subsequently, the homodimer reverts towards the open dimer state, lowering its affinity for the membrane-bound receptor, and returning it to the cytosol to initiate a new round of targeting. Homodimer. Belongs to the arsA ATPase family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +May be involved as a regulatory molecule in GPR24/MCH-R1 signaling. Interacts with GPR24/MCH-R1. +Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF2. Belongs to the prokaryotic/mitochondrial release factor family. +Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln). Also essential during biosynthesis of the molybdenum cofactor. Acts by mediating the C-terminal thiocarboxylation of sulfur carriers URM1 and MOCS2A. Its N-terminus first activates URM1 and MOCS2A as acyl-adenylates (-COAMP), then the persulfide sulfur on the catalytic cysteine is transferred to URM1 and MOCS2A to form thiocarboxylation (-COSH) of their C-terminus. The reaction probably involves hydrogen sulfide that is generated from the persulfide intermediate and that acts as nucleophile towards URM1 and MOCS2A. Subsequently, a transient disulfide bond is formed. Does not use thiosulfate as sulfur donor; NFS1 probably acting as a sulfur donor for thiocarboxylation reactions. [molybdopterin-synthase sulfur-carrier protein]-C-terminal Gly-Gly + ATP + H(+) = [molybdopterin-synthase sulfur-carrier protein]-C-terminal Gly-Gly-AMP + diphosphate [molybdopterin-synthase sulfur-carrier protein]-C-terminal Gly-Gly-AMP + AH2 + S-sulfanyl-L-cysteinyl-[cysteine desulfurase] = [molybdopterin-synthase sulfur-carrier protein]-C-terminal Gly-NH-CH2-C(O)SH + A + AMP + H(+) + L-cysteinyl-[cysteine desulfurase] Binds 1 zinc ion per subunit. tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis. Cofactor biosynthesis; molybdopterin biosynthesis. In the N-terminal section; belongs to the HesA/MoeB/ThiF family. UBA4 subfamily. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +DNA helicase that plays an important role in DNA replication, transcription and repair. Binds to the RNA polymerase II subunit POLR2A during transcription elongation and suppresses transcription-associated genomic instability. Associates also with POLR1A and enforces the stability of ribosomal DNA arrays. Plays an important role in mitotic chromosome separation after cross-over events and cell cycle progress. Mechanistically, removes RAD51 filaments protecting stalled replication forks at common fragile sites and stimulates MUS81-EME1 endonuclease leading to mitotic DNA synthesis. Required for efficient DNA repair, including repair of inter-strand cross-links. Stimulates DNA decatenation mediated by TOP2A. Prevents sister chromatid exchange and homologous recombination. ATP + H2O = ADP + H(+) + phosphate Monomer. Interacts with TOP2A, TOP3A and TOP3B. Interacts with RNA polymerase II subunit POLR2A. Identified in a complex with the RNA polymerase II core bound to DNA. Interacts with RAD51. Interacts with WRN; this interaction stimulates WRN helicase activity on DNA fork duplexes. Interacts with MUS1; this interaction promotes MUS81-dependent mitotic DNA synthesis. Recruited to sites of DNA damage, such as single-strand breaks and inter-strand cross-links, and at stalled replication forks. Phosphorylated by CDK1 at Ser-728; this phosphorylation is required for RECQL5-mediated disruption of RAD51 filaments on stalled replication forks. Belongs to the helicase family. RecQ subfamily. +Provides the silk fibroin thread with a sticky coating. Acts as a cement by sticking silk threads together. Produced exclusively in the middle (MSG) section of silk glands. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiC family. +Belongs to the bacterial ribosomal protein bL27 family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Essential for thiamine biosynthesis. The kinase activity is involved in the salvage synthesis of TH-P from the thiazole. Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate 5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphooxyethyl)-thiazole + ADP + H(+) Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-methyl-5-(2-phosphoethyl)-thiazole from 5-(2-hydroxyethyl)-4-methylthiazole: step 1/1. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Homooctamer. In the N-terminal section; belongs to the thiamine-phosphate synthase family. In the C-terminal section; belongs to the Thz kinase family. +Belongs to the UPF0509 family. +Has quercetin 2,3-dioxygenase activity in vitro. Its physiological role is unknown; however, may provide a mechanism that would avoid inhibition of key cellular proteins, such as DNA gyrase, by quercetin (By similarity). O2 + quercetin = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO Binds 1 divalent metal cation, Zn(2+), Co(2+) or Fe(2+). Flavonoid metabolism; quercetin degradation. Is composed of two structurally similar domains arranged face to face. Quercetin is a flavonoid compound synthesized by a variety of plants, including foods for human consumption. Belongs to the pirin family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. Cyanobacterial PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins PsbO, PsbU, PsbV and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbJ family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +Antibacterial and antifungal activity. Presents chitin-binding activity (By similarity). Cytoplasmic granules of hemocytes and to a lesser extent in small granules of hemocytes. Belongs to the penaeidin family. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Mitochondrial membrane ATP synthase (F(1)F(o) ATP synthase) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain (PubMed:19436713, PubMed:29247468). F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(o) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk (PubMed:19436713, PubMed:29247468, PubMed:29440423). During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Subunits alpha and beta form the catalytic core in F(1) (PubMed:19436713, PubMed:29440423). Rotation of the central stalk against the surrounding alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits (Probable). Contrary to the procyclic, insect form that requires F(1)F(o) ATP synthase for ATP synthesis, the bloodstream form relies on ATP hydrolysis by F(1)F(o) ATP synthase to maintain its mitochondrial membrane potential (PubMed:29247468). F-type ATPases have 2 components, F(1) - the catalytic core - and F(o) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1), plus the additional subunit P18 (Tb427.05.1710) that is not present in F(1)F(o) ATP synthase from metazoa (PubMed:19436713, PubMed:29247468, PubMed:29440423). Subunit P18 (Tb927.5.1710) interacts with the alpha subunit with a 1:1 stoichiometry; the interaction is direct (PubMed:29440423). Subunit gamma is part of the central stalk (PubMed:29440423). F(o) has three main subunits: a, b and c (PubMed:19436713). The trypanosomal ATPase complex contains additional subunits that are not present in the F(1)F(o) ATP synthase from metazoa (PubMed:19436713, PubMed:29247468, PubMed:29440423). Belongs to the ATPase epsilon chain family. +Catalyzes the oxidation of malonate semialdehyde (MSA) and methylmalonate semialdehyde (MMSA) into acetyl-CoA and propanoyl-CoA, respectively. 3-oxopropanoate + CoA + NAD(+) = acetyl-CoA + CO2 + NADH 2-methyl-3-oxopropanoate + CoA + H2O + NAD(+) = H(+) + hydrogencarbonate + NADH + propanoyl-CoA Polyol metabolism; myo-inositol degradation into acetyl-CoA; acetyl-CoA from myo-inositol: step 7/7. Homotetramer. Belongs to the aldehyde dehydrogenase family. IolA subfamily. +Catalyzes the NADPH-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5-carboxylate. L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 2/2. Belongs to the gamma-glutamyl phosphate reductase family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds 2 heme A groups non-covalently per subunit. Binds a copper B center. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of a catalytic core of 3 subunits and several supernumerary subunits. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII). Belongs to the heme-copper respiratory oxidase family. +Required during biogenesis of c-type cytochromes (cytochrome c6 and cytochrome f) at the step of heme attachment. May interact with Ccs1. Belongs to the CcmF/CycK/Ccl1/NrfE/CcsA family. +Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. ATP + CoA + succinate = ADP + phosphate + succinyl-CoA Binds 1 Mg(2+) ion per subunit. Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. Heterotetramer of two alpha and two beta subunits. Belongs to the succinate/malate CoA ligase beta subunit family. +Belongs to the CDV3 family. +Provides the cells with the ability to utilize trehalose at high osmolarity by splitting it into glucose molecules that can subsequently be taken up by the phosphotransferase-mediated uptake system. alpha,alpha-trehalose + H2O = alpha-D-glucose + beta-D-glucose Monomer. Belongs to the glycosyl hydrolase 37 family. +May be involved in a process influencing telomere capping. Belongs to the RTC5 family. +Probable transcription factor that may be involved in stress responses. +The synthesis of this protein in the absorptive cells of the rat duodenum is vitamin D3-dependent. Belongs to the S-100 family. Was originally thought to originate from chick. +Translocates 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol (alpha-L-Ara4N-phosphoundecaprenol) from the cytoplasmic to the periplasmic side of the inner membrane. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Heterodimer of ArnE and ArnF. Belongs to the ArnE family. +Plays an important role in the de novo pathway and in the salvage pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP (By similarity). GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Cotranslationally removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides. Binds 2 divalent metal cations per subunit. Has a high-affinity and a low affinity metal-binding site. The true nature of the physiological cofactor is under debate. The enzyme is active with cobalt, zinc, manganese or divalent iron ions. Most likely, methionine aminopeptidases function as mononuclear Fe(2+)-metalloproteases under physiological conditions, and the catalytically relevant metal-binding site has been assigned to the histidine-containing high-affinity site. Irreversibly inhibited by the fungal metabolite fumagillin and the fumagillin analog TNP470, antiangiogenic drugs. Belongs to the peptidase M24A family. Methionine aminopeptidase eukaryotic type 2 subfamily. +Involved in ribosomal large subunit assembly (By similarity). S-adenosyl-L-methionine-dependent methyltransferase that probably methylates the C(5) position of cytosine 1586 (m5C1586) in mitochondrial 26S rRNA (PubMed:26268215). May play a role in the regulation of the cell cycle and the increased nucleolar activity that is associated with the cell proliferation (By similarity). Seems involved in the regulation of cell proliferation (By similarity). a cytidine in rRNA + S-adenosyl-L-methionine = a 5-methylcytidine in rRNA + H(+) + S-adenosyl-L-homocysteine Normal levels of methylation at cytosine 2860 of 25S rRNA, but slight reduction of mitochondrial 26S rRNA cytosine 1586 (m5C1586). Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Functions as a heterodimeric glycoprotein hormone with GPHB5 able to bind and activate the thyroid-stimulating hormone receptor (TSHR), leading to increased cAMP production. Plays a central role in controlling thyroid cell metabolism. Heterodimer with GPHB5; this heterodimer interacts with thyroid-stimulating hormone receptor (TSHR), and hence stimulates cAMP production. Belongs to the glycoprotein hormones subunit alpha family. +Catalyzes the phosphorylation of N-acetylmannosamine (ManNAc) to ManNAc-6-P. an N-acyl-D-mannosamine + ATP = ADP + an N-acyl-D-mannosamine 6-phosphate + H(+) Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 2/5. Homodimer. Belongs to the ROK (NagC/XylR) family. NanK subfamily. +May act as a GTPase-activating protein for Rab family protein(s). Homodimer (PubMed:18186464). Interacts with ACBD3 and ARFGEF1. Interacts with YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ and YWHAZ (PubMed:23572552). +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. Belongs to the FlgH family. +Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system. ATP + H2O + phosphate(out) = ADP + H(+) + 2 phosphate(in) The complex is composed of two ATP-binding proteins (PstB), two transmembrane proteins (PstC and PstA) and a solute-binding protein (PstS). Belongs to the ABC transporter superfamily. Phosphate importer (TC 3.A.1.7) family. +Expressed in roots, stems and flowers. Starts to be expressed at the end of S phase, reaches a peak at mitosis and then decreases. Belongs to the cyclin family. Cyclin AB subfamily. +Functions as a sodium-dependent vesicular transporter selective for proline, glycine, leucine and alanine. In contrast to other members of this neurotransmitter transporter family, does not appear to be chloride-dependent (By similarity). Localizes at synaptic junctions - at both pre- and post-synaptic sites - particularly in excitatory glutamatergic terminals. Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A17 subfamily. +Plays a role in the regulation of lipogenesis, especially in lactating mammary gland. Important for the biosynthesis of triglycerides with medium-length fatty acid chains. May modulate lipogenesis by interacting with MID1IP1 and preventing its interaction with ACACA. May function as transcriptional coactivator. May modulate the transcription factor activity of THRB (By similarity). Homodimer. Heterodimer with MID1IP1. Interacts with THRB and PLAGL1 (By similarity). Mainly expressed in tissues that synthesize triglycerides. Decreased lipid synthesis in the lactating mammary gland. Milk has reduced triglyceride content, causing reduced weight gain in nursing pups. Adults exhibit reduced body fat content. No effect on lipid synthesis in liver. No effect on the expression of thyroid hormone-induced lipogenic genes. Belongs to the SPOT14 family. +Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Belongs to the thiamine-phosphate synthase family. +Beta toxins bind voltage-independently at site-4 of sodium channels (Nav) and shift the voltage of activation toward more negative potentials thereby affecting sodium channel activation and promoting spontaneous and repetitive firing. Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). Does not affect the cardiac Nav1.5/SCN5A, the peripheral nerve channel Nav1.7/SCN9A, and the voltage-dependent potassium channel Kv1.5/KCNA5. Belongs to the long (4 C-C) scorpion toxin superfamily. Sodium channel inhibitor family. Beta subfamily. +Belongs to the bacterial ribosomal protein bL35 family. +Involved in transport from the endoplasmic reticulum to the Golgi apparatus. Interacts with BZIP28. Belongs to the small GTPase superfamily. SAR1 family. +E3 ubiquitin-protein ligase that plays a key role in innate antiviral immunity by mediating ubiquitination of CGAS and STING1 (PubMed:21289118, PubMed:29426904). In response to pathogen- and host-derived double-stranded DNA (dsDNA), targets STING1 to 'Lys-63'-linked ubiquitination, thereby promoting its homodimerization, a step required for the production of type I interferon IFN-beta (By similarity). Also mediate monoubiquitination of CGAS, thereby promoting CGAS oligomerization and subsequent activation (PubMed:29426904). Independently of its E3 ubiquitin ligase activity, positive regulator of TLR3 signaling. Potentiates extracellular double stranded RNA (dsRNA)-induced expression of IFNB1 and interferon-stimulated genes ISG15, IFIT1/ISG56, CXCL10, OASL and CCL5/RANTES (PubMed:22948160). Promotes establishment of an antiviral state by TLR3 ligand and TLR3-mediated chemokine induction following infection by hepatitis C virus (PubMed:22948160). S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Homooligomer. Interacts with STING1 (By similarity). Interacts with TICAM1 (PubMed:22948160). Widely expressed (at protein level). Up-regulated by IFN-alpha. Autoubiquitinated. Belongs to the TRIM/RBCC family. Extended N-terminus. Truncated N-terminus. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF-1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. PrfC subfamily. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +May play a role in the molecular organization of synapses and neuronal cell signaling. Could be an adapter protein linking ion channel to the subsynaptic cytoskeleton. May induce enrichment of PSD-95/SAP90 at the plasma membrane. Interacts with DLG4/PSD-95. Postsynaptic density of neuronal cells. Expressed in various brain areas. Belongs to the SAPAP family. +Catalyzes the NAD(+)-dependent oxidation of L-threonine to 2-amino-3-ketobutyrate. L-threonine + NAD(+) = (2S)-2-amino-3-oxobutanoate + H(+) + NADH Binds 2 Zn(2+) ions per subunit. Amino-acid degradation; L-threonine degradation via oxydo-reductase pathway; glycine from L-threonine: step 1/2. Homotetramer. Belongs to the zinc-containing alcohol dehydrogenase family. +Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+). Homodimer. Eukaryotic topoisomerase I and II can relax both negative and positive supercoils, whereas prokaryotic enzymes relax only negative supercoils. Belongs to the type II topoisomerase family. Extended C-terminus. Wrong genetic code used for translating the sequence. +Plays a role in maintaining the mitochondrial genome and in controlling the mtDNA escape. Involved in the regulation of mtDNA nucleotide structure and number. May have a dispensable role in early maturation of pre-rRNA (By similarity). Belongs to the YME2 family. +Belongs to the bacterial ribosomal protein bL36 family. +A probable RNA chaperone. Forms a complex with KhpB which binds to cellular RNA and controls its expression. Plays a role in peptidoglycan (PG) homeostasis and cell length regulation. Forms a complex with KhpB. Belongs to the KhpA RNA-binding protein family. +Spliced protein is a DNA polymerase used in PCR reactions. PI-TfuI recognizes and cleaves a minimal sequence of 16 base pairs (bp, 5'-TTTTAGGTCGCTATAT-3') cutting after T-8 in supercoiled DNA with either Mn(2+) or Mg(2+) as cofactor. Yields 5'-phosphate and 3'-OH ends. It only cleaves linear DNA with Mn(2+) and requires a 19-bp minimal recognition sequence. PI-TfuII is a highly active homing endonuclease using Mg(2+) as cofactor. Its minimal recognition and cleavage site is 21 bp (5'-ACGCGGATACAGACGGCTTTT-3') cutting after -7 on both linear or circular DNA substrates. Yields 5'-phosphate and 3'-OH ends. Its endonuclease activity is strongly inhibited by the 3' digestion product, which remains bound to the enzyme after the cleavage reaction. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) For PI-TfuII intein endonuclease. For PI-TfuI intein endonuclease. Optimum temperature is 70 degrees Celsius. This protein undergoes a protein self splicing that involves a post-translational excision of the two intervening regions (inteins) followed by peptide ligation. Belongs to the DNA polymerase type-B family. +Part of the ABC transporter complex RbsABC involved in ribose import. Responsible for energy coupling to the transport system. ATP + D-ribose(out) + H2O = ADP + D-ribose(in) + H(+) + phosphate The complex is composed of an ATP-binding protein (RbsA), two transmembrane proteins (RbsC) and a solute-binding protein (RbsB). Belongs to the ABC transporter superfamily. Ribose importer (TC 3.A.1.2.1) family. +Homotetramer. +Prenyltransferase that catalyzes in vivo the transfer of the heptaprenyl moiety of heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP). This reaction is an ether-bond-formation step in the biosynthesis of archaea-type G1P-based membrane lipids found in Bacillales. all-trans-heptaprenyl diphosphate + sn-glycerol 1-phosphate = 3-heptaprenyl-sn-glycero-1-phosphate + diphosphate Membrane lipid metabolism; glycerophospholipid metabolism. Homodimer. Belongs to the GGGP/HepGP synthase family. Group I subfamily. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Catalyzes the relaxation of negatively supercoiled DNA in the presence of ATP or dATP but not other nucleotides. Individual subunits have no activity. Not able to negatively supercoil DNA, it can however introduce positive supercoils in DNA. Relaxes positive supercoils in an ATP-dependent manner. Catenates and decatenates DNA. Generates dsDNA breaks in the presence of the quinolone antibiotic ciprofloxacin, showing it is a topoisomerase (PubMed:16313624). ATP-dependent breakage, passage and rejoining of double-stranded DNA. Maximal DNA relaxation at 5.0 mM MgCl(2) (PubMed:16313624). Inhibited by quinolone antibiotic ciprofloxacin and coumarin antibiotic novobiocin, but at much higher concentrations than is usual for DNA gyrase/topoisomerase (PubMed:16313624). A complex of TopoN and TopoM, possibly a heterotetramer (PubMed:16313624). Belongs to the type II topoisomerase GyrA/ParC subunit family. +This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. 16 ATP + 16 H2O + N2 + 8 reduced [2Fe-2S]-[ferredoxin] = 16 ADP + 6 H(+) + H2 + 2 NH4(+) + 8 oxidized [2Fe-2S]-[ferredoxin] + 16 phosphate Binds 1 [8Fe-7S] cluster per heterodimer. Binds 1 [7Fe-Mo-9S-C-homocitryl] cluster per subunit. Tetramer of two alpha and two beta chains. Forms complex with the iron protein (nitrogenase component 2). Belongs to the NifD/NifK/NifE/NifN family. +Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) Binds 1 zinc ion per subunit. Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. Belongs to the class-II aminoacyl-tRNA synthetase family. +Promotes the exchange of GDP for GTP in EF-1-alpha/GDP, thus allowing the regeneration of EF-1-alpha/GTP that could then be used to form the ternary complex EF-1-alpha/GTP/AAtRNA. Belongs to the EF-1-beta/EF-1-delta family. +Catalyzes the sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine. H2O + L-histidinol + 2 NAD(+) = 3 H(+) + L-histidine + 2 NADH Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 9/9. Belongs to the histidinol dehydrogenase family. +Homodimer. Belongs to the CutC family. Once thought to be involved in copper homeostasis, experiments in E.coli have shown this is not the case. +Murein-degrading enzyme that degrades murein glycan strands and insoluble, high-molecular weight murein sacculi, with the concomitant formation of a 1,6-anhydromuramoyl product. Lytic transglycosylases (LTs) play an integral role in the metabolism of the peptidoglycan (PG) sacculus. Their lytic action creates space within the PG sacculus to allow for its expansion as well as for the insertion of various structures such as secretion systems and flagella. Exolytic cleavage of the (1->4)-beta-glycosidic linkage between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues in peptidoglycan, from either the reducing or the non-reducing ends of the peptidoglycan chains, with concomitant formation of a 1,6-anhydrobond in the MurNAc residue. Attached to the inner leaflet of the outer membrane. The N-terminal domain does not have lytic activity and probably modulates enzymatic activity. The C-terminal domain is the catalytic active domain. In the N-terminal section; belongs to the bacterial solute-binding protein 3 family. In the C-terminal section; belongs to the transglycosylase Slt family. +Associates with the mother centriole. Truncated N-terminus. +Component of TORC2, which regulates cell cycle-dependent polarization of the actin-cytoskeleton and cell wall integrity. TORC2 controls polarity of the actin cytoskeleton, which is required for orienting the secretory pathway toward discrete growth sites, via the RHO1/PKC1/MAPK cell integrity pathway. The target of rapamycin complex 2 (TORC2) is composed of at least AVO1, AVO2, BIT61, LST8, TOR2 and TSC11. TORC2 likely forms a homodimer. Contrary to TORC1, TORC2 does not bind to and is not sensitive to FKBP-rapamycin. AVO2 is peripherally associated to AVO1 and TSC11. Present with 1180 molecules/cell in log phase SD medium. +Belongs to the carbohydrate kinase PfkB family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 1 family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. cyanate + 3 H(+) + hydrogencarbonate = 2 CO2 + NH4(+) Belongs to the cyanase family. +Catalyzes the hydrolysis of methenyl-H(4)MPT(+) to 5-formyl-H(4)MPT. 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H2O = H(+) + N(5)-formyl-5,6,7,8-tetrahydromethanopterin One-carbon metabolism; formaldehyde degradation; formate from formaldehyde (H(4)MPT route): step 3/5. Belongs to the MCH family. +Acts as a signaling molecule that communicates proliferative growth signals from the cytoplasm to the nucleus. It is involved in the positive regulation of cell cycle progression (PubMed:29851065). Plays a role for the localization and accumulation of the survival motor neuron protein SMN1 in sub-nuclear bodies, including gems and Cajal bodies. Induces neuron differentiation and stimulates axonal growth and formation of growth cone in spinal cord motor neurons. Plays a role in the splicing of cellular pre-mRNAs. May be involved in H(2)O(2)-induced neuronal cell death. Component of an import snRNP complex composed of KPNB1, SNUPN, SMN1 and ZNF259. Interacts (via C-terminal region) with SMN1 (via C-terminal region); the interaction occurs after treatment with serum. Interacts with elongation factor 1-alpha EEF1A1; the interaction occurs in a epidermal growth factor (EGF)-dependent manner. Interacts (via zinc fingers) with EGFR (via C-terminal cytoplasmic kinase domain); the interaction is negatively regulated in response to epidermal growth factor (EGF) stimulation and the EGFR kinase activity. May also bind to the PDGFR receptor. Colocalized with SMN1 in Gemini of coiled bodies (gems), Cajal bodies, axon and growth cones of neurons (By similarity). Localized predominantly in the cytoplasm in serum-starved cells growth arrested in G0 of the mitotic cell cycle. Localized both in the nucleus and cytoplasm at the G1 phase of the mitotic cell cycle. Accumulates in the subnuclear bodies during progression into the S phase of the mitotic cell cycle. Diffusely localized throughout the cell during mitosis. Colocalized with NPAT and SMN1 in nuclear bodies including gems (Gemini of coiled bodies) and Cajal bodies in a cell cycle-dependent manner. Translocates together with EEF1A1 from the cytoplasm to the nucleolus after treatment with mitogens. Colocalized with EGFR in the cytoplasm of quiescent cells. Translocates from the cytoplasm to the nucleus in a epidermal growth factor (EGF)-dependent manner. Expressed in fibroblast; weakly expressed in fibroblast of spinal muscular atrophy (SMA) patients. The disease may be caused by variants affecting the gene represented in this entry. Belongs to the ZPR1 family. +Transcriptional regulator that specifically binds DNA of heat shock promoter elements (HSE). Homotrimer. Hardly expressed in young leaves at 14 days after sowing (DAS). Expression detected in adult leaves at 28 DAS and increases with growing stage. By heat stress. The hydrophobic-rich region (HR-A/B) corresponds to the oligomerization domain. AHA motifs are transcriptional activator elements. Exhibits temperature-dependent phosphorylation. Belongs to the HSF family. Class A subfamily. +Histones H1 are necessary for the condensation of nucleosome chains into higher-order structures. Belongs to the histone H1/H5 family. +Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a regulator of ion transport in the distal nephron. The BCR(KLHL3) complex acts by mediating ubiquitination of WNK4, an inhibitor of potassium channel KCNJ1, leading to WNK4 degradation (By similarity). The BCR(KLHL3) complex also mediates ubiquitination and degradation of CLDN8, a tight-junction protein required for paracellular chloride transport in the kidney (By similarity). Protein modification; protein ubiquitination. Homodimer. Component of the BCR(KLHL3) E3 ubiquitin ligase complex, at least composed of CUL3 and KLHL3 and RBX1 (By similarity). Interacts with SLC12A3 (By similarity). Interacts with WNK1 and WNK4 (By similarity). Interacts with CLDN8 (By similarity). Phosphorylation at Ser-433 by PKA decreases the interaction with WNK4, Leading to inhibit WNK4 degradation by the BCR(KLHL3) complex. Phosphorylation at Ser-433 is increased by insulin. +A possible D,D-carboxypeptidase, that releases amino acids sequentially from a proteins C-terminus (PubMed:7972112, PubMed:12196546). Has zinc-dependent carboxypeptidase activity on synthetic depsipeptide substrates (PubMed:7972112). May serve to decrease cross-linking of peptidoglycan, promoting the highly sinusous motility of this spirochaete (Probable). Overexpression of the whole protein in E.coli leads to aberrant cell morphology and extrusion of the cytoplasm, while overexpression of a construct with the first 62 resides of the protein fused to PhoA does have this effect, suggesting the whole protein, not the lipoprotein moiety, is toxic (PubMed:7972112). Binds penicillin (PubMed:2647634, PubMed:7972112). Penicillin binding is covalent, does not require lipidation, and is zinc-dependent (PubMed:7972112, PubMed:12196546). While this protein has beta-lactamase activity in vitro, that is probably not its role in vivo, as T.pallidum is very sensitive to penicillin antibiotics (PubMed:12196546). A pathogen-specific membrane antigen (PubMed:2642466, PubMed:1372297). Most abundant of the membrane lipoproteins, only found in pathogenic treponemes, suggesting that it is an important structural moiety in the cell envelope of virulent treponemal subspecies. A lipopeptide corresponding to the first 6 mature residues induces host (human and mouse) cytokine release by monocyte cell lines via TLR2 and CD14; nonlipidated protein does not stimulate host cells (PubMed:10426995). Stimulates host (human) dendritic cell maturation to become MHC class II-positive antigen presenting cells via TLR2, which depends on lipidation; nonlipidated protein does not stimulate maturation (PubMed:11160304). Carboxypeptidase activity is stimulated by zinc (PubMed:7972112). Penicillin-binding is stimulated by zinc (PubMed:12196546). Probably a monomer; a non-lipidated construct (residues 22-434) is monomeric in solution but crystallizes as a homodimer. The N-terminus is blocked (PubMed:2642466). Present as a doublet of low abundance 48 kDa and high abundance 47 kDa proteins (PubMed:2647634, PubMed:2668192, PubMed:1372297). The longer form is probably due to readthrough of the stop codon; the extra amino acids at the C-terminus would be X-Lys-Arg-Gly-Val-Leu-Ser-Arg-Val-Ser, a peptide antibody against this sequence detects only the 48 kDa form (PubMed:2668192). A recombinant non-lipidated form (residues 20-434) is recognized by human antisera, indicating the lipidation site is not essential for antigenicity, although the acylated lipopeptide clearly is antigenic (PubMed:1372297, PubMed:10426995). The non-lipidated form binds also penicillin (PubMed:7972112). +Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA. guanosine(2445) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(2)-methylguanosine(2445) in 23S rRNA + S-adenosyl-L-homocysteine guanosine(2069) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(2)-methylguanosine(2069) in 23S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RlmKL family. +Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor. (S)-dihydroorotate + a quinone = a quinol + orotate Binds 1 FMN per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (quinone route): step 1/1. Monomer. Belongs to the dihydroorotate dehydrogenase family. Type 2 subfamily. +Implicated in mitochondrial protein import and macromolecular assembly. May facilitate the correct folding of imported proteins. May also prevent misfolding and promote the refolding and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix (By similarity). Forms a single seven-member ring complex, in tight association with the p63 protein. Testis. From the second half of the larval final-instar, through the first two days of pupal development. Shows ATPase activity. Belongs to the chaperonin (HSP60) family. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Some bacteria have evolved a zinc-coordinating structure that stabilizes the LID domain. Belongs to the adenylate kinase family. +Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis. ATP + beta-D-fructose 6-phosphate = ADP + beta-D-fructose 1,6-bisphosphate + H(+) Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 3/4. Homotetramer. Belongs to the phosphofructokinase type A (PFKA) family. +Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. However, the true cosubstrate could be (R)-1-amino-2-propanol O-2-phosphate, leading to cobinamide phosphate. Cofactor biosynthesis; adenosylcobalamin biosynthesis. Belongs to the CobD/CbiB family. +acetyl-CoA + H2O + oxaloacetate = citrate + CoA + H(+) Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate from oxaloacetate: step 1/2. Belongs to the citrate synthase family. +ATP-dependent DNA helicase required for initiation of viral DNA replication. It forms a complex with the viral E2 protein. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins. During the initial step, a dimer of E1 interacts with a dimer of protein E2 leading to a complex that binds the viral origin of replication with high specificity. Then, a second dimer of E1 displaces the E2 dimer in an ATP-dependent manner to form the E1 tetramer. Following this, two E1 monomers are added to each half of the site, which results in the formation of two E1 trimers on the viral ori. Subsequently, two hexamers will be created. The double hexamer acts as a bi-directional helicase machinery and unwinds the viral DNA and then recruits the host DNA polymerase to start replication. ATP + H2O = ADP + H(+) + phosphate Can form hexamers. Interacts with E2 protein; this interaction increases E1 DNA binding specificity. Interacts with host DNA polymerase subunit POLA2. Interacts with host single stranded DNA-binding protein RPA1. Interacts with host TOP1; this interaction stimulates the enzymatic activity of TOP1. Phosphorylated. Sumoylated. Belongs to the papillomaviridae E1 protein family. +Belongs to the ABC transporter superfamily. ABCC family. Conjugate transporter (TC 3.A.1.208) subfamily. +Belongs to the NAD(P)-dependent epimerase/dehydratase family. +Stealth proteins are part of a protein family that is conserved from bacteria to higher eukaryotes. Family members were first identified in microbes as proteins that help pathogens to elude the host innate immune system. Microbial stealth proteins are involved in the biosynthesis of exopolysaccharides. Stealth proteins are predicted to function as hexose-1-phosphoryltransferases. Belongs to the stealth family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 1 Zn(2+) ion per subunit. In cyanobacteria the RNAP catalytic core is composed of 2 alpha, 1 beta, 1 beta', 1 gamma and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. RpoC1 subfamily. +Phosphorylation-dependent transcription factor that stimulates transcription upon binding to the DNA cAMP response element (CRE), a sequence present in many viral and cellular promoters. Transcription activation is enhanced by the TORC coactivators which act independently of Ser-119 phosphorylation. Involved in different cellular processes including the synchronization of circadian rhythmicity and the differentiation of adipose cells. Interacts with PPRC1. Binds DNA as a dimer. This dimer is stabilized by magnesium ions. Interacts, through the bZIP domain, with the coactivators TORC1/CRTC1, TORC2/CRTC2 and TORC3/CRTC3. Interacts (phosphorylated form) with TOX3 (By similarity). When phosphorylated on Ser-119, binds CREBBP. Interacts with ARRB1. Binds to HIPK2 (By similarity). Interacts with SGK1 (By similarity). Interacts with CREBL2; regulates CREB1 phosphorylation, stability and transcriptional activity. Interacts with TSSK4; this interaction facilitates phosphorylation on Ser-119 (By similarity). Forms a complex with KMT2A and CREBBP (By similarity). Interacts with TOX4; CREB1 is required for full induction of TOX4-dependent activity and the interaction is increased by cAMP and inhibited by insulin (PubMed:34914893). At least 6 isoforms may be produced. Ubiquitously expressed. Phosphorylation of Ser-119 allows CREBBP binding. Stimulated by phosphorylation. Phosphorylated Ser-128 can be detected in the suprachiasmatic nucleus (SCN), the amygdala, the cortex, and the hippocampus but not in the striatum nor in the cerebellum. In the SCN, phosphorylation of Ser-128 and Ser-119 are stimulated by light exposure and submitted to circadian oscillations. In the retina, only phosphorylation of Ser-119 can be detected upon light exposure. Phosphorylation of both Ser-119 and Ser-128 in the SCN regulates the activity of CREB and participates in circadian rhythm generation. Phosphorylated upon calcium influx by CaMK4 and CaMK2 on Ser-119. CaMK4 is much more potent than CAMK2 in activating CREB. Phosphorylated by CaMK2 on Ser-128. Phosphorylation of Ser-128 blocks CREB-mediated transcription even when Ser-119 is phosphorylated. Phosphorylated by CaMK1. Phosphorylation of Ser-271 by HIPK2 in response to genotoxic stress promotes CREB1 activity, facilitating the recruitment of the coactivator CBP (By similarity). Phosphorylated at Ser-119 by RPS6KA3, RPS6KA4 and RPS6KA5 in response to mitogenic or stress stimuli. CREBL2 positively regulates phosphorylation at Ser-119 thereby stimulating CREB1 transcriptional activity. In liver, phosphorylation is induced by fasting or glucagon in a circadian fashion. Phosphorylated by TSSK4 on Ser-119 (By similarity). Sumoylated with SUMO1. Sumoylation on Lys-290, but not on Lys-271, is required for nuclear localization of this protein. Sumoylation is enhanced under hypoxia, promoting nuclear localization and stabilization (By similarity). Belongs to the bZIP family. +ATP-binding (A) component of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. In this organism these probably include biotin, thiamine precursor, niacin, pantothenic acid, queuosine precursor, riboflavin and thiamine. Uptake of niacin or riboflavin into proteosomes containing EcfA1A2T and Niax or RibU has been demonstrated. Uptake requires hydrolyzable Mg-ATP and is substrate-specific; NiaX-containing proteosomes did not transport riboflavin. Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). In L.lactis forms a stable complex with EcfA' and EcfT and substrate-binding components. In E.coli forms a stable complex with EcfA, EcfT and individually with 3 tested substrate-binding components (BioY, NiaX and ThiT) with a stoichiometry of 1.1:1:1. The core ECF complex interacts with a number of substrate-specific binding components, including BioY, BioY2, HmpT, NiaX, PanT, QueT, RibU and ThiT. Belongs to the ABC transporter superfamily. Energy-coupling factor EcfA family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Catalyzes the transfer of the carbamoyl group from carbamoyl phosphate to the delta-amino group of N(2)-acetyl-L-ornithine to produce N(2)-acetyl-L-citrulline. This is a step in an alternative arginine biosynthesis pathway. The enzyme has no activity with ornithine. carbamoyl phosphate + N(2)-acetyl-L-ornithine = H(+) + N(2)-acetyl-L-citrulline + phosphate Carboxylation at Lys-302 increases the catalytic activity of the enzyme (PubMed:20695527). Is potently inhibited by N(alpha)-acetyl-N(delta)-phosphonoacetyl-L-ornithine (PALAO) (PubMed:16585758). Amino-acid biosynthesis; L-arginine biosynthesis. Homotrimer. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. AOTCase family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +There are at least 12 different components in Midge globin. Belongs to the globin family. +RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs. Homohexamer. Belongs to the Hfq family. +May play a role in neuronal and neurobehavioral development. Belongs to the UPF0524 family. Contaminating sequence. Potential poly-A sequence. +diphosphate + H2O = H(+) + 2 phosphate Binds tightly a transition metal ion; prefers Co(2+) over Mn(2+). Mg(2+) ions are required for optimal catalytic activity. Inhibited by AMP and ADP with 25% and 35% of activity remaining, respectively, at saturating conditions. Activated 5-fold by diadenosine polyphosphates(Ap[n]A) with n>2 (Ap3A, Ap4A, Ap5A, Ap6A) at saturating conditions. Homodimer. Belongs to the PPase family. +Belongs to the herpesviridae UL92 family. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. Required for limiting lipid storage in lipid droplets (By similarity). Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits. The coatomer is cytoplasmic or polymerized on the cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it. Present within the clusters of tubulo-vesicular structures of Golgi membrane and cis-Golgi membranes. +Methyltransferase that performs automethylation at Met-207 (By similarity). No other methyl-accepting substrate has been identified yet (By similarity). Component of the velvet transcription factor complex that acts as a global regulator for secondary metabolite gene expression (PubMed:15075281). Controls the expression of the sterigmatocystin, penicillin, and lovastatin gene clusters (PubMed:15075281). Controls light-dependent formation of the velB-vosA complex, veA protein modification, and is required for light-mediated inhibition of sexual development (By similarity). Within the velvet complex, controls light-dependent secondary metabolism (By similarity). Involved in the defense response against Drosophila melanogaster larval grazing (By similarity). L-methionyl-[protein] + S-adenosyl-L-methionine = S-adenosyl-L-homocysteine + S-methyl-L-methionyl-[protein] Component of the heterotrimeric velvet complex composed of laeA, veA and velB; VeA acting as a bridging protein between laeA and velB (By similarity). Expression is negatively regulated by the transcription factor AflR, as well as by two signal transduction elements, protein kinase A and RasA. Self-methylates at Met-207. Reduces secondary metabolite production, including sterigmatocystin, a carcinogen biochemically related to the agricultural contaminant aflatoxin (PubMed:15075281). Belongs to the methyltransferase superfamily. LaeA methyltransferase family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Catalytic component of the signal peptidase complex (SPC) which catalyzes the cleavage of N-terminal signal sequences from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum (By similarity). Specifically cleaves N-terminal signal peptides that contain a hydrophobic alpha-helix (h-region) shorter than 18-20 amino acids (By similarity). Cleavage of hydrophobic, N-terminal signal or leader sequences from secreted and periplasmic proteins. Component of the signal peptidase complex (SPC) composed of a catalytic subunit SEC11 and three accessory subunits SPC1, SPC2 and SPC3 (By similarity). The complex induces a local thinning of the ER membrane which is used to measure the length of the signal peptide (SP) h-region of protein substrates. This ensures the selectivity of the complex towards h-regions shorter than 18-20 amino acids (By similarity). SPC associates with the translocon complex (By similarity). The C-terminal short (CTS) helix is essential for catalytic activity. It may be accommodated as a transmembrane helix in the thinned membrane environment of the complex, similarly to the signal peptide in the complex substrates. Belongs to the peptidase S26B family. +Catalyzes the hydrolysis of methenyl-H(4)MPT(+) to 5-formyl-H(4)MPT. 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H2O = H(+) + N(5)-formyl-5,6,7,8-tetrahydromethanopterin One-carbon metabolism; formaldehyde degradation; formate from formaldehyde (H(4)MPT route): step 3/5. Belongs to the MCH family. +The S-layer is a paracrystalline mono-layered assembly of proteins which coat the surface of bacteria. This bacterium is covered by a S-layer with oblique (p2) symmetry. +Calcium/calmodulin-dependent protein kinase that functions autonomously after Ca(2+)/calmodulin-binding and autophosphorylation, and is involved in sarcoplasmic reticulum Ca(2+) transport in skeletal muscle and may function in dendritic spine and synapse formation and neuronal plasticity. In slow-twitch muscles, is involved in regulation of sarcoplasmic reticulum (SR) Ca(2+) transport and in fast-twitch muscle participates in the control of Ca(2+) release from the SR through phosphorylation of the ryanodine receptor-coupling factor triadin. In the central nervous system, it is involved in the regulation of neurite formation and arborization. It may participate in the promotion of dendritic spine and synapse formation and maintenance of synaptic plasticity which enables long-term potentiation (LTP) and hippocampus-dependent learning (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by Ca(2+)/calmodulin. Binding of calmodulin results in conformational change that relieves intrasteric autoinhibition and allows autophosphorylation of Thr-287 which turns the kinase in a constitutively active form and confers to the kinase a Ca(2+)-independent activity. CAMK2 is composed of 4 different chains: alpha (CAMK2A), beta (CAMK2B), gamma (CAMK2G), and delta (CAMK2D). The different isoforms assemble into homo- or heteromultimeric holoenzymes composed of 12 subunits with two hexameric rings stacked one on top of the other (By similarity). Additional isoforms seem to exist. By cocaine in cardiomyocytes. The CAMK2 protein kinases contain a unique C-terminal subunit association domain responsible for oligomerization. Autophosphorylation of Thr-287 following activation by Ca(2+)/calmodulin. Phosphorylation of Thr-287 locks the kinase into an activated state (By similarity). Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. CaMK subfamily. +Involved in a peptide intake transport system that plays a role in the resistance to antimicrobial peptides. Part of the sapA-sapB-sapC-sapD-sapF operon, RNA detected in mid-log phase cells. Loss of resistance to protamine. Belongs to the binding-protein-dependent transport system permease family. OppBC subfamily. +Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). H(+) + orotidine 5'-phosphate = CO2 + UMP Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. Homodimer. Belongs to the OMP decarboxylase family. Type 1 subfamily. +Catalyzes the specific phosphorylation of 1,6-anhydro-N-acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. Is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling. 1,6-anhydro-N-acetyl-beta-muramate + ATP + H2O = ADP + H(+) + N-acetyl-D-muramate 6-phosphate Amino-sugar metabolism; 1,6-anhydro-N-acetylmuramate degradation. Cell wall biogenesis; peptidoglycan recycling. Belongs to the anhydro-N-acetylmuramic acid kinase family. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Catalyzes the irreversible NADPH-dependent deamination of GMP to IMP. It functions in the conversion of nucleobase, nucleoside and nucleotide derivatives of G to A nucleotides, and in maintaining the intracellular balance of A and G nucleotides. IMP + NADP(+) + NH4(+) = GMP + 2 H(+) + NADPH Belongs to the IMPDH/GMPR family. GuaC type 2 subfamily. +G-protein coupled receptor for the bioactive lysosphingolipid sphingosine 1-phosphate (S1P) that seems to be coupled to the G(i) subclass of heteromeric G proteins. Signaling leads to the activation of RAC1, SRC, PTK2/FAK1 and MAP kinases. Plays an important role in cell migration, probably via its role in the reorganization of the actin cytoskeleton and the formation of lamellipodia in response to stimuli that increase the activity of the sphingosine kinase SPHK1. Required for normal chemotaxis toward sphingosine 1-phosphate. Required for normal embryonic heart development and normal cardiac morphogenesis. Plays an important role in the regulation of sprouting angiogenesis and vascular maturation. Inhibits sprouting angiogenesis to prevent excessive sprouting during blood vessel development. Required for normal egress of mature T-cells from the thymus into the blood stream and into peripheral lymphoid organs. Plays a role in the migration of osteoclast precursor cells, the regulation of bone mineralization and bone homeostasis. Plays a role in responses to oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine by pulmonary endothelial cells and in the protection against ventilator-induced lung injury. Interacts with GNAI1 and GNAI3. Recruited to caveolin-enriched plasma membrane microdomains in response to oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine. Ligand binding leads to receptor internalization (By similarity). Expressed in a wide variety of tissues with highest levels in brain, heart and spleen. Lower levels found in kidney, liver, lung, muscle, placenta, thymus, and uterus. Very low levels in intestine, stomach and testis. According to PubMed:9931453, expressed modestly in apparent endothelial cells surrounding some blood vessels (e.g. aortic trunk). Palmitoylated by ZDHHC5. Palmitoylation is required for targeting to plasma membrane, enabling G(i) coupling. Embryonic lethality, due to impaired vascular maturation and defects in heart development. Embryos appear normal up to 11.5 dpc, but after that they display massive hemorrhage. They have a normally arborized vascular network, but present excessive sprouting angiogenesis and severe aberrations in vessel size. Their aorta and other arteries are not properly enveloped by vascular smooth muscle cells, causing hemorrhage. Likewise, small blood vessels show a marked reduction in the number of vascular pericytes. In addition, mutants display defects in heart morphogenesis, with reduced myocardial tissue and altered morphology of the heart wall and the trabeculae (PubMed:11032855, PubMed:14732704, PubMed:21668976, PubMed:22951644). At 12.5 dpc, mutant embryos also show a massive cell loss in the forebrain (PubMed:16314531). Conditional knockout in endothelial cells leads to the same vascular maturation defect as that seen in homozygous knockout mice (PubMed:12869509). Conditional knockout in fibroblasts leads to defects in chemotaxis, probably due to defects in the activation of SRC and PTK2/FAK1, resulting in defects in the reorganization of the actin cytoskeleton and lamellipodia formation (PubMed:11726541). A T-cell-specific knockout leads to a defect in the egress of mature T-cells from the thymus into the periphery (PubMed:14737169). Conditional knockout in osteoclast precursors leads to osteoporosis, due to impaired migration of osteoclast precursors and increased osteoclast attachment to the bone (PubMed:19204730). Belongs to the G-protein coupled receptor 1 family. +Transcriptional repressor of genes that require a bHLH protein for their transcription. May act as a negative regulator of myogenesis by inhibiting the functions of MYOD1 and ASH1. Binds DNA on N-box motifs: 5'-CACNAG-3' with high affinity and on E-box motifs: 5'-CANNTG-3' with low affinity. May play a role in a functional FA core complex response to DNA cross-link damage, being required for the stability and nuclear localization of FA core complex proteins, as well as for FANCD2 monoubiquitination in response to DNA damage (By similarity). Interacts with SIRT1. Interacts weakly with TLE2. Interacts with HES6 (By similarity). Transcription repression requires formation of a complex with a corepressor protein of the Groucho/TLE family. Interacts (via WPRW motif) with TLE1. Interacts with an FA complex, composed of FANCA, FANCF, FANCG and FANCL, but not of FANCC, nor FANCE (By similarity). Present in all tissues examined but highest in epithelial cells and in mesoderm-derived tissues such as embryonal muscle cells. Has a particular type of basic domain (presence of a helix-interrupting proline) that binds to the N-box (CACNAG), rather than the canonical E-box (CANNTG). The C-terminal WRPW motif is a transcriptional repression domain necessary for the interaction with Groucho/TLE family members, transcriptional corepressors recruited to specific target DNA by Hairy-related proteins. The bHLH, as well as cooperation between the central Orange domain and the C-terminal WRPW motif, is required for transcriptional repressor activity. +Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. Cleavage of peptide bonds with very broad specificity. The formation of the proteasomal ATPase PAN-20S proteasome complex, via the docking of the C-termini of PAN into the intersubunit pockets in the alpha-rings, triggers opening of the gate for substrate entry. Interconversion between the open-gate and close-gate conformations leads to a dynamic regulation of the 20S proteasome proteolysis activity. The 20S proteasome core is composed of 14 alpha and 14 beta subunits that assemble into four stacked heptameric rings, resulting in a barrel-shaped structure. The two inner rings, each composed of seven catalytic beta subunits, are sandwiched by two outer rings, each composed of seven alpha subunits. The catalytic chamber with the active sites is on the inside of the barrel. Has a gated structure, the ends of the cylinder being occluded by the N-termini of the alpha-subunits. Is capped at one or both ends by the proteasome regulatory ATPase, PAN. Belongs to the peptidase T1B family. +Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate. (2R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (2S)-2-acetolactate + H(+) + NADPH (2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP(+) = (S)-2-ethyl-2-hydroxy-3-oxobutanoate + H(+) + NADPH Binds 2 magnesium ions per subunit. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 2/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 2/4. Belongs to the ketol-acid reductoisomerase family. +May act as a serine protease inhibitor, since it possess the kazal serine protease inhibitor signature (Probable). The recombinant peptide does not produce toxic effects on insects (PubMed:31870846). Expressed by the venom gland. Monoisotopic mass. The peptide presented here consists of a single Kazal domain but is suggested to be derived from a multidomain Kazal protein after proteolytic cleavage. +Belongs to the eukaryotic ribosomal protein eL14 family. +GTPase activator for the nuclear Ras-related regulatory protein GSP1 (Ran), converting it to the putatively inactive GDP-bound state. Causes conditional lethality. Strains bearing this mutation do not grow at temperatures exceeding 30 degrees Celsius. Present with 52200 molecules/cell in log phase SD medium. Belongs to the RNA1 family. +Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) Binds 1 zinc ion per subunit. Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. Belongs to the class-II aminoacyl-tRNA synthetase family. +Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. Homohexamer. The homohexamer assembles into an open ring structure. Belongs to the Rho family. +Converts stearoyl-ACP to oleoyl-ACP by introduction of a cis double bond between carbons 9 and 10 of the acyl chain. 2 H(+) + O2 + octadecanoyl-[ACP] + 2 reduced [2Fe-2S]-[ferredoxin] = (9Z)-octadecenoyl-[ACP] + 2 H2O + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 2 Fe(2+) ions per subunit. Lipid metabolism; fatty acid metabolism. Homodimer. In green tissue, found in chloroplasts. In non-photosynthetic tissue, found in plastids. Belongs to the fatty acid desaturase type 2 family. +Mediates secretion of glycanase ExsH. Part of a type I secretion system composed of PrsD and PrsE. Belongs to the ABC transporter superfamily. Extended N-terminus. +Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction: the enzyme is irreversibly inactivated. a 6-O-methyl-2'-deoxyguanosine in DNA + L-cysteinyl-[protein] = a 2'-deoxyguanosine in DNA + S-methyl-L-cysteinyl-[protein] a 4-O-methyl-thymidine in DNA + L-cysteinyl-[protein] = a thymidine in DNA + S-methyl-L-cysteinyl-[protein] This enzyme catalyzes only one turnover and therefore is not strictly catalytic. According to one definition, an enzyme is a biocatalyst that acts repeatedly and over many reaction cycles. Belongs to the MGMT family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Methylates ribosomal protein L11. L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. PrmA family. +Belongs to the aromatic acid exporter ArAE (TC 2.A.85) family. +Involved in the import of GDP-mannose from the cytoplasm into the Golgi lumen. Homooligomer. Belongs to the TPT transporter family. SLC35D subfamily. +Type IV dipeptidyl-peptidase which removes N-terminal dipeptides sequentially from polypeptides having unsubstituted N-termini provided that the penultimate residue is proline. Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, from a polypeptide, preferentially when Yaa is Pro, provided Zaa is neither Pro nor hydroxyproline. Lysosome-like vacuoles. Belongs to the peptidase S9B family. +Belongs to the IIV-6 357R family. +GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Toroid-shaped homodecamer, composed of two pentamers of five dimers. Belongs to the GTP cyclohydrolase I family. +Involved in synthesis of starch. Catalyzes the synthesis of ADP-glucose, a molecule that serves as an activated glycosyl donor for alpha-1,4-glucan synthesis. Essential for starch synthesis in leaf chloroplasts and endosperm amyloplasts. alpha-D-glucose 1-phosphate + ATP + H(+) = ADP-alpha-D-glucose + diphosphate Activated by 3'phosphoglycerate, inhibited by orthophosphate. Allosteric regulation. Glycan biosynthesis; starch biosynthesis. Heterotetramer composed of two small and two large subunits. Expressed in leaves and stems. Expressed in developing seeds from 10 to 12 days after flowering (DAF). Belongs to the bacterial/plant glucose-1-phosphate adenylyltransferase family. +Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O Binds 1 Mg(2+) ion per subunit. Homooctamer; tetramer of dimers. Reaction proceeds via a syn dehydration. Belongs to the mandelate racemase/muconate lactonizing enzyme family. RhamD subfamily. +Belongs to the recoverin family. +Binds to 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL14 family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Almost completely overlaps APS1. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +a 6-phospho-beta-D-galactoside + H2O = an alcohol + D-galactose 6-phosphate Carbohydrate metabolism; lactose degradation; D-galactose 6-phosphate and beta-D-glucose from lactose 6-phosphate: step 1/1. Belongs to the glycosyl hydrolase 1 family. +Structural component of striated muscles which plays a role in myofibrillogenesis. Probably involved in the assembly of myosin into sarcomeric A bands in striated muscle (PubMed:11448995, PubMed:16205939). Has serine/threonine protein kinase activity and phosphorylates N-cadherin CDH2 and sodium/potassium-transporting ATPase subunit ATP1B1 (By similarity). Binds (via the PH domain) strongly to phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), and to a lesser extent to phosphatidylinositol 3-phosphate (PtdIns(3)P), phosphatidylinositol 4-phosphate (PtdIns(4)P), phosphatidylinositol 5-phosphate (PtdIns(5)P) and phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) (PubMed:28826662). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts (via protein kinase domain 2) with CDH2 and (via protein kinase domain 1) with ATP1B1 (By similarity). Isoform 3 interacts with TTN/titin and calmodulin (PubMed:11448995, PubMed:11717165). Isoform 3 interacts with ANK1 isoform Mu17/ank1.5 (PubMed:12527750). In differentiating skeletal muscle cells, isoform 3 primarily localizes to the sarcomeric M-line and less frequently to the Z-disk (PubMed:12527750). Isoform 3 colocalizes with ANK1 isoform Mu17/ank1.5 at the M-line in differentiated skeletal muscle cells (PubMed:12527750). Colocalizes with CDH2 and ATP1B1 to the sarcolemma and to intercalating disks in cardiac muscles. Colocalizes with ATP1B1 to M line and Z line in cardiac muscles. Additional isoforms seem to exist. Autophosphorylated by protein kinase domains 1 and 2. A chromosomal aberration involving OBSCN has been found in Wilms tumor. Translocation t(1;7)(q42;p15) with PTHB1. Lacks the kinase domain. Initially described as obscurin. Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. Initially the name obscurin was used to describe isoform 3 which lacks the kinase domains. +Hexosyltransferase involved in N-glycan biosynthetic pathway that takes place under low-salt conditions (1.75 M instead of 3.4 M). Participates in the formation of the tetrasaccharide present at 'Asn-532' of S-layer glycoprotein Csg, consisting of a sulfated hexose, 2 hexoses and rhamnose. Involved in the addition of sugar 3 to the disaccharide-charged dolichol phosphate in the tetrasaccharide. Protein modification; protein glycosylation. Cell surface structure biogenesis; S-layer biogenesis. Impaired formation of the tetrasaccharide present at 'Asn-532' of S-layer glycoprotein Csg. No effect on 'Asn-47' and 'Asn-117' glycosylation of S-layer glycoprotein Csg. Belongs to the glycosyltransferase group 1 family. +Probably oxidoreductase that, when reduced, rapidly reacts with molecular oxygen, a hallmark of flavoprotein oxidases. A large panel of alcohols, including carbohydrates, steroids and secondary alcohols were tested as potential substrates, but none has been identified so far. Binds 1 FAD per subunit in a bicovalent manner. The FAD cofactor is bound via a bicovalent 6-S-cysteinyl, 8alpha-N1-histidyl FAD linkage. Belongs to the oxygen-dependent FAD-linked oxidoreductase family. +Converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP. H2O + holo-[ACP] = (R)-4'-phosphopantetheine + apo-[ACP] + H(+) Belongs to the AcpH family. Could be the product of a pseudogene. The N-terminus is shorter than in related proteins. +Shows antibacterial activity against S.aureus and S.uberis. Expressed by the skin dorsal glands. +Acts as a major beta-cyanoalanine synthase. The cyanoalanine synthesis reaction is more efficient than the cysteine synthase activity. Probably unable to interact with SAT and to form the decameric Cys synthase complex (CSC) and is therefore not an enzymatically true OASTL protein. Probably involved in the detoxification of cyanide that arises from ethylene biosynthesis. Maintains a low level of cyanide for proper root hair development. hydrogen sulfide + O-acetyl-L-serine = acetate + L-cysteine hydrogen cyanide + L-cysteine = 3-cyano-L-alanine + H(+) + hydrogen sulfide kcat is 120 min(-1) for O(3)-acetyl-L-serine for the cysteine synthase activity, kcat is 90 min(-1) for Na(2)S for the cysteine synthase activity, kcat is 160 min(-1) for cysteine for the L-3-cyanoalanine synthase activity, kcat is 130 min(-1) for KCN for the L-3-cyanoalanine synthase activity. Mainly expressed in mature rosette leaves. Also detected in roots, young rosette leaves, stems, cauline leaves, and flowers. Defective in root hair formation and accumulates cyanide in root tissues. No effects on growth. Belongs to the cysteine synthase/cystathionine beta-synthase family. +Ca(2+)-regulated actin-binding protein (By similarity). Binds actin microfilaments (MFs). Involved in actin filament bundling, severing and capping. Caps the barbed end of actin filaments and is able to sever them in a calcium-dependent manner (By similarity). Belongs to the villin/gelsolin family. +Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12. [sulfur carrier]-SH + AH2 + L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 2 S-adenosyl-L-methionine = 3-methylsulfanyl-L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Belongs to the methylthiotransferase family. RimO subfamily. +May be involved in copper-dependent ATP7A trafficking between the trans-Golgi network and vesicles in the cell periphery. Belongs to the CCDC93 family. +Catalyzes the transfer of succinyl-CoA to arginine to produce N(2)-succinylarginine. L-arginine + succinyl-CoA = CoA + H(+) + N(2)-succinyl-L-arginine Amino-acid degradation; L-arginine degradation via AST pathway; L-glutamate and succinate from L-arginine: step 1/5. Belongs to the arginine N-succinyltransferase family. +This protein is an aporepressor. When complexed with L-tryptophan it binds the operator region of the trp operon (5'-ACTAGT-'3') and prevents the initiation of transcription. The complex also regulates trp repressor biosynthesis by binding to its regulatory region. Homodimer. Belongs to the TrpR family. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Catalyzes the transfer of L-fucose, from a guanosine diphosphate-beta-L-fucose, to the N-acetyl glucosamine (GlcNAc) of a distal alpha2,3 sialylated lactosamine unit of a glycoprotein- or glycolipid-linked sialopolylactosamines chain or of a distal or internal lactosamine unit of a neutral glycoprotein- or glycolipid-linked polylactosamines chain through an alpha-1,3 glycosidic linkage and participates in surface expression of the sialyl Lewis X (sLe(x)), Lewis X (Le(x)) and non sialylated VIM2 determinants. Moreover transfers fucose to H-type 2 (Fucalpha1-2Galbeta1-4GlcNAc) chain acceptor substrates and participates in difucosylated sialyl Lewis x determinants. Also fucosylates a polylactosamine substrate having a 6 sulfate modification at the GlcNAc moiety and gives rise to sialyl and non-sialyl 6-sulfo lewis X. Does not have activity towards type 1 ((Galbeta1-3GlcNAc)) and H-type 1 chain (Fucalpha1-2Galbeta1-3GlcNAc) acceptors substrates. a beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + GDP-beta-L-fucose = a beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl derivative + GDP + H(+) an N-acetyl-alpha-neuraminyl-(2->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + GDP-beta-L-fucose = an alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-beta-D-GlcNAc derivative + GDP + H(+) an alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-beta-D-GlcNAc derivative + GDP-beta-L-fucose = an alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-beta-D-GlcNAc derivative + GDP + H(+) beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + GDP-beta-L-fucose = beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + GDP + H(+) beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + GDP-beta-L-fucose = beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + GDP + H(+) GDP-beta-L-fucose + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide = GDP + H(+) + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide beta-D-galactosyl-(1->4)-N-acetyl-D-glucosamine + GDP-beta-L-fucose = beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-D-glucosamine + GDP + H(+) GDP-beta-L-fucose + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosamine = GDP + H(+) + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosamine GDP-beta-L-fucose + lactose = beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-D-glucose + GDP + H(+) alpha-L-Fuc-(1->2)-beta-D-Gal-(1->4)-D-Glc + GDP-beta-L-fucose = alpha-L-Fuc-(1->2)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-D-Glc + GDP + H(+) a beta-D-galactosyl-(1->4)-N-acetyl-beta-D-6-sulfooxy-glucosaminyl derivative + GDP-beta-L-fucose = a beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-6-sulfooxy-glucosaminyl derivative + GDP + H(+) Protein modification; protein glycosylation. Homodimer and monomer. Monomer (secreted form). Membrane-bound form in trans cisternae of Golgi. N-glycosylated. Proteolytic cleavage releases a secreted glycoform of 43 kDa. Belongs to the glycosyltransferase 10 family. +Receptor for TNFSF18. Seems to be involved in interactions between activated T-lymphocytes and endothelial cells and in the regulation of T-cell receptor-mediated cell death. Mediated NF-kappa-B activation via the TRAF2/NIK pathway (By similarity). Binds to TRAF1, TRAF2, and TRAF3, but not TRAF5 and TRAF6 (By similarity). Binds through its C-terminus to SIVA1/SIVA. Preferentially expressed in activated T lymphocytes. Up-regulated in peripherical mononuclear cells after antigen stimulation/lymphocyte activation. +Catalyzes the oxidation of mono- and o-diphenols to o-diquinones. 2 catechol + O2 = 2 1,2-benzoquinone + 2 H2O Binds 2 copper ions per subunit. Belongs to the tyrosinase family. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. Belongs to the FlgI family. +ATP + oxaloacetate = ADP + CO2 + phosphoenolpyruvate Carbohydrate biosynthesis; gluconeogenesis. Homodimer. Belongs to the phosphoenolpyruvate carboxykinase (ATP) family. +Homodimer. In response to low temperature. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient (By similarity). a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 6 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Paired-like homeobox transcription factor involved in embryogenesis (PubMed:27578796, PubMed:30479355). May act as a regulator of embryo genome activation (PubMed:27578796). Binds to a 36 bp DNA elements containing a 5'-TAATCC-3' sequence motif, referred to as EEA motif (EGA-enriched Alu-motif), present in the promoters of target genes activated in early embryos (PubMed:27578796, PubMed:30479355). Inactive transcriptional activity. During early embryo development, its expression is restricted to the 4-cell to 8-cell stage of the preimplantation embryo. The homeobox contain essential residues (Ile-54, Lys-57, Ala-61) for binding to the 5'-TAATCC-3' motif of the targe gene promoters. The homeobox is incomplete and cannot bind to the 36 bp motif found in the promoters of the target genes. The 9aaTAD motif is a conserved putative nine amino acid transactivation motifs in C-terminus of the LEUTX region. Belongs to the paired homeobox family. +Metallocarboxypeptidase that mediates deglutamylation of tubulin and non-tubulin target proteins. Catalyzes the removal of polyglutamate side chains present on the gamma-carboxyl group of glutamate residues within the C-terminal tail of alpha- and beta-tubulin. Cleaves alpha- and gamma-linked polyglutamate tubulin side-chain, as well as the branching point glutamate. Also catalyzes the removal of alpha-linked glutamate residues from the carboxy-terminus of alpha-tubulin. Mediates deglutamylation of nucleotidyltransferase CGAS, leading to CGAS antiviral defense response activation. gamma-L-glutamyl-L-glutamyl-[protein] + H2O = L-glutamate + L-glutamyl-[protein] (L-glutamyl)(n+1)-gamma-L-glutamyl-L-glutamyl-[protein] + H2O = (L-glutamyl)(n)-gamma-L-glutamyl-L-glutamyl-[protein] + L-glutamate C-terminal L-alpha-aminoacyl-L-glutamyl-[tubulin] + H2O = C-terminal L-alpha-aminoacyl-[tubulin] + L-glutamate C-terminal L-alpha-aminoacyl-L-glutamyl-L-glutamyl-[tubulin] + H2O = C-terminal L-alpha-aminoacyl-L-glutamyl-[tubulin] + L-glutamate Binds 1 zinc ion per subunit. Mainly cytoplasmic. Slight accumulation in the nucleus is observed. Colocalizes with alpha-tubulin in the mitotic spindle and with midbody microtubules in the intercellular bridges formed during cytokinesis. Belongs to the peptidase M14 family. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit. S-adenosyl-L-methionine + uridine(2552) in 23S rRNA = 2'-O-methyluridine(2552) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase RlmE family. +Protein modifier that is covalently attached to lysine residues of substrate proteins, thereby targeting them for proteasomal degradation. The tagging system is termed pupylation. Protein degradation; proteasomal Pup-dependent pathway. Strongly interacts with the proteasome-associated ATPase ARC through a hydrophobic interface; the interacting region of Pup lies in its C-terminal half. There is one Pup binding site per ARC hexamer ring. The N-terminal unstructured half of Pup provides a signal required to initiate unfolding and degradation by the proteasome but is not needed for pupylation, while the C-terminal helical half of Pup interacts with ARC to target proteins to the proteasome. Is modified by deamidation of its C-terminal glutamine to glutamate by the deamidase Dop, a prerequisite to the subsequent pupylation process. Belongs to the prokaryotic ubiquitin-like protein family. +Responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox center in the PyrD type B subunit to the ultimate electron acceptor NAD(+). Binds 1 [2Fe-2S] cluster per subunit. Binds 1 FAD per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (NAD(+) route): step 1/1. Heterotetramer of 2 PyrK and 2 PyrD type B subunits. Belongs to the PyrK family. +Required for assembly or stability of RuBisCO. Acts at a postchaperonin step to fold and/or assemble the large subunit (rbcL) into RuBisCO. RAF1 brackets an rbcL dimer (rbcL(2)), leading to rbcL(8)-RAF1(4) complex formation. In the next step, RBCS displaces RAF1, thus resulting in holoenzyme formation. Homodimer. Has 3 domains, the N-terminal alpha-helical domain, an extended flexible linker and the C-terminal beta-sheet domain. The N-terminal alpha-helical domain stabilizes RbcL dimers and RbcL dimer-dimer interactions, facilitating RbcL(8) formation (PubMed:26237510). The C-terminal beta-sheet domain probably dimerizes Raf1 (Probable). The 2 C-terminal beta-sheet domains are swapped and pack against each other to form the dimer interface (By similarity). Belongs to the RAF family. +Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS11 family. +H2O + L-glutamate + NAD(+) = 2-oxoglutarate + H(+) + NADH + NH4(+) Homohexamer. Belongs to the Glu/Leu/Phe/Val dehydrogenases family. +Phosphatidylinositol (PtdIns) phosphatase that specifically hydrolyzes the 5-phosphate of phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P3) to produce PtdIns(3,4)P2, thereby negatively regulating the PI3K (phosphoinositide 3-kinase) pathways. Plays a central role in regulation of PI3K-dependent insulin signaling, although the precise molecular mechanisms and signaling pathways remain unclear. While overexpression reduces both insulin-stimulated MAP kinase and Akt activation, its absence does not affect insulin signaling or GLUT4 trafficking. Confers resistance to dietary obesity. May act by regulating AKT2, but not AKT1, phosphorylation at the plasma membrane. Part of a signaling pathway that regulates actin cytoskeleton remodeling. Required for the maintenance and dynamic remodeling of actin structures as well as in endocytosis, having a major impact on ligand-induced EGFR internalization and degradation. Participates in regulation of cortical and submembraneous actin by hydrolyzing PtdIns(3,4,5)P3 thereby regulating membrane ruffling (By similarity). Regulates cell adhesion and cell spreading. Required for HGF-mediated lamellipodium formation, cell scattering and spreading. Acts as a negative regulator of EPHA2 receptor endocytosis by inhibiting via PI3K-dependent Rac1 activation. Acts as a regulator of neuritogenesis by regulating PtdIns(3,4,5)P3 level and is required to form an initial protrusive pattern, and later, maintain proper neurite outgrowth. Acts as a negative regulator of the FC-gamma-RIIA receptor (FCGR2A). Mediates signaling from the FC-gamma-RIIB receptor (FCGR2B), playing a central role in terminating signal transduction from activating immune/hematopoietic cell receptor systems. Involved in EGF signaling pathway. Upon stimulation by EGF, it is recruited by EGFR and dephosphorylates PtdIns(3,4,5)P3. Plays a negative role in regulating the PI3K-PKB pathway, possibly by inhibiting PKB activity. Down-regulates Fc-gamma-R-mediated phagocytosis in macrophages independently of INPP5D/SHIP1. In macrophages, down-regulates NF-kappa-B-dependent gene transcription by regulating macrophage colony-stimulating factor (M-CSF)-induced signaling. May also hydrolyze PtdIns(1,3,4,5)P4, and could thus affect the levels of the higher inositol polyphosphates like InsP6. Involved in endochondral ossification (By similarity). a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3,4,5-trisphosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3,4-bisphosphate) + phosphate 1,2-dioctanoyl-sn-glycero-3-phospho-(1D-myo-inositol-3,4,5-trisphosphate) + H2O = 1,2-dioctanoyl-sn-glycero-3-phospho-(1D-myo-inositol-3,4-bisphosphate) + phosphate 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol-3,4,5-trisphosphate) + H2O = 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol-3,4-bisphosphate) + phosphate Activated upon translocation to the sites of synthesis of PtdIns(3,4,5)P3 in the membrane. Enzymatic activity is enhanced in the presence of phosphatidylserine (By similarity). Interacts with tyrosine phosphorylated form of SHC1. Interacts with EGFR. Upon stimulation by the EGF signaling pathway, it forms a complex with SHC1 and EGFR. Interacts with cytoskeletal protein SORBS3/vinexin, promoting its localization to the periphery of cells. Forms a complex with filamin (FLNA or FLNB), actin, GPIb (GP1BA or GP1BB) that regulates cortical and submembraneous actin. Interacts with c-Met/MET, when c-Met/MET is phosphorylated on 'Tyr-1356'. Interacts with p130Cas/BCAR1. Interacts with CENTD3/ARAP3 via its SAM domain. Interacts with c-Cbl/CBL and CAP/SORBS1. Interacts with activated EPHA2 receptor. Interacts with receptors FCGR2A. Interacts with FCGR2B. Interacts with tyrosine kinase ABL1. Interacts with tyrosine kinase TEC. Interacts with CSF1R. Interacts (via N-terminus) with SH3YL1 (via SH3 domain). Interacts (via SH2 domain) with tyrosine phosphorylated KLRC1 (via ITIM). Translocates to membrane ruffles when activated, translocation is probably due to different mechanisms depending on the stimulus and cell type. Partly translocated via its SH2 domain which mediates interaction with tyrosine phosphorylated receptors such as the FC-gamma-RIIB receptor (FCGR2B). Tyrosine phosphorylation may also participate in membrane localization. Insulin specifically stimulates its redistribution from the cytosol to the plasma membrane. Recruited to the membrane following M-CSF stimulation. In activated spreading platelets, localizes with actin at filopodia, lamellipodia and the central actin ring. The SH2 domain interacts with tyrosine phosphorylated forms of proteins such as SHC1 or FCGR2A. It also mediates the interaction with p130Cas/BCAR1 (By similarity). The NPXY sequence motif found in many tyrosine-phosphorylated proteins is required for the specific binding of the PID domain. Tyrosine phosphorylated by the members of the SRC family after exposure to a diverse array of extracellular stimuli such as insulin, growth factors such as EGF or PDGF, chemokines, integrin ligands and hypertonic and oxidative stress. May be phosphorylated upon IgG receptor FCGR2B-binding. Phosphorylated at Tyr-987 following cell attachment and spreading. Phosphorylated at Tyr-1161 following EGF signaling pathway stimulation (By similarity). Variant Cys-1142 found in diabetic GK strain may be a cause of diabete in this strain. Genetic variations in Inppl1 may also be a cause of susceptibility to hypertension. Belongs to the inositol 1,4,5-trisphosphate 5-phosphatase family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 4L family. +Photoreceptor that binds cis-retinaldehydes (By similarity). Contributes to pupillar reflex, photoentrainment and other non-image forming responses to light (By similarity). May be involved in the optokinetic visual tracking response (By similarity). May be involved in the regulation of retinal hyaloid vessel growth and regression (By similarity). Belongs to the G-protein coupled receptor 1 family. Opsin subfamily. +Belongs to the serpin family. +Transfers mannosyl residues to the hydroxyl group of serine or threonine residues. Coexpression of both POMT1 and POMT2 is necessary for enzyme activity, expression of either POMT1 or POMT2 alone is insufficient. Essentially dedicated to O-mannosylation of alpha-DAG1 and few other proteins but not of cadherins and protocaherins. a dolichyl beta-D-mannosyl phosphate + L-seryl-[protein] = 3-O-(alpha-D-mannosyl)-L-seryl-[protein] + a dolichyl phosphate + H(+) a dolichyl beta-D-mannosyl phosphate + L-threonyl-[protein] = 3-O-(alpha-D-mannosyl)-L-threonyl-[protein] + a dolichyl phosphate + H(+) Protein modification; protein glycosylation. Expressed ubiquitously at low level after 7.5 dpc. At 8.5 dpc high levels of expression are detected throughout the neural tube, and in the dorsal aspects of the neural folds of the future midbrain region and the somites. At 9.0 dpc high levels of expression are detected in the ventral domain of the neural tube, developing eye, floor plate, notochord, and gut endothelium. At 10.5 dpc expression high levels of expression are detected in the dermomyotome of the somites, limb-bud mesenchyme, mantle layer of the dorsal neural tube, and developing trigeminal ganglion. Mice suffer of developmental arrest around 7.5 dpc and die between 7.5 dpc and 9.5 dpc. Defects are observed in the formation of Reichert's membrane that are probably due to abnormal glycosylation and maturation of dystroglycan and impaired recruitment of laminin. Belongs to the glycosyltransferase 39 family. +May help in the organization of the PsaL subunit. Belongs to the PsaI family. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +May function as sodium-coupled metabolite transporter across the chloroplast envelope. Belongs to the bile acid:sodium symporter (BASS) (TC 2.A.28) family. +Involved in the biosynthesis of the exopolysaccharide xanthan, a polymer that is comprised of repeating pentasaccharide units with the structure of a beta-(1,4)-linked D-glucose backbone with trisaccharide side chains composed of mannose-beta-(1,4)-glucuronic acid-beta-(1,2)-mannose attached to alternate glucose residues in the backbone by alpha-(1,3) linkages. Xanthan is involved in pathogenicity but has also been used in a variety of applications as a specialty polymer for commercial applications, including food additives, where they act as viscosifying, stabilizing, emulsifying, or gelling agents. beta-D-Glc-(1->4)-alpha-D-Glc-di-trans,octa-cis-undecaprenyl diphosphate + GDP-alpha-D-mannose = alpha-D-Man-(1->3)-beta-D-Glc-(1->4)-alpha-D-Glc-1-di-trans,octa-cis-undecaprenyl diphosphate + GDP + H(+) Belongs to the glycosyltransferase group 1 family. Glycosyltransferase 4 subfamily. +Belongs to the bacterial ribosomal protein bS16 family. +Catalyzes the deamination of dCTP to dUTP. dCTP + H(+) + H2O = dUTP + NH4(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 1/2. Homotrimer. Belongs to the dCTP deaminase family. +Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetE route): step 1/1. Belongs to the vitamin-B12 independent methionine synthase family. +Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively. Component of the CSN complex, composed of COPS1/GPS1, COPS2, COPS3, COPS4, COPS5, COPS6, COPS7 (COPS7A or COPS7B), COPS8 and COPS9 isoform 1 (PubMed:11337588, PubMed:18850735, PubMed:26456823). In the complex, it probably interacts directly with COPS1, COPS2, COPS4, COPS5, COPS6 and COPS8. Interacts with PMF1 (PubMed:12020345). Interacts with the translation initiation factor EIF3S6 (PubMed:12220626). Interacts with CK2 and PKD (PubMed:12628923). Interacts directly with ID3 (By similarity). (Microbial infection) Interacts with vaccinia virus protein C9L. Widely expressed. Expressed at high level in brain, heart and skeletal muscle. Phosphorylated by CK2 and PKD kinases. Belongs to the CSN7/EIF3M family. CSN7 subfamily. +Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa. Belongs to the peptidase S1 family. +May function as RNase and regulate the levels of target RNA species. Belongs to the ZC3H12 family. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Transcription coactivator that plays a role in the regulation of cell expansion in leaf and cotyledons tissues (By similarity). Component of a network formed by miR396, the GRFs and their interacting factors (GIFs) acting in the regulation of meristem function, at least partially through the control of cell proliferation (By similarity). GIFs are involved in the positive regulation of cell proliferation of lateral organs in a functionally redundant manner. Interacts with GRF1. Predominantly expressed in shoot tips containing the shoot apical meristem (SAM) and flower buds. Also expressed in mature flowers. Belongs to the SS18 family. +Part of the ABC transporter complex PhnCDE involved in phosphonates import. Responsible for energy coupling to the transport system. ATP + H2O + phosphonate(out) = ADP + H(+) + phosphate + phosphonate(in) The complex is composed of two ATP-binding proteins (PhnC), two transmembrane proteins (PhnE) and a solute-binding protein (PhnD). Belongs to the ABC transporter superfamily. Phosphonates importer (TC 3.A.1.9.1) family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity (By similarity). Belongs to the universal ribosomal protein uS4 family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein. Monomer. Belongs to the LolB family. +Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Belongs to the thiamine-phosphate synthase family. +Catalyzes the conversion of pppGpp to ppGpp. Guanosine pentaphosphate (pppGpp) is a cytoplasmic signaling molecule which together with ppGpp controls the 'stringent response', an adaptive process that allows bacteria to respond to amino acid starvation, resulting in the coordinated regulation of numerous cellular activities. guanosine 3'-diphosphate 5'-triphosphate + H2O = guanosine 3',5'-bis(diphosphate) + H(+) + phosphate Purine metabolism; ppGpp biosynthesis; ppGpp from GTP: step 2/2. Belongs to the GppA/Ppx family. GppA subfamily. +Belongs to the sodium:galactoside symporter (TC 2.A.2) family. Extended N-terminus. +Essential for recycling GMP and indirectly, cGMP. ATP + GMP = ADP + GDP Belongs to the guanylate kinase family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity). Belongs to the bacterial ribosomal protein bL20 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. Cleavage of peptide bonds with very broad specificity. The formation of the proteasomal ATPase PAN-20S proteasome complex, via the docking of the C-termini of PAN into the intersubunit pockets in the alpha-rings, triggers opening of the gate for substrate entry. Interconversion between the open-gate and close-gate conformations leads to a dynamic regulation of the 20S proteasome proteolysis activity. The 20S proteasome core is composed of 14 alpha and 14 beta subunits that assemble into four stacked heptameric rings, resulting in a barrel-shaped structure. The two inner rings, each composed of seven catalytic beta subunits, are sandwiched by two outer rings, each composed of seven alpha subunits. The catalytic chamber with the active sites is on the inside of the barrel. Has a gated structure, the ends of the cylinder being occluded by the N-termini of the alpha-subunits. Is capped at one or both ends by the proteasome regulatory ATPase, PAN. Belongs to the peptidase T1B family. +Component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane. Component of the mitochondrial large ribosomal subunit (mt-LSU). Mature yeast 74S mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S small subunit contains a 15S ribosomal RNA (15S mt-rRNA) and 34 different proteins. The 54S large subunit contains a 21S rRNA (21S mt-rRNA) and 46 different proteins. Mitoribosomes are tethered to the mitochondrial inner membrane and spatially aligned with the membrane insertion machinery through two distinct membrane contact sites, formed by the 21S rRNA expansion segment 96-ES1 and the inner membrane protein MBA1. Present with 1200 molecules/cell in log phase SD medium. Belongs to the universal ribosomal protein uL30 family. +Involved in the proteasome-dependent degradation of fructose-1,6-bisphosphatase. Belongs to the FYV10 family. +Protects the hemoglobin in erythrocytes from oxidative breakdown. In platelets, plays a crucial role of glutathione peroxidase in the arachidonic acid metabolism. 2 glutathione + H2O2 = glutathione disulfide + 2 H2O (12S)-hydroperoxy-(5Z,8Z,10E,14Z)-eicosatetraenoate + 2 glutathione = (12S)-hydroxy-(5Z,8Z,10E,14Z)-eicosatetraenoate + glutathione disulfide + H2O Homotetramer. Interacts with MIEN1 (By similarity). During periods of oxidative stress, Sec-47 may react with a superoxide radical, irreversibly lose hydroselenide and be converted to dehydroalanine. Belongs to the glutathione peroxidase family. +Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation. Responsible for the sulfation of cholesterol (PubMed:19589875, PubMed:12145317). Catalyzes sulfation of the 3beta-hydroxyl groups of steroids, such as, pregnenolone and dehydroepiandrosterone (DHEA) (PubMed:9799594, PubMed:12145317, PubMed:21855633, PubMed:16855051). Preferentially sulfonates cholesterol, while it has also significant activity with pregnenolone and DHEA (PubMed:12145317, PubMed:21855633). Plays a role in epidermal cholesterol metabolism and in the regulation of epidermal proliferation and differentiation (PubMed:28575648). Sulfonates pregnenolone but not cholesterol. 3'-phosphoadenylyl sulfate + an alcohol = adenosine 3',5'-bisphosphate + an alkyl sulfate + H(+) 3'-phosphoadenylyl sulfate + 3beta-hydroxyandrost-5-en-17-one = adenosine 3',5'-bisphosphate + dehydroepiandrosterone 3-sulfate + H(+) (24S)-hydroxycholesterol + 3'-phosphoadenylyl sulfate = (24S)-hydroxycholesterol 3-sulfate + adenosine 3',5'-bisphosphate + H(+) 3'-phosphoadenylyl sulfate + cholesterol = adenosine 3',5'-bisphosphate + cholesterol sulfate + H(+) 3'-phosphoadenylyl sulfate + pregnenolone = adenosine 3',5'-bisphosphate + H(+) + pregnenolone sulfate Optimum temperature is 37 degrees Celsius. Retains 70% and 20% of activity when incubated at 42 degrees Celsius for 45 and 120 minutes, respectively. Activity is lost after 200 minutes incubation at 42 degrees Celsius. Phosphorylation of Ser-348 is required for translocation to the nucleus. Expressed in the stratum granulosum-stratum corneum junction in the skin (at protein level) (PubMed:28575648). Expressed highly in placenta, prostate and trachea and lower expression in the small intestine and lung (PubMed:9799594). The C-terminus, which contains a proline/serine-rich region is involved in nuclear translocation and enzymatic thermostability. Phosphorylated. The disease is caused by variants affecting the gene represented in this entry. Belongs to the sulfotransferase 1 family. +Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate. adenosylcob(III)inamide-GDP + alpha-ribazole = adenosylcob(III)alamin + GMP + H(+) adenosylcob(III)inamide-GDP + alpha-ribazole 5'-phosphate = adenosylcob(III)alamin 5'-phosphate + GMP + H(+) Cofactor biosynthesis; adenosylcobalamin biosynthesis; adenosylcobalamin from cob(II)yrinate a,c-diamide: step 7/7. Belongs to the CobS family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a(1), b(1), b'(1) and c(9-12). Belongs to the ATPase alpha/beta chains family. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +Mediates visceral muscle contractile activity (myotropic activity). Corpora cardiaca. Belongs to the pyrokinin family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Participates in initiation and elongation during chromosome replication; it exhibits DNA-dependent ATPase activity. ATP + H2O = ADP + H(+) + phosphate Belongs to the helicase family. DnaB subfamily. +Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Responsible for energy coupling to the transport system. ATP + H2O + (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran-[AI-2-binding protein]Side 1 = ADP + phosphate + (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuranSide 2 + [AI-2-binding protein]Side 1. The complex is composed of two ATP-binding proteins (LsrA), two transmembrane proteins (LsrC and LsrD) and a solute-binding protein (LsrB). Belongs to the ABC transporter superfamily. AI-2 autoinducer porter (TC 3.A.1.2.8) family. +Fructose-bisphosphatase hydrolyzing fructose-2,6-bisphosphate as well as fructose-1,6-bisphosphate (By similarity). Acts as a negative regulator of glycolysis by lowering intracellular levels of fructose-2,6-bisphosphate in a p53/TP53-dependent manner, resulting in the pentose phosphate pathway (PPP) activation and NADPH production (PubMed:23726973). Contributes to the generation of reduced glutathione to cause a decrease in intracellular reactive oxygen species (ROS) content, correlating with its ability to protect cells from oxidative or metabolic stress-induced cell death (PubMed:23726973). Plays a role in promoting protection against cell death during hypoxia by decreasing mitochondria ROS levels in a HK2-dependent manner through a mechanism that is independent of its fructose-bisphosphatase activity (By similarity). In response to cardiac damage stress, mediates p53-induced inhibition of myocyte mitophagy through ROS levels reduction and the subsequent inactivation of BNIP3 (PubMed:22044588). Reduced mitophagy results in an enhanced apoptotic myocyte cell death, and exacerbates cardiac damage (PubMed:22044588). Plays a role in adult intestinal regeneration; contributes to the growth, proliferation and survival of intestinal crypts following tissue ablation (PubMed:23726973). Plays a neuroprotective role against ischemic brain damage by enhancing PPP flux and preserving mitochondria functions (PubMed:24872551). Protects glioma cells from hypoxia- and ROS-induced cell death by inhibiting glycolysis and activating mitochondrial energy metabolism and oxygen consumption in a TKTL1-dependent and p53/TP53-independent manner. Plays a role in cancer cell survival by promoting DNA repair through activating PPP flux in a CDK5-ATM-dependent signaling pathway during hypoxia and/or genome stress-induced DNA damage responses (By similarity). Involved in intestinal tumor progression (PubMed:23726973). beta-D-fructose 2,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Interacts with HK2; the interaction increases hexokinase HK2 activity in a hypoxia- and HIF1A-dependent manner, resulting in the regulation of mitochondrial membrane potential, thus increasing NADPH production and decreasing intracellular ROS levels. Translocated to the mitochondria during hypoxia in a HIF1A-dependent manner. Colocalizes with HK2 in the mitochondria during hypoxia. Translocated to the nucleus during hypoxia and/or genome stress-induced DNA damage responses in cancer cells (By similarity). Translocation to the mitochondria is enhanced in ischemic cortex after reperfusion and/or during oxygen and glucose deprivation (OGD)/reoxygenation insult in primary neurons (PubMed:24872551). Expressed in olfactory bulb, cerebellum, and cortex (PubMed:24872551). Expressed in neurons and astrocytes (PubMed:24872551) (at protein level). Expressed in intestinal crypt (PubMed:23726973). Up-regulated by hypoxia in cardiac myocytes in a p53/TP53-dependent manner (PubMed:20935145). Up-regulated in ischemic cortex after reperfusion in a p53/TP5-independent manner (PubMed:24872551). Up-regulated in primary neurons by oxygen and glucose deprivation (OGD)/reoxygenation insult in a p53/TP5-independent manner (at protein level) (PubMed:24872551). Up-regulated in ischemic myocardium in a p53/TP5-dependent manner (PubMed:22044588). Up-regulated in small intestine after gamma irradiation damage (PubMed:23726973). Mice are viable and fertile and show no obvious developmental defects (PubMed:23726973). Following intestine ablation by gamma irradiation, adult mice display a reduction in the size and number of proliferating intestinal crypts and an increase in cell death (PubMed:23726973). Mice display reduced intestinal tumor progression compared to wild-type mice (PubMed:23726973). In response to ischemic myocardium injury, display an increase in the ability to stimulate myocyte mitophagy in ischemic border zones through a ROS-induced and BNIP3 activation dependent manner leading to a reduction of defective mitochondria and myocyte cell death, and hence a better recovery of cardiac function (PubMed:22044588). Belongs to the phosphoglycerate mutase family. Not expected to have any kinase activity. +Receptor for the C-terminal sequence motif K-D-E-L that is present on endoplasmic reticulum resident proteins and that mediates their recycling from the Golgi back to the endoplasmic reticulum. Upon ligand binding the receptor oligomerizes and interacts with components of the transport machinery such as ARFGAP1 and ARF1. Localized in the Golgi in the absence of bound proteins with the sequence motif K-D-E-L. Trafficks back to the endoplasmic reticulum together with cargo proteins containing the sequence motif K-D-E-L. Phosphorylation by PKA at Ser-209 is required for endoplasmic reticulum retention function. Belongs to the ERD2 family. +Homodimer. +Belongs to the GST superfamily. Beta family. +Seems to play a role in the dimerization of PSII. Belongs to the PsbT family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +Catalyzes the hydroxylation of n-alkanes in the presence of a NADH-rubredoxin reductase and rubredoxin. It preferably hydroxylases long-chain-length alkanes with at least 12 carbon atoms. 2 H(+) + O2 + octane + 2 reduced [rubredoxin] = H2O + octan-1-ol + 2 oxidized [rubredoxin] Binds 2 Fe(3+) ions per subunit. Hydrocarbon metabolism; alkane degradation. Induced by AlkR and n-alkanes only in stationary phase. Repressed by oxidized alkane derivatives. Belongs to the fatty acid desaturase type 1 family. AlkB subfamily. +Belongs to the BolA/IbaG family. +The isoform alpha-1B gives rise to N-type calcium currents. N-type calcium channels belong to the 'high-voltage activated' (HVA) group (By similarity). Multisubunit complex consisting of alpha-1, alpha-2, beta and delta subunits in a 1:1:1:1 ratio. The channel activity is directed by the pore-forming and voltage-sensitive alpha-1 subunit. In many cases, this subunit is sufficient to generate voltage-sensitive calcium channel activity. The auxiliary subunits beta and alpha-2/delta linked by a disulfide bridge regulate the channel activity (By similarity). Additional isoforms seem to exist. Expression is higher in the electric lobe than in the forebrain. Each of the four internal repeats contains five hydrophobic transmembrane segments (S1, S2, S3, S5, S6) and one positively charged transmembrane segment (S4). S4 segments probably represent the voltage-sensor and are characterized by a series of positively charged amino acids at every third position. Phosphorylated in vitro by CaM-kinase II, PKA, PKC and CGPK. Belongs to the calcium channel alpha-1 subunit (TC 1.A.1.11) family. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiC family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in chloroplasts and mitochondria. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Subunit of the heterotrimeric GatCAB amidotransferase (AdT) complex, composed of A, B and C subunits. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the GatB/GatE family. GatB subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity (By similarity). Belongs to the universal ribosomal protein uS4 family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds 2 heme A groups non-covalently per subunit. Binds a copper B center. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of a catalytic core of 3 subunits and several supernumerary subunits. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII). Belongs to the heme-copper respiratory oxidase family. +Plays a role in intracellular trafficking and contributes to the macromolecular organization of group 1 metabotropic glutamate receptors (mGluRs) at synapses. Heteromer. Composed of TAMALIN, CYTH2 and at least one GRM1. Also interacts with CYTH3, GRM2, GRM3 and GRM5 (By similarity). +alpha-D-glucose 1-phosphate + H(+) + UTP = diphosphate + UDP-alpha-D-glucose Carbohydrate metabolism; nucleotide-sugar metabolism. Capsule biogenesis; capsule polysaccharide biosynthesis. Belongs to the UDPGP type 2 family. +Bactericidal activity (effective inhibitor of L.monocytogenes). Belongs to the bacteriocin class IIA/YGNGV family. +Regulates the GDP/GTP exchange reaction of most Rab proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them. Promotes the dissociation of GDP-bound Rab proteins from the membrane and inhibits their activation. Promotes the dissociation of RAB1A, RAB3A, RAB5A and RAB10 from membranes. Interacts with RHOH (By similarity). Interacts with the non-phosphorylated forms of RAB1A, RAB3A, RAB5A, RAB5B, RAB5C, RAB8A, RAB8B, RAB10, RAB12, RAB35, and RAB43 (By similarity). High expression in brain, lower in other tissues. Belongs to the Rab GDI family. +May bind long-chain fatty acids, such as palmitate, and may play a role in lipid transport or fatty acid metabolism. +May bind to and transport cholesterol and may play a role in ecdysteroid biosynthesis. Expressed in larval prothoracic gland cells (at protein level). Detected in larval ring gland, imaginal disk and salivary gland and in adult head, ovary and testis. Expressed in nurse cells of stage 10 egg chambers in 2-day-old adult ovary. No expression detected in adult brain. Expressed in the embryo from stage 16. In the larva, abundant at the end of both the second and third instar but is almost undetectable in freshly hatched third instar larvae and declines in white prepupae. Also expressed in the adult. +Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; fumarate reductase is used in anaerobic growth, and succinate dehydrogenase is used in aerobic growth. Anchors the catalytic components of the fumarate reductase complex to the cell inner membrane, binds quinones. Part of an enzyme complex containing four subunits: a flavoprotein (FrdA), an iron-sulfur protein (FrdB), and two hydrophobic anchor proteins (FrdC and FrdD). Belongs to the FrdD family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the proton channel; it may play a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Component of an ATP synthase complex composed of ATP5PB, ATP5MC1, ATP5F1E, ATP5PD, ATP5ME, ATP5PF, ATP5MF, MT-ATP6, MT-ATP8, ATP5F1A, ATP5F1B, ATP5F1D, ATP5F1C, ATP5PO, ATP5MG, ATP5MK and ATP5MJ (By similarity). Interacts with DNAJC30; interaction is direct (By similarity). Belongs to the ATPase A chain family. +Hydrolyzes cAMP to 5'-AMP. Plays an important regulatory role in modulating the intracellular concentration of cAMP, thereby influencing cAMP-dependent processes. Specifically required for regulation of virulence factors. Can also hydrolyze cGMP, but cGMP is unlikely to be synthesized by P.aeruginosa and cAMP is probably the biologically relevant substrate for CpdA in vivo. 3',5'-cyclic AMP + H2O = AMP + H(+) Binds 2 metal cations per subunit. Site 1 may preferentially bind Fe(3+) ions, while site 2 may have a preference for Fe(2+) ions. Activated by iron. Other divalent metal ions have no effect. Monomer. Positively regulated by Vfr in response to elevated intracellular cAMP. Mutants show increased levels of cellular cAMP. In rich medium, mutants exhibit a significantly reduced growth rate compared to wild-type strain. Belongs to the cyclic nucleotide phosphodiesterase class-III family. +Belongs to the N-Me-Phe pilin family. +Involved in the efflux of sugars. The physiological role may be the reduction of the intracellular concentration of toxic sugars or sugar metabolites. Belongs to the major facilitator superfamily. SotB (TC 2.A.1.2) family. +May be involved in the transport of PQQ or its precursor to the periplasm, in association with PQQ biosynthesis, but is not absolutely required for this synthesis. Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. Belongs to the PqqB family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Binds to actin on the surface of endothelial cells; once bound, angiogenin is endocytosed and translocated to the nucleus. Stimulates ribosomal RNA synthesis including that containing the initiation site sequences of 45S rRNA. Cleaves tRNA within anticodon loops to produce tRNA-derived stress-induced fragments (tiRNAs) which inhibit protein synthesis and triggers the assembly of stress granules (SGs) (By similarity). Angiogenin induces vascularization of normal and malignant tissues. Angiogenic activity is regulated by interaction with RNH1 in vivo (By similarity). Homodimer. Interacts with and forms a tight 1:1 complex with RNH1. Dimerization of two such complexes may occur (By similarity). Rapidly endocytosed by target cells and translocated to the nucleus where it accumulates in the nucleolus and binds to DNA (By similarity). Belongs to the pancreatic ribonuclease family. +Involved in ATP-driven sodium extrusion. Belongs to the V-ATPase G subunit family. Extended N-terminus. +Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. 3 H2O + hydrogen sulfide + 3 NADP(+) = 4 H(+) + 3 NADPH + sulfite Binds 1 siroheme per subunit. Binds 1 [4Fe-4S] cluster per subunit. Sulfur metabolism; hydrogen sulfide biosynthesis; hydrogen sulfide from sulfite (NADPH route): step 1/1. Alpha(8)-beta(8). The alpha component is a flavoprotein, the beta component is a hemoprotein. Belongs to the nitrite and sulfite reductase 4Fe-4S domain family. +Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 magnesium ions per subunit. Monomer. Belongs to the DNA polymerase type-Y family. +Catalytic component of the SET1 complex that specifically di- and trimethylates 'Lys-4' of histone H3 and is the main di- and trimethyltransferase throughout development. Set1-dependent trimethylation regulates chromatin changes at active promoters that ensure optimal RNA polymerase II release into productive elongation, thereby contributing to optimal transcription. L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-homocysteine Component of the SET1 complex, composed at least of the catalytic subunit Set1, wds/WDR5, Wdr82, Rbbp5, ash2, Cfp1/CXXC1, hcf and Dpy-30L1. Interacts with ash2 and wds. Colocalizes with di- and trimethylated H3 'Lys-4' and with phosphorylated RNA polymerase II at transcriptional puffs on polytene chromosomes. Belongs to the class V-like SAM-binding methyltransferase superfamily. Contaminating sequence. Potential poly-A sequence. Contaminating sequence. Potential poly-A sequence. +Serine protease inhibitor that inhibits plasma kallikrein (Ki=1.7 nM), and plasmin (Ki=33.0 nM). Expressed by the venom gland. Belongs to the venom Kunitz-type family. Attempts to clone the transcript coding for this protein failed. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +Catalyzes the hydroxylation of L-kynurenine (L-Kyn) to form 3-hydroxy-L-kynurenine (L-3OHKyn). Required for synthesis of quinolinic acid. H(+) + L-kynurenine + NADPH + O2 = 3-hydroxy-L-kynurenine + H2O + NADP(+) Cofactor biosynthesis; NAD(+) biosynthesis; quinolinate from L-kynurenine: step 1/3. Belongs to the aromatic-ring hydroxylase family. KMO subfamily. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Belongs to the polyribonucleotide nucleotidyltransferase family. +Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and/or repair of Fe-S clusters in biosynthetic enzymes. Monomer. Belongs to the Fe(2+)-trafficking protein family. +hexadecanoyl-CoA + L-cysteinyl-[protein] = CoA + S-hexadecanoyl-L-cysteinyl-[protein] The DHHC domain is required for palmitoyltransferase activity. Belongs to the DHHC palmitoyltransferase family. +Bone marrow-derived monocyte and paracrine-acting protein that promotes cardiac myocyte survival and adaptive angiogenesis for cardiac protection and/or repair after myocardial infarction (MI). Stimulates endothelial cell proliferation through a MAPK1/3-, STAT3- and CCND1-mediated signaling pathway. Inhibits cardiac myocyte apoptosis in a PI3K/AKT-dependent signaling pathway. The C-terminal RTEL motif may provide retention in the endoplasmic reticulum. Expressed in prostate, spleen and lung, and weakly expressed in the left ventricle (LF) and liver. Expressed predominantly in inflammatory cells, such as monocytes and macrophages, and weakly expressed in neutrophils, T-cells, B-cells, endothelial cells and cardiac myocytes, after myocardial infarction (MI) (at protein level). Up-regulated by ischemia/hypoxia and reperfusion (IR) injury in the left ventricle (at protein level) (PubMed:25581518). Up-regulated during adipocyte differentiation (at protein level) (PubMed:15378209). Mice show normal postnatal body mass gain, develop normally and are fertile. Show larger infarct collagen-rich scars and more severe heart contractile dysfunction compared to wild-type mice after ischemia and reperfusion (IR) injury. Belongs to the MYDGF family. Was originally thought to signal lymphoid cells to proliferate via thymic shared antigen 1 (PubMed:11714798). This work was later retracted (PubMed:12538725). It has been reported that MYDGF is secreted into blood plasma (PubMed:15378209, PubMed:25581518). However, another report studying human MYDGF shows resident localization to the endoplasmic reticulum and Golgi apparatus and secretion when the two most C-terminal residues of the RTEL motif are abolished (By similarity). +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +The RIC1-RGP1 complex acts as a guanine nucleotide exchange factor (GEF), which activates RAB6A by exchanging bound GDP for free GTP and may thereby required for efficient fusion of endosome-derived vesicles with the Golgi compartment. The RIC1-RGP1 complex participates in the recycling of mannose-6-phosphate receptors. Forms a complex with RIC1; the interaction enhances RAB6A GTPase activity. Interacts with RIC1. Interacts with RAB6A; the interaction is direct with a preference for RAB6A-GDP. Interacts with RAB33B. Belongs to the RGP1 family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA. Homotetramer, a dimer of dimers. One homotetramer interacts with 1 SecA dimer. Belongs to the SecB family. +The pigment-dispersing hormone causes the migration of the distal retinal pigment into the proximal end of the pigment chromatophore cells and thus decreases the amount of light entering the retinulas. May also function as a neurotransmitter and/or neuromodulator (By similarity). Eyestalk sinus gland. Belongs to the arthropod PDH family. +Belongs to the UPF0758 family. YicR subfamily. +Antimicrobial peptide. Synthetic peptide shows higher potency against Gram-negative bacteria than against Gram-positive bacteria. Has a very week hemolytic activity. Expressed by the skin glands. Belongs to the ascaphin family. +Part of the ABC transporter complex TauABC involved in taurine import. Responsible for energy coupling to the transport system. ATP + H2O + taurine(out) = ADP + H(+) + phosphate + taurine(in) The complex is composed of two ATP-binding proteins (TauB), two transmembrane proteins (TauC) and a solute-binding protein (TauA). Belongs to the ABC transporter superfamily. Taurine importer (TC 3.A.1.17.1) family. +Potent and specific cellular inhibitor of CaM-kinase II (CAMK2) (PubMed:9724800, PubMed:17942605). Traps Ca(2+)/calmodulin on CAMK2 (PubMed:17942605). Interacts with CAMK2A and CAMK2B in the presence of Ca(2+)/calmodulin or after autophosphorylation. Excluded from nucleus when coexpressed with activated CAMK2. Expressed in forebrain, hippocampus, midbrain, cerebellum, and testis. Expressed in forebrain, hippocampus, midbrain, and cerebellum (at protein level). In the cortex expressed more in laminae II and III than in laminae IV-VI. Expressed within the pyramidal layer of the hippocampus and granular layer of the dentate gyrus as well as in the olfactory bulb. Diffusely expressed within the caudate-putamen and globus pallidus. Diffusely expressed throughout regions of the midbrain. In cerebellum, expressed within the Purkinje and granular layer. Stronger expressed in the cerebellum. Highly expressed in frontal cortex, hippocampus, olfactory bulb, caudate-putamen and cerebellum exhibit (at protein level). Belongs to the CAMK2N family. +Belongs to the chlamydial CPn_0512/CT_425/TC_0708 family. +Belongs to the FAH family. +Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Once loaded onto DNA, double hexamers can slide on dsDNA in the absence of ATPase activity. ATP + H2O = ADP + H(+) + phosphate Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6-MCM4-MCM7-MCM3-MCM5; loaded onto DNA, forms a head-head double hexamer. Interacts with CSM1 and MCM10. Present with 166 molecules/cell in log phase SD medium. Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex. Belongs to the MCM family. +Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type B subfamily. +Part of the ABC transporter complex XylFGH involved in xylose import. Responsible for energy coupling to the transport system. ATP + D-xylose(out) + H2O = ADP + D-xylose(in) + H(+) + phosphate The complex is composed of two ATP-binding proteins (XylG), two transmembrane proteins (XylH) and a solute-binding protein (XylF). Belongs to the ABC transporter superfamily. Xylose importer (TC 3.A.1.2.4) family. +Ubiquitin-like modifier involved in autophagosomes formation. With ATG4, mediates the delivery of the autophagosomes to the vacuole via the microtubule cytoskeleton. Required for selective autophagic degradation of the nucleus (nucleophagy) as well as for mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. Participates also in membrane fusion events that take place in the early secretory pathway. Also involved in endoplasmic reticulum-specific autophagic process and is essential for the survival of cells subjected to severe ER stress. The ATG8-PE conjugate mediates tethering between adjacent membranes and stimulates membrane hemifusion, leading to expansion of the autophagosomal membrane during autophagy. The C-terminal 2 residues are removed by ATG4 to expose Gly-116 at the C-terminus. The c-terminal Gly is then amidated with phosphatidylethanolamine by an activating system similar to that for ubiquitin. Belongs to the ATG8 family. +Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA. Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding. Interacts with PCNA. Three molecules of FEN1 bind to one PCNA trimer with each molecule binding to one PCNA monomer. PCNA stimulates the nuclease activity without altering cleavage specificity. Resides mostly in the nucleoli and relocalizes to the nucleoplasm upon DNA damage. Phosphorylated. Phosphorylation upon DNA damage induces relocalization to the nuclear plasma. Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily. +Overexpression affects chitinase expression, cell separation and budding pattern, and increases trehalose accumulation and heat resistance by inhibiting protein kinase CBK1. Overexpression also suppresses temperature-induced hyperosmosensitivity and sensitivity to cell wall degrading enzymes. Overexpression of both LRE1 and PBN1 confers resistance to laminarinase. Phosphorylated by CDC28/CDK1. +Catalyzes oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs. AH2 + O2 + uridine(34) in tRNA = 5-hydroxyuridine(34) in tRNA + A + H2O Belongs to the TrhO family. +SIII, also known as elongin, is a general transcription elongation factor that increases the RNA polymerase II transcription elongation past template-encoded arresting sites. Subunit A is transcriptionally active and its transcription activity is strongly enhanced by binding to the dimeric complex of the SIII regulatory subunits B and C (elongin BC complex) (By similarity). The elongin BC complex seems to be involved as an adapter protein in the proteasomal degradation of target proteins via different E3 ubiquitin ligase complexes. Belongs to the SKP1 family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Belongs to the FAM221 family. +Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. (2S,6S)-2,6-diaminoheptanedioate = meso-2,6-diaminoheptanedioate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. Homodimer. Belongs to the diaminopimelate epimerase family. +DNA-binding transcription factor that specifically binds heat shock promoter elements (HSE) and activates transcription. Homotrimer (By similarity). Homotrimerization increases the affinity of HSF1 to DNA (By similarity). Belongs to the HSF family. +Involved in iron-sulfur (Fe-S) cluster assembly. May act as a regulator of Fe-S biogenesis. Belongs to the frataxin family. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +It has a serine and a weak tyrosine phosphatase activity with ratios of serine to tyrosine phosphatase activity as high as 200:1. It is essential for growth or germination at 37 degrees Celsius. May have a role in the heat shock response. Involved in tRNA splicing and cell separation. H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 magnesium or manganese ions per subunit. Manganese is about 20 times more efficient than magnesium. Interacts with NBP2 and PBS2. Present with 1520 molecules/cell in log phase SD medium. Belongs to the PP2C family. +Serine protease inhibitor (By similarity). Does not inhibit plasmin, and does not reduce blood loss in the mouse tail vein blood loss model. Expressed by the venom gland. Belongs to the venom Kunitz-type family. +Acts as a GTPase-activating protein (GAP) for SAR1 (PubMed:24947508). Contrary to its SEC23 homolog, NEL1 does not associate with SEC24 and its homologs, nor does it associate with the COPII components, suggesting that it is unlikely that NEL1 functions as a structural component of the vesicle coat machinery (PubMed:24947508). May function as a signaling molecule (PubMed:24947508). Is diffusely localized throughout the cytosol, and does not accumulate at ER exit sites (ERES). Leads to a significant growth defect in the temperature-sensitive SAR1-D32G mutant background. Present with 450 molecules/cell in log phase SD medium. Belongs to the SEC23/SEC24 family. SEC23 subfamily. +carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Heterooligomer of catalytic and regulatory chains. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family. +Core component of the 3M and Cul7-RING(FBXW8) complexes, which mediates the ubiquitination of target proteins. Core component of the 3M complex, a complex required to regulate microtubule dynamics and genome integrity. It is unclear how the 3M complex regulates microtubules, it could act by controlling the level of a microtubule stabilizer. Interaction with CUL9 is required to inhibit CUL9 activity and ubiquitination of BIRC5. Core component of a Cul7-RING ubiquitin-protein ligase with FBXW8, which mediates ubiquitination and consequent degradation of target proteins such as GORASP1, IRS1 and MAP4K1/HPK1. Ubiquitination of GORASP1 regulates Golgi morphogenesis and dendrite patterning in brain (PubMed:21572988). Mediates ubiquitination and degradation of IRS1 in a mTOR-dependent manner: the Cul7-RING(FBXW8) complex recognizes and binds IRS1 previously phosphorylated by S6 kinase (RPS6KB1 or RPS6KB2). The Cul7-RING(FBXW8) complex also mediates ubiquitination of MAP4K1/HPK1: recognizes and binds autophosphorylated MAP4K1/HPK1, leading to its degradation, thereby affecting cell proliferation and differentiation. Acts as a regulator in trophoblast cell epithelial-mesenchymal transition and placental development. Does not promote polyubiquitination and proteasomal degradation of p53/TP53. While the Cul7-RING(FBXW8) and the 3M complexes are associated and involved in common processes, CUL7 and the Cul7-RING(FBXW8) complex may be have additional functions (By similarity). Protein modification; protein ubiquitination. Component of the 3M complex, composed of core components CUL7, CCDC8 and OBSL1. Part of a Cul7-RING complex consisting of CUL7, RBX1, SKP1 and FBXW8. Interacts with a complex of SKP1 and FBXW8, but not with SKP1 alone. Interacts with CUL9; leading to inhibit CUL9 activity. Interacts with FBXW8; interaction is mutually exclusive of binding to CUL9 or p53/TP53. Interacts with p53/TP53; the interaction preferentially involves tetrameric and dimeric p53/TP53. The CUL7-CUL9 heterodimer seems to interact specifically with p53/TP53. Interacts with CUL1; the interactions seems to be mediated by FBXW8 (By similarity). Interacts with OBSL1 and FBXW8. Interacts (as part of the 3M complex) with HDAC4 and HDAC5; it is negatively regulated by ANKRA2 (By similarity). During mitosis, localizes to the mitotic apparatus. CCDC8 is required for centrosomal location (By similarity). Colocalizes with FBXW8 at the Golgi apparatus in neurons; localization to Golgi is mediated by OBSL1. Belongs to the cullin family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. In this organism, the P 'protein' is a heterodimer of two subunits. Belongs to the GcvP family. N-terminal subunit subfamily. +Component of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum (ER) and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis, and function in nonvesicular lipid trafficking between the ER and mitochondria. Mdm12 is required for the interaction of the ER-resident membrane protein mmm1 and the outer mitochondrial membrane-resident beta-barrel protein mdm10. The mdm12-mmm1 subcomplex functions in the major beta-barrel assembly pathway that is responsible for biogenesis of all mitochondrial outer membrane beta-barrel proteins, and acts in a late step after the SAM complex. The mdm10-mdm12-mmm1 subcomplex further acts in the TOM40-specific pathway after the action of the mdm12-mmm1 complex. Essential for establishing and maintaining the structure of mitochondria and maintenance of mtDNA nucleoids. Component of the ER-mitochondria encounter structure (ERMES) or MDM complex, composed of mmm1, mdm10, mdm12 and mdm34. A mmm1 homodimer associates with one molecule of mdm12 on each side in a pairwise head-to-tail manner, and the SMP-LTD domains of mmm1 and mdm12 generate a continuous hydrophobic tunnel for phospholipid trafficking. The ERMES/MDM complex localizes to a few discrete foci (around 10 per single cell), that represent mitochondria-endoplasmic reticulum junctions. These foci are often found next to mtDNA nucleoids. The SMP-LTD domain is a barrel-like domain that can bind various types of glycerophospholipids in its interior and mediate their transfer between two adjacent bilayers. Belongs to the MDM12 family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +Isoform Holin: Accumulates harmlessly in the cytoplasmic membrane until it reaches a critical concentration that triggers the formation of micron-scale pores (holes) causing host cell membrane disruption and endolysin escape into the periplasmic space (PubMed:12813073, PubMed:16030234). Determines the precise timing of host cell lysis (By similarity). Participates with the endolysin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles from the host cell (By similarity). Isoform Antiholin: Counteracts the aggregation of the holin molecules and thus of pore formation. Homomultimer. Isoform Holin: Interacts with isoform Antiholin; this interaction blocks the holin homomultimerization and delays host cell lysis. Classified as a class I holin. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Homodimer. Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily. +Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). H2O + O2 + pyridoxamine 5'-phosphate = H2O2 + NH4(+) + pyridoxal 5'-phosphate O2 + pyridoxine 5'-phosphate = H2O2 + pyridoxal 5'-phosphate Binds 1 FMN per subunit. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1. Homodimer. Belongs to the pyridoxamine 5'-phosphate oxidase family. +Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis. Monomer. Belongs to the pyridoxal phosphate-binding protein YggS/PROSC family. +With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS5 family. +Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. 2 D-sedoheptulose 7-phosphate = D-glycero-alpha-D-manno-heptose 7-phosphate + D-glycero-beta-D-manno-heptose 7-phosphate Binds 1 zinc ion per subunit. Carbohydrate biosynthesis; D-glycero-D-manno-heptose 7-phosphate biosynthesis; D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate from sedoheptulose 7-phosphate: step 1/1. Homotetramer. The reaction produces a racemic mixture of D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate. Belongs to the SIS family. GmhA subfamily. +Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors. [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H(+) Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 51 family. +RNA-dependent RNA polymerase that plays an essential role in the virus replication. Induces the reorganization of host mitochondria and the formation of structures with numerous dilations surrounded by double membranes, which may provide a protected environment to viral replication. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) This protein is translated as a fusion protein by episodic readthrough of P29 termination codon. Readthrough of the terminator codon TAG occurs between the codons for 268-Asn and 270-Gly. Belongs to the tombusviridae RNA polymerase family. +Involved in specifying the paraxial, but not dorsal, mesoderm. May regulate the expression of T-box transcription factors required for mesoderm formation and differentiation (By similarity). Expressed in the presomitic mesoderm preceding the formation of somites. At stage 4 expressed in and around the primitive streak. During subsequent development, expression domain persists, and gradually retracts in parallel to the retracting Hensen's node towards the caudal end. Expression begins to accumulate in gastrulating mesoderm and is later restricted to paraxial mesoderm, prior to the onset of somite formation. No expression is seen within somites, nor in the tailbud mesoderm. +Catalyzes the ATP- as well as the pyrophosphate-dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK/P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P-Ser-HPr). The two antagonistic activities of HprK/P are regulated by several intracellular metabolites, which change their concentration in response to the absence or presence of rapidly metabolisable carbon sources (glucose, fructose, etc.) in the growth medium. Also phosphorylates/dephosphorylates the HPr-like catabolite repression protein crh on a specific serine residue. Therefore, by controlling the phosphorylation state of HPr and crh, HPrK/P is a sensor enzyme that plays a major role in the regulation of carbon metabolism and sugar transport: it mediates carbon catabolite repression (CCR), and regulates PTS-catalyzed carbohydrate uptake and inducer exclusion (By similarity). [HPr protein]-L-serine + ATP = [HPr protein]-O-phospho-L-serine + ADP + H(+) [HPr protein]-O-phospho-L-serine + H(+) + phosphate = [HPr protein]-L-serine + diphosphate Homohexamer. The Walker A ATP-binding motif also binds Pi and PPi. Both phosphorylation and phosphorolysis are carried out by the same active site and suggest a common mechanism for both reactions. Belongs to the HPrK/P family. In this second copy of HPRK/P in O.iheyensis, Ala-202 and Glu-243 are present instead of the conserved Glu and Arg which are respectively expected to be part of the active site. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation (By similarity). This fusion protein includes a component of the F(0) channel (subunit b) and of the F(1) subunit (subunit delta). Two copies of subunit b and one of delta together form the peripheral 'stator' stalk which links F(1) to F(0) (By similarity). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains (By similarity). In the N-terminal section; belongs to the ATPase B chain family. In the C-terminal section; belongs to the ATPase delta chain family. +The predicted gene At1g24000 has been split into 3 genes: At1g24000, At1g24010 and At1g24020. +Involved in spore wall assembly. May be a component of the mitochondrial RNase MRP (MtMRP), a ribonucleoprotein endoribonuclease involved in the cleaving RNA transcripts to generate primers for DNA replication in mitochondria. Component of the mitochondria-localized RNase mitochondrial RNA-processing (RNase MRP) composed of one single RNA encoded by the NME1 gene and at least 31 proteins. Absent in the nucleus-localized RNase MRP (NuMRP). Belongs to the SHE10 family. +Belongs to the ycf66 family. +This protein produces a dimethylation of the adenine residue at position 2085 in 23S rRNA, resulting in reduced affinity between ribosomes and macrolide-lincosamide-streptogramin B antibiotics. adenosine(2085) in 23S rRNA + 2 S-adenosyl-L-methionine = 2 H(+) + N(6)-dimethyladenosine(2085) in 23S rRNA + 2 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. In the genome of Neisseria meningitidis (serogroup B), the gene for this protein is present (NMB0066). It was introduced as part of a construct built to neutralize the virulence of the bacterium. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Homodimer. Belongs to the IspH family. +Catalyzes the oxidative demethylation of N-methyl-L-tryptophan. H2O + N(alpha)-methyl-L-tryptophan + O2 = formaldehyde + H2O2 + L-tryptophan Binds 1 FAD per subunit. Monomer. Belongs to the MSOX/MTOX family. MTOX subfamily. +Involved in the post-translational modification of the lantibiotic subtilin. Possibly associated with, and anchored to, the cytoplasmic side of the membrane. To S.epidermidis EpiB and L.lactis NisB. Was originally proposed to code for two separate adjacent ORFs, SpaE and SpaD. +Snake venom zinc metalloproteinase that causes hemorrhage by provoking the degradation of the sub-endothelial matrix proteins (fibronectin, laminin, type IV collagen, nidogen, and gelatins). Cleavage of 5-His-|-Leu-6, 10-His-|-Leu-11, 14-Ala-|-Leu-15, 16-Tyr-|-Leu-17 and 23-Gly-|-Phe-24 of insulin B chain. With small molecule substrates prefers hydrophobic residue at P2' and small residue such as Ala, Gly at P1. Binds 1 zinc ion per subunit. Monomer. Expressed by the venom gland. The N-terminus is blocked. Belongs to the venom metalloproteinase (M12B) family. P-I subfamily. +Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS11 family. +May be involved in transcriptional regulation. Belongs to the krueppel C2H2-type zinc-finger protein family. +Avian ovomucoid consists of three homologous, tandem Kazal family inhibitory domains. This is the only ovomucoid third domain known to be not glycosylated. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide. May have a role in cell-wall turnover. D-alanyl-D-alanine + H2O = 2 D-alanine Binds 1 zinc ion per subunit. kcat is 310 sec(-1) with D-Ala-D-Ala. kcat is 110 sec(-1) with L-Ala-D-Ala. Belongs to the peptidase M15D family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Part of the ABC transporter complex CntABCDF (Opp1) involved in the uptake of metal in complex with the metallophore staphylopine (StP). May be involved in the import of a large array of divalent metals ions such as nickel, cobalt, zinc, copper and iron. Probably responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (CntD and CntF), two transmembrane proteins (CntB and CntC) and a solute-binding protein (CntA). Up-regulated in metal-poor media. Deletion of the cntABCDF genes decreases StP intracellular levels and decreases the import of iron, zinc, nickel and cobalt. Belongs to the ABC transporter superfamily. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Belongs to the histone H4 family. +This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA. Binds to the 5S rRNA independently of L5 and L18. Belongs to the bacterial ribosomal protein bL25 family. CTC subfamily. +Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccA family. +Core component of the type II secretion system required for the energy-dependent secretion of extracellular factors such as proteases and toxins from the periplasm. Pseudopilin (pilin-like) protein that polymerizes to form the pseudopilus. Further polymerization triggers pseudopilus growth. Type II secretion system is composed of four main components: the outer membrane complex, the inner membrane complex, the cytoplasmic secretion ATPase and the periplasm-spanning pseudopilus. Forms homomultimers. Cleaved by the prepilin peptidase. Methylated by prepilin peptidase at the amino group of the N-terminal phenylalanine once the leader sequence is cleaved. Belongs to the GSP G family. +By temperature-induced mass conversion from opaque to white colonies. WH11 is abruptly activated at the second cell doubling. To yeast HSP12/GLP1 and S.pombe hsp9. +This protein binds specifically to 23S rRNA. The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Belongs to the GMC oxidoreductase family. +Component of the small ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains about 33 different proteins and 1 molecule of RNA (18S). The 60S subunit contains about 49 different proteins and 3 molecules of RNA (25S, 5.8S and 5S). Belongs to the eukaryotic ribosomal protein eS1 family. +Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form the product. After dissociation, two additional enzymatic reactions on the tRNA convert PreQ1 to queuine (Q), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine). 7-aminomethyl-7-carbaguanine + guanosine(34) in tRNA = 7-aminomethyl-7-carbaguanosine(34) in tRNA + guanine Binds 1 zinc ion per subunit. tRNA modification; tRNA-queuosine biosynthesis. Homodimer. Within each dimer, one monomer is responsible for RNA recognition and catalysis, while the other monomer binds to the replacement base PreQ1. Belongs to the queuine tRNA-ribosyltransferase family. +Binds to the TGF-beta receptors sma-6 and daf-4, and enhances TGF-beta signaling activity in vitro. Has a role in regulation of body size. Interacts with sma-6 and daf-1. Expressed in the hypodermis. Expressed in the pharynx from the embryonic stage to adulthood. Small body size phenotype. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 6 family. +May be involved in vacuolar sorting and osmoregulation. Binds 2 Zn(2+) ions per subunit. Belongs to the peptidase M28 family. +F-actin-capping proteins bind in a Ca(2+)-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike other capping proteins (such as gelsolin and severin), these proteins do not sever actin filaments (By similarity). Heterodimer of an alpha and a beta subunit. Belongs to the F-actin-capping protein alpha subunit family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +Elicitor of plant defense. Belongs to the brassicaceae elicitor peptide family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +(6S)-10-formyltetrahydrofolate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide = (6S)-5,6,7,8-tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide H2O + IMP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide Purine metabolism; IMP biosynthesis via de novo pathway; 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide (10-formyl THF route): step 1/1. Purine metabolism; IMP biosynthesis via de novo pathway; IMP from 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide: step 1/1. The IMP cyclohydrolase activity resides in the N-terminal region. Belongs to the PurH family. +Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Belongs to the thiamine-phosphate synthase family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Adenosine deaminase that may contribute to the degradation of extracellular adenosine, a signaling molecule that controls a variety of cellular responses. Requires elevated adenosine levels for optimal enzyme activity. Binds to cell surfaces via proteoglycans and may play a role in the regulation of cell proliferation and differentiation, independently of its enzyme activity (By similarity). adenosine + H(+) + H2O = inosine + NH4(+) Binds 1 zinc ion per subunit. Homodimer. Interacts with adenosine receptors. Binds heparin (By similarity). The PRB domain is involved in receptor binding, and may be responsible for the cytokine-like growth factor activity due to it's sharing of several structural properties with chemokines. High-affinity binding to heparin/glycosaminoclycan (GAG) is mediated by a large, highly positively charged surface at the interface of dimer's subunits involving approximately residues 30-45, 389-396, and 422-428. Belongs to the metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. ADGF subfamily. +Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 1 subfamily. +IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. Monomer. Belongs to the IF-3 family. +Provides oxygen to the bacteroids. This role is essential for symbiotic nitrogen fixation. Monomer. Root nodules. Belongs to the plant globin family. +Glutamate-gated receptor that probably acts as non-selective cation channel. May be involved in light-signal transduction and calcium homeostasis via the regulation of calcium influx into cells. May form heteromers. Expressed predominantly in roots. Belongs to the glutamate-gated ion channel (TC 1.A.10.1) family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Belongs to the UppP family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the radical SAM superfamily. Lipoyl synthase family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly. Belongs to the UreE family. +E3 ubiquitin ligase that plays a role in antifungal immunity by mediating 'Lys-27'-linked ubiquitination of CARD9 downstream of C-type lectin receptors; leading to CARD9 activation, followed by activation of NF-kappa-B and MAP kinase p38 pathways (PubMed:26488816). E3 ubiquitin ligase activity is dependent on E2 ubiquitin-conjugating enzyme UBE2D2 (PubMed:23402750). S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Interacts with the ubiquitin-conjugating enzyme, UBE2D2. The RING finger is required for ubiquitin ligase activity. Polyubiquitinated, autoubiquitinated in the presence of UBE2D2. Belongs to the TRIM/RBCC family. +Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-aspartyl-tRNA(Asx) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +Beta-type chain found in early embryos. Heterotetramer of two epsilon chains and two alpha chains. Red blood cells. Belongs to the globin family. +Efflux pump for various substrates. Belongs to the major facilitator superfamily. TCR/Tet family. +Key structural component of the deuterosome, a structure that promotes de novo centriole amplification in multiciliated cells. Deuterosome-mediated centriole amplification occurs in terminally differentiated multiciliated cells and can generate more than 100 centrioles. Probably sufficient for the specification and formation of the deuterosome inner core. Interacts with CEP152 and recruits PLK4 to activate centriole biogenesis (By similarity). Interacts with CEP152; the interaction is mutually exclusive with CEP63. Localizes to the deuterosome. Belongs to the CEP63 family. It is uncertain whether Met-1 or Met-22 is the initiator. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Kinesin family. KIN-14 subfamily. Was originally thought to correspond to two different genes Os02g0229500 and Os02g0229600. Was originally thought to correspond to two different genes Os02g0229500 and Os02g0229600. +Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser) ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec) Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. Homodimer. The tRNA molecule binds across the dimer. Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily. +Transcriptional regulator that controls expression of some virulence factors in a cell density-dependent manner. Belongs to the SarA family. +Plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis. Belongs to the YciB family. +May operate as a cation/H(+) antiporter. Expressed in roots. Belongs to the monovalent cation:proton antiporter 2 (CPA2) transporter (TC 2.A.37) family. CHX (TC 2.A.37.4) subfamily. +Is involved in the catabolism of quinate. Allows the utilization of quinate as carbon source via the beta-ketoadipate pathway. 3-dehydroquinate = 3-dehydroshikimate + H2O Aromatic compound metabolism; 3,4-dihydroxybenzoate biosynthesis; 3,4-dihydroxybenzoate from 3-dehydroquinate: step 1/2. Homododecamer. Adopts a ring-like structure, composed of an arrangement of two hexameric rings stacked on top of one another. Belongs to the type-II 3-dehydroquinase family. +Multifunctional dioxygenase; part of the gene cluster B that mediates the biosynthesis of austinol and dehydroaustinol, two fungal meroterpenoids (PubMed:22329759). The first step of the pathway is the synthesis of 3,5-dimethylorsellinic acid by the polyketide synthase ausA (PubMed:22329759). 3,5-dimethylorsellinic acid is then prenylated by the polyprenyl transferase ausN (PubMed:22329759). Further epoxidation by the FAD-dependent monooxygenase ausM and cyclization by the probable terpene cyclase ausL lead to the formation of protoaustinoid A (PubMed:22329759). Protoaustinoid A is then oxidized to spiro-lactone preaustinoid A3 by the combined action of the FAD-binding monooxygenases ausB and ausC, and the dioxygenase ausE (PubMed:22329759, PubMed:23865690). Acid-catalyzed keto-rearrangement and ring contraction of the tetraketide portion of preaustinoid A3 by ausJ lead to the formation of preaustinoid A4 (PubMed:22329759). The aldo-keto reductase ausK, with the help of ausH, is involved in the next step by transforming preaustinoid A4 into isoaustinone which is in turn hydroxylated by the P450 monooxygenase ausI to form austinolide (PubMed:22329759). Finally, the cytochrome P450 monooxygenase ausG modifies austinolide to austinol (PubMed:22329759). Austinol can be further modified to dehydroaustinol which forms a diffusible complex with diorcinol that initiates conidiation (PubMed:22234162, PubMed:22329759). Due to genetic rearrangements of the clusters and the subsequent loss of some enzymes, the end products of the Emericella nidulans austinoid biosynthesis clusters are austinol and dehydroaustinol, even if additional enzymes, such as the O-acetyltransferase ausQ and the cytochrome P450 monooxygenase ausR are still functional (PubMed:29076725). 2-oxoglutarate + O2 + preaustinoid A1 = CO2 + H2O + preaustinoid A2 + succinate 2-oxoglutarate + O2 + preaustinoid A2 = CO2 + H2O + preaustinoid A3 + succinate 2-oxoglutarate + berkeleyone A + O2 = CO2 + H2O + preaustinoid A + succinate Secondary metabolite biosynthesis; terpenoid biosynthesis. Homodimer. Residues at positions 150 and 232 are important for the type of reaction catalyzed, using identical substrate (PubMed:29317628). Both ausE and prhA accept preaustinoid A1 as a substrate to form divergent products through dynamic skeletal rearrangement (PubMed:29317628). AusE (containing 'Leu-150' and 'Ser-232') first desaturates at C1-C2 to form preaustinoid A2, followed by rearrangement leading to the formation of the spiro-lactone in preaustinoid A3 (PubMed:29317628). In contrast, prhA (containing 'Val-150' and 'Ala-232') first desaturates at C5-C6 to form berkeleyone B, followed by rearrangement of the A/B-ring to form the cycloheptadiene moiety in berkeleydione (PubMed:22234162). Impairs the synthesis of austinol and dehydroaustinol (PubMed:22329759). In A.calidoustus, the austinoid gene cluster lies on a contiguous DNA region, while clusters from E.nidulans and P.brasilianum are split in their respective genomes. Genetic rearrangements provoked variability among the clusters and E.nidulans produces the least number of austionoid derivatives with the end products austinol and dehydroaustinol, while P.brasilianum can produce until acetoxydehydroaustin, and A.calidoustus produces the highest number of identified derivatives. Belongs to the PhyH family. +Plays a major role in protein secretion by helping the post-translocational extracellular folding of several secreted proteins. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the PrsA family. +Plays an important role in promoting lung pathology in both primary viral infection and secondary bacterial infection. Promotes alteration of mitochondrial morphology, dissipation of mitochondrial membrane potential, and cell death. Alternatively, inhibits the production of interferon in the infected cell at the level of host mitochondrial antiviral signaling MAVS. Its level of expression differs greatly depending on which cell type is infected, in a manner that is independent of the levels of expression of other viral proteins. Monocytic cells are more affected than epithelial cells. Seems to disable virus-infected monocytes or other host innate immune cells. During early stage of infection, predisposes the mitochondria to permeability transition through interaction with host SLC25A6/ANT3 and VDAC1. These proteins participate in the formation of the permeability transition pore complex (PTPC) responsible of the release of mitochondrial products that triggers apoptosis. Oligomer. Interacts with human SLC25A6/ANT3 and VDAC1. Interacts with host MAVS. Inner mitochondrial membrane in most cells types. Otherwise is detected in the nucleus and cytosol. Is not encoded in all strains, and seems to be dispensable for replication. Belongs to the influenza viruses PB1-F2 family. +Non-SCF-type F-box protein involved in the endocytic with the vacuolar sorting pathway. Acts as a repressor of YPT52 by inhibiting the formation of active, GTP-bound, YPT52. Involved in the defense mechanism against methylmercury toxicity. Interacts with SKP1 and YPT32; SKP1 is required for the interaction with YPT32. Expression is RSF1 and RSF2 dependent. The F-box domain is required for interaction with SKP1 and defense against methylmercury toxicity. Present with 3080 molecules/cell in log phase SD medium. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +Belongs to the MEMO1 family. +Probably catalyzes the addition of a phosphoethanolamine moiety to lipid A. Phosphoethanolamine modification of lipid A gives polymyxin resistance (PubMed:26603172). Confers resistance to polymyxin-type antibiotics; expression of the Mcr-1 protein in E.coli increases colistin and polymyxin B minimal inhibitory concentration (MIC) from 0.5 mg/ml to 2.0 mg/ml. The pHNSHP45 plasmid can transfer efficiently (0.1 to 0.001) to other E.coli strains by conjugation and increases polymxin MIC by 8- to 16-fold; it may not require selective pressure to be maintained in the cell. When transformed into K.pneumoniae or P.aeruginosa it also increases polymxin MIC 8- to 16-fold. In a murine (BALB/c mice) thigh infection study using an mcr1-encoding plasmid isolated from a human patient, the plasmid confers in vivo protection against colistin (PubMed:26603172). This is the first (as of November 2015) reported plasmid-mediated resistance to polymyxin antibiotics; although it does not confer a high MIC it protects against colistin treatment in an infection model. Colistin is one of the last-resort antibiotics available for multidrug-resistant Gram-negative bacteria such as K.pneumoniae, P.aeruginosa and Acinetobacter. First identified from a pig farm in Shanghai, China in July 2013, retrospective screening detects the gene in (slowly) increasing proportions between 2011 and 2015 from pigs and chickens, and also in hospitalized patients in China. Colistin is very widely used in veterinary agriculture (PubMed:26603172). Belongs to the phosphoethanolamine transferase family. +In elementary bodies (EBs, the infectious stage, which is able to survive outside the host cell) provides the structural integrity of the outer envelope through disulfide cross-links with the large cysteine-rich periplasmic protein and the major outer membrane porin. It has been described in publications as the Sarkosyl-insoluble COMC (Chlamydia outer membrane complex), and serves as the functional equivalent of peptidoglycan (By similarity). Part of a disulfide cross-linked outer membrane complex (COMC) composed of the major outer membrane porin (MOMP), the small cysteine-rich protein (OmcA) and the large cysteine-rich periplasmic protein (OmcB). The protein moiety probably penetrates into the periplasm. It is present but the disulfide bonds are reduced in reticulate bodies (RBs). +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Belongs to the archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit family. +Involved in the non-oxidative decarboxylation and detoxification of phenolic derivatives under anaerobic conditions, however the precise biochemical function in metabolism of phenolic acid is unknown. It is not known, if phenolic acid decarboxylase forms a complex composed of EdcB, EdcC and EdcD. The term subunit is often used in reference to the operon, however there is no experimental evidence to prove the existence of the complex. +Catalyzes the reduction of FMN to FMNH2 which is used to reduce pyrimidine by RutA via the Rut pathway. FMNH2 + NAD(+) = FMN + 2 H(+) + NADH Belongs to the non-flavoprotein flavin reductase family. RutF subfamily. +Component of the large ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Component of the large ribosomal subunit (By similarity). May bind IPO9 with low affinity (By similarity). Detected on cytosolic polysomes (By similarity). Detected in ribosomes that are associated with the rough endoplasmic reticulum (By similarity). Belongs to the eukaryotic ribosomal protein eL6 family. +Catalyzes the epimerization of trans-4-hydroxy-L-proline (t4LHyp) to cis-4-hydroxy-D-proline (c4DHyp). May be involved in a degradation pathway of t4LHyp. Can also catalyze the epimerization of trans-3-hydroxy-L-proline (t3LHyp) to cis-3-hydroxy-D-proline (c3DHyp) in vitro. Displays no proline racemase activity. trans-4-hydroxy-L-proline = cis-4-hydroxy-D-proline kcat is 1.3 sec(-1) for t4LHyp epimerization. kcat is 0.75 sec(-1) for t3LHyp epimerization. Belongs to the proline racemase family. +Catalyzes the first and rate-limiting reaction of the four reactions that constitute the long-chain fatty acids elongation cycle. This endoplasmic reticulum-bound enzymatic process allows the addition of 2 carbons to the chain of long- and very long-chain fatty acids (VLCFAs) per cycle. Condensing enzyme that acts specifically toward polyunsaturated acyl-CoA with the higher activity toward C18:3(n-6) acyl-CoA. May participate in the production of monounsaturated and of polyunsaturated VLCFAs of different chain lengths that are involved in multiple biological processes as precursors of membrane lipids and lipid mediators (By similarity). In conditions where the essential linoleic and alpha linoleic fatty acids are lacking it is also involved in the synthesis of Mead acid from oleic acid (PubMed:24184513). a very-long-chain acyl-CoA + H(+) + malonyl-CoA = a very-long-chain 3-oxoacyl-CoA + CO2 + CoA (6Z,9Z,12Z)-octadecatrienoyl-CoA + H(+) + malonyl-CoA = (8Z,11Z,14Z)-3-oxoeicosatrienoyl-CoA + CO2 + CoA (9Z,12Z,15Z)-octadecatrienoyl-CoA + H(+) + malonyl-CoA = (11Z,14Z,17Z)-3-oxoeicosatrienoyl-CoA + CO2 + CoA (9Z)-hexadecenoyl-CoA + H(+) + malonyl-CoA = 3-oxo-(11Z)-octadecenoyl-CoA + CO2 + CoA (9Z)-octadecenoyl-CoA + H(+) + malonyl-CoA = (11Z)-3-oxoicosenoyl-CoA + CO2 + CoA (11Z)-octadecenoyl-CoA + H(+) + malonyl-CoA = 3-oxo-(13Z)-eicosenoyl-CoA + CO2 + CoA (9Z,12Z)-octadecadienoyl-CoA + H(+) + malonyl-CoA = (11Z,14Z)-3-oxoicosa-11,14-dienoyl-CoA + CO2 + CoA (6Z,9Z,12Z,15Z)-octadecatetraenoyl-CoA + H(+) + malonyl-CoA = (8Z,11Z,14Z,17Z)-3-oxoicosatetraenoyl-CoA + CO2 + CoA (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA + H(+) + malonyl-CoA = (7Z,10Z,13Z,16Z)-3-oxodocosatetraenoyl-CoA + CO2 + CoA (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA + H(+) + malonyl-CoA = (7Z,10Z,13Z,16Z,19Z)-3-oxodocosapentaenoyl-CoA + CO2 + CoA Lipid metabolism; polyunsaturated fatty acid biosynthesis. In Purkinje cells, the protein localizes to the soma and proximal portion of the dendritic tree. Belongs to the ELO family. ELOVL5 subfamily. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit (By similarity). 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +Specifically methylates the N7 position of a guanine in 16S rRNA. Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of lipoate-dependent enzymes. (R)-lipoate + ATP + L-lysyl-[lipoyl-carrier protein] = (R)-N(6)-lipoyl-L-lysyl-[lipoyl-carrier protein] + AMP + diphosphate + H(+) Protein modification; protein lipoylation via exogenous pathway; protein N(6)-(lipoyl)lysine from lipoate: step 1/2. Protein modification; protein lipoylation via exogenous pathway; protein N(6)-(lipoyl)lysine from lipoate: step 2/2. Monomer. In the transfer reaction, the free carboxyl group of lipoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LplA family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Collagen receptor involved in collagen-induced platelet adhesion and activation. Plays a key role in platelet procoagulant activity and subsequent thrombin and fibrin formation. This procoagulant function may contribute to arterial and venous thrombus formation. The signaling pathway involves the FcR gamma-chain, the Src kinases (likely FYN or LYN) and SYK, the adapter protein LAT and leads to the activation of PLCG2. Associated with Fc receptor gamma chain. The GPVI:FcRgamma complex is associated with the Src kinase family FYN and LYN (PubMed:10961879, PubMed:9295288). Interacts with TRAF4 (PubMed:20946164). Interacts with COL1A1, but not with COL4A4 (By similarity). (Microbial infection) Interacts with Staphylococcus aureus protein SSL5. Megakaryocytes and platelets. N-linked glycosylation at Asn-92 is not required for the cell surface expression, but contributes to maximal adhesion to type I collagen, collagen-related peptide (CRP), and, to a lesser extent, to the snake venom C-type lectin convulxin (CVX). The disease is caused by variants affecting the gene represented in this entry. Has no transmembrane domain. Does not interact with Fc receptor gamma chain. Does not bind to collagen-like peptides. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Acts as component of the nascent polypeptide-associated complex (NAC), which promotes mitochondrial protein import by enhancing productive ribosome interactions with the outer mitochondrial membrane. Also blocks the inappropriate interaction of ribosomes translating non-secretory nascent polypeptides with translocation sites in the membrane of the endoplasmic reticulum. BTT1 may act as a transcription factor that exert a negative effect on the expression of several genes that are transcribed by RNA polymerase II (By similarity). Part of the nascent polypeptide-associated complex (NAC), consisting of EGD2 and either EGD1 or BTT1. NAC associates with ribosomes via EGD1 or BTT1 (By similarity). Predominantly cytoplasmic, may also transiently localize to the nucleus. Belongs to the NAC-beta family. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Also binds steroids, bilirubin, carcinogens and numerous organic anions. Has dichloromethane dehalogenase activity. glutathione + RX = a halide anion + an S-substituted glutathione + H(+) Homodimer. Belongs to the GST superfamily. Theta family. +An adapter protein which plays a role in the regulation of immunoreceptor signaling, including PLC-gamma-mediated B-cell antigen receptor (BCR) signaling and FC-epsilon R1-mediated mast cell degranulation (By similarity). Together with FGR, it acts as a negative regulator of natural killer cell-activating receptors and inhibits interferon-gamma production (By similarity). Acts as a positive regulator of both T-cell receptor and natural killer T (NKT) cell receptor signaling in CD4-positive NKT cells (By similarity). Together with MAP4K1, it enhances CD3-triggered activation of T-cells and subsequent IL2 production (By similarity). May be involved in tumor necrosis factor induced cell death by promoting reactive oxidative species generation, and MLKL oligomerization, ultimately leading to necrosis (By similarity). Involved in phosphorylation of LAT (By similarity). May be involved in high affinity immunoglobulin epsilon receptor signaling in mast cells (By similarity). When phosphorylated, interacts with PLCG1, PLCG2, GRB2, VAV and LAT (By similarity). Interacts with LBR and AGO2 (PubMed:26009488). Interacts with FGR (By similarity). Part of a complex consisting of CLNK, SKAP1 and FYB1 (By similarity). Interacts (via SH2 domain) with FYB1; this interaction allows SKAP1 and FYB1 to promote tyrosine phosphorylation of CLNK by LYN (By similarity). Interacts (via SH2 domain) with MAP4K1 (By similarity). The N-terminal proline-rich region interacts with the SH3 domain of PLCG1. The SH2 domain is important for restoration of BCR-induced calcium response and JNK2 activation in BLNK-deficient DT40 cells expressing LAT. Tyrosine-phosphorylated upon BCR cross-linking. Tyrosine phosphorylation at both Tyr-69 and Tyr-96 are required for BCR-induced calcium response and are essential to restore PLCG2-mediated signaling in BLNK-deficient DT40 cells, but this phosphorylation is dispensable in cells expressing LAT. Interacts with the SH2 domain of PLCG1 via phosphorylated Tyr-96 (By similarity). Tyrosine phosphorylation is increased when complexed with SKAP1 and FYB1 (By similarity). +Belongs to the bacterial ribosomal protein bL35 family. +Transcriptional activator that specifically binds 5'-GATA-3' or 5'-GAT-3' motifs within gene promoters. By drought and salt stresses. Belongs to the type IV zinc-finger family. Class C subfamily. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis. Belongs to the YciB family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +This protein binds specifically to 23S rRNA. The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Trans-enoyl reductase; part of the gene cluster that mediates the biosynthesis of HIV-1 integrase inhibitor equisetin and of fusarisetin A, both trans-fused decalin-containing tetramic acids showing also antimicrobial activity (PubMed:25770422). The PKS module of fsa1 together with the enoylreductase fsa3 catalyze the formation of the polyketide unit which is then conjugated to L-serine by the condensation domain of the fsa1 NRPS module (PubMed:25770422). Activity of the Dieckmann cyclase domain (RED) results in release of the Dieckmann product intermediate (PubMed:25770422). Diels-Alderase fsa2 is involved in endo-selective Diels-Alder cycloaddition to form the decalin ring, leading to the production of N-desmethylequisetin also called trichosetin (PubMed:25770422, PubMed:28401214, PubMed:29972614, PubMed:34121297). Subsequent N-methylation is carried out by fsa4 to give equisetin (PubMed:25770422). The enzymatic gene responsible for the conversion of equisetin to fusarisetin A has not been identified yet and is probably located outside of the fsa cluster (PubMed:28401214). acetyl-CoA + ATP + 11 H(+) + L-serine + 7 malonyl-CoA + 8 NADPH + 2 S-adenosyl-L-methionine = (5S)-3-[(2E,6R,8E,10E,12E)-2,6-dimethyltetradeca-2,8,10,12-tetraenoyl]-5-(hydroxymethyl)pyrrolidine-2,4-dione + AMP + 7 CO2 + 8 CoA + diphosphate + 6 H2O + 8 NADP(+) + 2 S-adenosyl-L-homocysteine Mycotoxin biosynthesis. Monomer. Results in the loss of production of equisetin and fusarisetin A (PubMed:25770422). Belongs to the zinc-containing alcohol dehydrogenase family. +Involved in the synthesis of Nod factor, a sulfated N-acyl-beta-1,4-tetrasaccharide of N-acetylglucosamine which initiates a series of events in the host plant species leading eventually to nodulation. Belongs to the NodC/HAS family. +Catalyzes the conversion of lactate to pyruvate. (S)-lactate + NAD(+) = H(+) + NADH + pyruvate Allosterically activated by fructose 1,6-bisphosphate (FBP). Fermentation; pyruvate fermentation to lactate; (S)-lactate from pyruvate: step 1/1. Homotetramer. Belongs to the LDH/MDH superfamily. LDH family. +Catalyzes the NADPH-dependent reduction of succinic semialdehyde to gamma-hydroxybutyrate. May have an important role in producing the neuromodulator gamma-hydroxybutyrate (GHB). Has broad substrate specificity. Can reduce the dialdehyde protein-binding form of aflatoxin B1 (AFB1) to the non-binding AFB1 dialcohol. May be involved in protection of liver against the toxic and carcinogenic effects of AFB1, a potent hepatocarcinogen (By similarity). 4-hydroxybutanoate + NADP(+) = H(+) + NADPH + succinate semialdehyde Inhibited by citrate, succinate and tartrate. Homodimer. Expressed in liver, kidney, testis and brain with low levels in skeletal muscle, spleen, heart and lung. Belongs to the aldo/keto reductase family. Aldo/keto reductase 2 subfamily. +Belongs to the UPF0235 family. +Non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA. Homodimer. The ends of the coiled-coil dimer bind to each other, forming polymers. Interacts with FtsZ. Localizes to the septum at mid-cell, in a FtsZ-like pattern. Belongs to the ZapB family. +Atypical bHLH transcription factor probably unable to bind DNA. Negatively regulates brassinosteroid signaling. Homodimer (Probable). Interacts with PRE3. +Immunity component of one of 6 LXG toxin-immunity modules in this strain. They promote kin selection, mediate competition in biofilms, and drive spatial segregation of different strains, indicating that LXG toxins may help avoid warfare between strains in biofilms. Mediates intercellular competition during biofilm formation; disruption of the operon disadvantages the bacteria, but overexpression of the cognate immunity protein restores growth in competition with wild-type. In situ neutralizes the toxic effect of cognate toxin YqcG (PubMed:34280190). Neutralizes the toxic activity of cognate toxin YqcG upon expression in E.coli. Does not have immunity protein activity on other LXG toxins (PubMed:22200572). Probably interacts with cognate toxin YqcG but not with other non-cognate toxins. The interaction inhibits the toxic activity of YqcG (Probable). Expressed on rich and minimal solid media likely in early stationary phase; dependent on DegSU. Not expressed in liquid LB, but only under conditions that promote biofilm formation. Deletion of the yqcF-yqcG operon has no visible growth phenotype, however it is out-competed by wild-type cells. +Adds the terminal N-acetyl-D-glucosamine group on the glucose(II) group of LPS. UDP-N-acetyl-alpha-D-glucosamine + [lipopolysaccharide] = UDP + N-acetyl-alpha-D-glucosaminyl-[lipopolysaccharide]. Bacterial outer membrane biogenesis; LPS core biosynthesis. +Modulates transcription in response to changes in cellular NADH/NAD(+) redox state. Homodimer. Belongs to the transcriptional regulatory Rex family. +ATP + hydrogencarbonate + NH4(+) = ADP + carbamoyl phosphate + H(+) + H2O Metabolic intermediate metabolism; carbamoyl phosphate degradation; CO(2) and NH(3) from carbamoyl phosphate: step 1/1. Belongs to the carbamate kinase family. +Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation. Required for sporulation. Has a role late in meiosis following DNA replication. Part of the multisubunit TRAPP (transport protein particle) I complex composed of BET3, BET5, TRS20, TRS23, TRS31 and TRS33. Part of the multisubunit TRAPP (transport protein particle) II complex composed of BET3, BET5, TRS20, TRS23, TRS31, TRS33, TRS65, TRS85, TRS120 and TRS130. Part of the multisubunit TRAPP (transport protein particle) III complex composed of BET3, BET5, TRS20, TRS23, TRS31, TRS33 and TRS85. Belongs to the TRAPP small subunits family. BET3 subfamily. +5'-3' exonuclease acting preferentially on double-stranded DNA. +Belongs to the AAA ATPase family. +Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm. This transfer involves a cascade of disulfide bond formation and reduction steps. [protein]-dithiol + NAD(+) = [protein]-disulfide + H(+) + NADH [protein]-dithiol + NADP(+) = [protein]-disulfide + H(+) + NADPH Belongs to the thioredoxin family. DsbD subfamily. +Probable RNA methyltransferase. Embryonic lethality (PubMed:31145769). Conditional knockdown in ovary leads to female sterility, possibly caused by dysregulation of miRNAs and mRNAsso (PubMed:31145769). Belongs to the methyltransferase superfamily. +Belongs to the ubiquitin-conjugating enzyme family. FTS subfamily. Lacks the conserved Cys residue necessary for ubiquitin-conjugating enzyme E2 activity. +Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). diphosphate + N-(5-phospho-beta-D-ribosyl)anthranilate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate Binds 2 magnesium ions per monomer. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 2/5. Homodimer. Belongs to the anthranilate phosphoribosyltransferase family. +Catalyzes the irreversible NADPH-dependent deamination of GMP to IMP. It functions in the conversion of nucleobase, nucleoside and nucleotide derivatives of G to A nucleotides, and in maintaining the intracellular balance of A and G nucleotides. IMP + NADP(+) + NH4(+) = GMP + 2 H(+) + NADPH Belongs to the IMPDH/GMPR family. GuaC type 2 subfamily. +Plays an important role in DNA replication, recombination and repair. Binds to ssDNA and to an array of partner proteins to recruit them to their sites of action during DNA metabolism. Homotetramer. +Specific class of high-redox-potential 4Fe-4S ferredoxins. Functions in anaerobic electron transport in most purple and in some other photosynthetic bacteria and in at least one genus (Paracoccus) of halophilic, denitrifying bacteria. Homodimer. Belongs to the high-potential iron-sulfur protein (HiPIP) family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle. oxaloacetate + phosphate = hydrogencarbonate + phosphoenolpyruvate Belongs to the PEPCase type 1 family. +Probably a ribosomal protein or a ribosome-associated protein. Part of the 30S ribosomal subunit. Belongs to the chloroplast-specific ribosomal protein cS23 family. +Belongs to the UPF0758 family. +Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine. putrescine + S-adenosyl 3-(methylsulfanyl)propylamine = H(+) + S-methyl-5'-thioadenosine + spermidine Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1. Homodimer or homotetramer. Belongs to the spermidine/spermine synthase family. +Forms a proton-selective ion channel that is necessary for the efficient release of the viral genome during virus entry. After attaching to the cell surface, the virion enters the cell by endocytosis. Acidification of the endosome triggers M2 ion channel activity. The influx of protons into virion interior is believed to disrupt interactions between the viral ribonucleoprotein (RNP), matrix protein 1 (M1), and lipid bilayers, thereby freeing the viral genome from interaction with viral proteins and enabling RNA segments to migrate to the host cell nucleus, where influenza virus RNA transcription and replication occur. Also plays a role in viral proteins secretory pathway. Elevates the intravesicular pH of normally acidic compartments, such as trans-Golgi network, preventing newly formed hemagglutinin from premature switching to the fusion-active conformation. The M2 protein from most influenza A strains is inhibited by amantadine and rimantadine, resulting in viral uncoating incapacity. Emergence of amantadine-resistant variants is usually rapid. Homotetramer; composed of two disulfide-linked dimers held together by non-covalent interactions. May interact with matrix protein 1. Abundantly expressed at the apical plasma membrane in infected polarized epithelial cells, in close proximity to budding and assembled virions. Minor component of virions (only 16-20 molecules/virion). Only the first 9 residues are shared by the 2 isoforms. Cytoplasmic tail plays an important role in virion assembly and morphogenesis. When the channel is activated, one or more imidazole moieties of His-37 probably become bi-protonated. Belongs to the influenza viruses matrix protein M2 family. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG). 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + H(+) Optimum pH is between 5.6 and 6. Carbohydrate acid metabolism; 2-dehydro-3-deoxy-D-gluconate degradation; D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate: step 1/2. Belongs to the carbohydrate kinase pfkB family. +Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing. a 3'-end 3'-phospho-ribonucleotide-RNA + ATP = a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + AMP + diphosphate Belongs to the RNA 3'-terminal cyclase family. Type 1 subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Has low pectate lyase activity. Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends. Binds 1 Ca(2+) ion. Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-gluconate from pectin: step 2/5. Expressed in pollen (at protein level). N-glycosylated; consists of complex-type N-glycans containing the Lewis a antigen (Galbeta1-3(Fucalpha1-4)GlcNAcbeta1-). Causes an allergic reaction in human. Binds to IgE of patients allergic to mountain cedar (PubMed:10482836, PubMed:10482835, PubMed:14563374, PubMed:16423400). Binds to IgE in 71% of the 14 patients tested allergic to mountain cedar. Binds to IgE in 40% of the 35 patients tested allergic to Japanese cedar (PubMed:10482835). IgE-binding is significantly reduced by heat denaturation (75 degrees Celsius), chemical denaturation (guanidine treatment) and reductive alkylation in guanidine, but not by reductive alkylation alone, indicating the presence of conformational epitopes. On the other hand, heat and guanidine-induced denaturation increases binding to a mouse monoclonal antibody KW-S91, indicative of enhanced display of the linear epitope by these treatments (PubMed:16423400). Causes proliferation of the peripheral blood mononuclear cells (PBMCs) in patients allergic to mountain cedar (PubMed:10482835). Causes seasonal allergic rhinitis in North America (PubMed:10482836, PubMed:10482835, PubMed:14563374, PubMed:16423400). Belongs to the polysaccharide lyase 1 family. Amb a subfamily. +Acts as a transcriptional activator. Involved in neurogenesis. Plays important roles in the early stage of organogenesis of the CNS, as well as during dorsal spinal cord development and maturation of the cerebellum. Involved in the spatial distribution of mossy fiber (MF) neurons within the pontine gray nucleus (PGN). Plays a role in the regulation of MF axon pathway choice. Promotes MF migration towards ipsilaterally-located cerebellar territories. May have a role in shear flow mechanotransduction in osteocytes. Retains nuclear GLI1 and GLI3 in the cytoplasm. Binds to the minimal GLI-consensus sequence 5'-TGGGTGGTC-3' (By similarity). Interacts (via the C2H2-type domains 3, 4 and 5) with MDFIC (via the C2H2-type domains 3, 4 and 5). Interacts with GLI1; the interaction enhances transcription activation. Interacts with GLI2. Interacts with GLI3; the interaction enhances transcription activation (By similarity). Localizes in the cytoplasm in presence of MDFIC overexpression. CNS. A high level expression is seen in the cerebellum. Detected in the nuclei of the cerebellar granule cell lineage from the progenitor cells of the external germinal layer to the postmigrated cells of the internal granular layer. Detected in medulloblastoma (26/29 cases), but not present in all other tumors examined. The C2H2-type 3, 4 and 5 zinc finger domains are necessary for transcription activation. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the GLI C2H2-type zinc-finger protein family. +Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6-phosphate and D-lactate. H2O + N-acetyl-D-muramate 6-phosphate = (R)-lactate + N-acetyl-D-glucosamine 6-phosphate Amino-sugar metabolism; N-acetylmuramate degradation. Homodimer. A lyase-type mechanism (elimination/hydration) is suggested for the cleavage of the lactyl ether bond of MurNAc 6-phosphate, with the formation of an alpha,beta-unsaturated aldehyde intermediate with (E)-stereochemistry, followed by the syn addition of water to give product. Belongs to the GCKR-like family. MurNAc-6-P etherase subfamily. +NDH-1 shuttles electrons from an unknown electron donor, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH-1 can be composed of about 15 different subunits; different subcomplexes with different compositions have been identified which probably have different functions. Belongs to the complex I subunit 3 family. +Acts as an inhibitor of bacterial RNA polymerase by interacting with RpoC subunit and thus preventing promoter recognition by RpoE. Non-DNA-binding transcription factor that plays a role in the transcriptional switch that abolishes transcription of the viral early genes (class I) by the host RNA polymerase but allows transcription of late genes (class II and class III) by T7 RNA polymerase. Interacts with host RpoC; this interaction inhibits host RNA polymerase activity. +Involved in the processing of the 20S pre-rRNA. Belongs to the FYV7 family. +Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner. ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) Monomer. ValRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated threonine is translocated from the active site to the editing site. The C-terminal coiled-coil domain is crucial for aminoacylation activity. Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily. +Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain. acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine Binds 1 Mg(2+) ion per subunit. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; N-acetyl-alpha-D-glucosamine 1-phosphate from alpha-D-glucosamine 6-phosphate (route II): step 2/2. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; UDP-N-acetyl-alpha-D-glucosamine from N-acetyl-alpha-D-glucosamine 1-phosphate: step 1/1. Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. In the N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family. In the C-terminal section; belongs to the transferase hexapeptide repeat family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Packages viral RNA to form a viral nucleocapsid, and promotes virion budding (Probable). Participates in the viral particle production as a result of its interaction with the non-structural protein 5A (By similarity). Binds RNA and may function as a RNA chaperone to induce the RNA structural rearrangements taking place during virus replication (By similarity). Modulates viral translation initiation by interacting with viral IRES and 40S ribosomal subunit (By similarity). Affects various cell signaling pathways, host immunity and lipid metabolism (Probable). Prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) and IFN-gamma signaling pathways and by blocking the formation of phosphorylated STAT1 and promoting ubiquitin-mediated proteasome-dependent degradation of STAT1 (By similarity). Activates STAT3 leading to cellular transformation (By similarity). Regulates the activity of cellular genes, including c-myc and c-fos (By similarity). May repress the promoter of p53, and sequester CREB3 and SP110 isoform 3/Sp110b in the cytoplasm (By similarity). Represses cell cycle negative regulating factor CDKN1A, thereby interrupting an important check point of normal cell cycle regulation (By similarity). Targets transcription factors involved in the regulation of inflammatory responses and in the immune response: suppresses TNF-induced NF-kappa-B activation, and activates AP-1 (By similarity). Binds to dendritic cells (DCs) via C1QR1, resulting in down-regulation of T-lymphocytes proliferation (By similarity). Alters lipid metabolism by interacting with hepatocellular proteins involved in lipid accumulation and storage (By similarity). Induces up-regulation of FAS promoter activity, and thereby contributes to the increased triglyceride accumulation in hepatocytes (steatosis) (By similarity). Forms a heterodimer with envelope glycoprotein E2, which mediates virus attachment to the host cell, virion internalization through clathrin-dependent endocytosis and fusion with host membrane (By similarity). Fusion with the host cell is most likely mediated by both E1 and E2, through conformational rearrangements of the heterodimer required for fusion rather than a classical class II fusion mechanism (By similarity). E1/E2 heterodimer binds host apolipoproteins such as APOB and ApoE thereby forming a lipo-viro-particle (LVP) (By similarity). APOE associated to the LVP allows the initial virus attachment to cell surface receptors such as the heparan sulfate proteoglycans (HSPGs), syndecan-1 (SDC1), syndecan-1 (SDC2), the low-density lipoprotein receptor (LDLR) and scavenger receptor class B type I (SCARB1) (By similarity). The cholesterol transfer activity of SCARB1 allows E2 exposure and binding of E2 to SCARB1 and the tetraspanin CD81 (By similarity). E1/E2 heterodimer binding on CD81 activates the epithelial growth factor receptor (EGFR) signaling pathway (By similarity). Diffusion of the complex E1-E2-EGFR-SCARB1-CD81 to the cell lateral membrane allows further interaction with Claudin 1 (CLDN1) and occludin (OCLN) to finally trigger HCV entry (By similarity). Forms a heterodimer with envelope glycoprotein E1, which mediates virus attachment to the host cell, virion internalization through clathrin-dependent endocytosis and fusion with host membrane (By similarity). Fusion with the host cell is most likely mediated by both E1 and E2, through conformational rearrangements of the heterodimer required for fusion rather than a classical class II fusion mechanism (By similarity). The interaction between envelope glycoprotein E2 and host apolipoprotein E/APOE allows the proper assembly, maturation and infectivity of the viral particles (By similarity). This interaction is probably promoted via the up-regulation of cellular autophagy by the virus (By similarity). E1/E2 heterodimer binds host apolipoproteins such as APOB and APOE thereby forming a lipo-viro-particle (LVP) (By similarity). APOE associated to the LVP allows the initial virus attachment to cell surface receptors such as the heparan sulfate proteoglycans (HSPGs), syndecan-1 (SDC1), syndecan-1 (SDC2), the low-density lipoprotein receptor (LDLR) and scavenger receptor class B type I (SCARB1) (By similarity). The cholesterol transfer activity of SCARB1 allows E2 exposure and binding of E2 to SCARB1 and the tetraspanin CD81 (By similarity). E1/E2 heterodimer binding on CD81 activates the epithelial growth factor receptor (EGFR) signaling pathway (By similarity). Diffusion of the complex E1-E2-EGFR-SCARB1-CD81 to the cell lateral membrane allows further interaction with Claudin 1 (CLDN1) and occludin (OCLN) to finally trigger HCV entry (By similarity). Inhibits host EIF2AK2/PKR activation, preventing the establishment of an antiviral state (By similarity). Viral ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on dendritic cells (DCs), and on liver sinusoidal endothelial cells and macrophage-like cells of lymph node sinuses (By similarity). These interactions allow the capture of circulating HCV particles by these cells and subsequent facilitated transmission to permissive cells such as hepatocytes and lymphocyte subpopulations (By similarity). The interaction between E2 and host amino acid transporter complex formed by SLC3A2 and SLC7A5/LAT1 may facilitate viral entry into host cell (By similarity). Ion channel protein that acts as a viroporin and plays an essential role in the assembly, envelopment and secretion of viral particles (By similarity). Regulates the host cell secretory pathway, which induces the intracellular retention of viral glycoproteins and favors assembly of viral particles (By similarity). Creates a pore in acidic organelles and releases Ca(2+) and H(+) in the cytoplasm of infected cells, leading to a productive viral infection (By similarity). High levels of cytoplasmic Ca(2+) may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication (Probable). This ionic imbalance induces the assembly of the inflammasome complex, which triggers the maturation of pro-IL-1beta into IL-1beta through the action of caspase-1 (By similarity). Targets also host mitochondria and induces mitochondrial depolarization (By similarity). In addition of its role as a viroporin, acts as a lipid raft adhesion factor (By similarity). Cysteine protease required for the proteolytic auto-cleavage between the non-structural proteins NS2 and NS3 (By similarity). The N-terminus of NS3 is required for the function of NS2 protease (active region NS2-3) (By similarity). Promotes the initiation of viral particle assembly by mediating the interaction between structural and non-structural proteins (By similarity). Displays three enzymatic activities: serine protease with a chymotrypsin-like fold, NTPase and RNA helicase (By similarity). NS3 serine protease, in association with NS4A, is responsible for the cleavages of NS3-NS4A, NS4A-NS4B, NS4B-NS5A and NS5A-NS5B (By similarity). The NS3/NS4A complex prevents phosphorylation of host IRF3, thus preventing the establishment of dsRNA induced antiviral state (By similarity). The NS3/NS4A complex induces host amino acid transporter component SLC3A2, thus contributing to HCV propagation (By similarity). NS3 RNA helicase binds to RNA and unwinds both dsDNA and dsRNA in the 3' to 5' direction, and likely resolves RNA complicated stable secondary structures in the template strand (By similarity). Binds a single ATP and catalyzes the unzipping of a single base pair of dsRNA (By similarity). Inhibits host antiviral proteins TBK1 and IRF3 thereby preventing the establishment of an antiviral state (By similarity). Cleaves host MAVS/CARDIF thereby preventing the establishment of an antiviral state (By similarity). Cleaves host TICAM1/TRIF, thereby disrupting TLR3 signaling and preventing the establishment of an antiviral state (By similarity). Induces a specific membrane alteration that serves as a scaffold for the virus replication complex (By similarity). This membrane alteration gives rise to the so-called ER-derived membranous web that contains the replication complex (By similarity). NS4B self-interaction contributes to its function in membranous web formation (By similarity). Promotes host TRIF protein degradation in a CASP8-dependent manner thereby inhibiting host TLR3-mediated interferon signaling (By similarity). Disrupts the interaction between STING and TBK1 contributing to the inhibition of interferon signaling (By similarity). Phosphorylated protein that is indispensable for viral replication and assembly (By similarity). Both hypo- and hyperphosphorylated states are required for the viral life cycle (By similarity). The hyperphosphorylated form of NS5A is an inhibitor of viral replication (By similarity). Involved in RNA-binding and especially in binding to the viral genome (By similarity). Zinc is essential for RNA-binding (By similarity). Participates in the viral particle production as a result of its interaction with the mature viral core protein (By similarity). Its interaction with host VAPB may target the viral replication complex to vesicles (By similarity). Down-regulates viral IRES translation initiation (By similarity). Mediates interferon resistance, presumably by interacting with and inhibiting host EIF2AK2/PKR (By similarity). Prevents BIN1-induced apoptosis (By similarity). Acts as a transcriptional activator of some host genes important for viral replication when localized in the nucleus (By similarity). Via the interaction with host PACSIN2, modulates lipid droplet formation in order to promote virion assembly (By similarity). Modulates TNFRSF21/DR6 signaling pathway for viral propagation (By similarity). RNA-dependent RNA polymerase that performs primer-template recognition and RNA synthesis during viral replication. Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'. a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate ATP + H2O = ADP + H(+) + phosphate a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Activity of protease NS2 is dependent on zinc ions and completely inhibited by EDTA. This is probably due to the fact that NS2 protease activity needs NS3 N-terminus that binds a zinc atom (active region NS2-3). Binds 1 zinc ion, which has a structural role (By similarity). The magnesium ion is essential for the helicase activity (By similarity). Binds 2 magnesium ion that constitute a dinuclear catalytic metal center. Inhibited by the antiviral drug hexamethylene amiloride (By similarity). Inhibition by amantadine appears to be genotype-dependent (By similarity). Also inhibited by long-alkyl-chain iminosugar derivatives (By similarity). Activity is up-regulated by PRK2/PKN2-mediated phosphorylation. Homooligomer (By similarity). Interacts with E1 (via C-terminus) (By similarity). Interacts with the non-structural protein 5A (By similarity). Interacts (via N-terminus) with host STAT1 (via SH2 domain); this interaction results in decreased STAT1 phosphorylation and ubiquitin-mediated proteasome-dependent STAT1 degradation, leading to decreased IFN-stimulated gene transcription (By similarity). Interacts with host STAT3; this interaction constitutively activates STAT3 (By similarity). Interacts with host LTBR receptor (By similarity). Interacts with host TNFRSF1A receptor and possibly induces apoptosis (By similarity). Interacts with host HNRPK (By similarity). Interacts with host YWHAE (By similarity). Interacts with host UBE3A/E6AP (By similarity). Interacts with host DDX3X (By similarity). Interacts with host APOA2 (By similarity). Interacts with host RXRA protein (By similarity). Interacts with host SP110 isoform 3/Sp110b; this interaction sequesters the transcriptional corepressor SP110 away from the nucleus (By similarity). Interacts with host CREB3 nuclear transcription protein; this interaction triggers cell transformation (By similarity). Interacts with host ACY3 (By similarity). Interacts with host C1QR1 (By similarity). Interacts with host RBM24; this interaction, which enhances the interaction of the mature core protein with 5'-UTR, may inhibit viral translation and favor replication (By similarity). Interacts with host EIF2AK2/PKR; this interaction induces the autophosphorylation of EIF2AK2 (By similarity). Part of the viral assembly initiation complex composed of NS2, E1, E2, NS3, NS4A, NS5A and the mature core protein (By similarity). Forms a heterodimer with envelope glycoprotein E2 (By similarity). Interacts with mature core protein (By similarity). Interacts with protease NS2 (By similarity). The heterodimer E1/E2 interacts with host CLDN1; this interaction plays a role in viral entry into host cell (By similarity). Interacts with host SPSB2 (via C-terminus) (By similarity). Part of the viral assembly initiation complex composed of NS2, E1, E2, NS3, NS4A, NS5A and the mature core protein (By similarity). Forms a heterodimer with envelope glycoprotein E1 (By similarity). Interacts with host CD81 and SCARB1 receptors; these interactions play a role in viral entry into host cell (By similarity). Interacts with host EIF2AK2/PKR; this interaction inhibits EIF2AK2 and probably allows the virus to evade the innate immune response (By similarity). Interacts with host CD209/DC-SIGN and CLEC4M/DC-SIGNR (By similarity). Interact with host SPCS1; this interaction is essential for viral particle assembly (By similarity). Interacts with protease NS2 (By similarity). The heterodimer E1/E2 interacts with host CLDN1; this interaction plays a role in viral entry into host cell (By similarity). Part of the viral assembly initiation complex composed of NS2, E1, E2, NS3, NS4A, NS5A and the mature core protein (By similarity). Interacts with host SLC3A2/4F2hc; the interaction may facilitate viral entry into host cell (By similarity). Interacts with human PLSCR1 (By similarity). Homohexamer (By similarity). Homoheptamer (By similarity). Interacts with protease NS2 (By similarity). Homodimer (By similarity). Interacts with host SPCS1; this interaction is essential for viral particle assembly (By similarity). Interacts with envelope glycoprotein E1 (By similarity). Interacts with envelope glycoprotein E2 (By similarity). Interacts with viroporin p7 (By similarity). Interacts with serine protease/helicase NS3 (By similarity). Part of the replication complex composed of NS2, NS3, NS4A, NS4B, NS5A and the RNA-directed RNA polymerase embedded in an ER-derived membranous web (By similarity). Part of the viral assembly initiation complex composed of NS2, E1, E2, NS3, NS4A, NS5A and the mature core protein (By similarity). Interacts with protease NS2 (By similarity). Interacts with non-structural protein 4A; this interaction stabilizes the folding of NS3 serine protease (By similarity). NS3-NS4A interaction is essential for NS3 activation and allows membrane anchorage of the latter (By similarity). NS3/NS4A complex also prevents phosphorylation of host IRF3, thus preventing the establishment of dsRNA induced antiviral state (By similarity). Interacts with host MAVS; this interaction leads to the cleavage and inhibition of host MAVS (By similarity). Interacts with host TICAM1; this interaction leads to the cleavage and inhibition of host TICAM1 (By similarity). Interacts with host TANK-binding kinase/TBK1; this interaction results in the inhibition of the association between TBK1 and IRF3, which leads to the inhibition of IRF3 activation (By similarity). Interacts with host RBM24 (By similarity). Part of the replication complex composed of NS2, NS3, NS4A, NS4B, NS5A and the RNA-directed RNA polymerase embedded in an ER-derived membranous web (By similarity). Part of the viral assembly initiation complex composed of NS2, E1, E2, NS3, NS4A, NS5A and the mature core protein (By similarity). Interacts with NS3 serine protease; this interaction stabilizes the folding of NS3 serine protease (By similarity). NS3-NS4A interaction is essential for NS3 activation and allows membrane anchorage of the latter (By similarity). Interacts with non-structural protein 5A (via N-terminus) (By similarity). Part of the replication complex composed of NS2, NS3, NS4A, NS4B, NS5A and the RNA-directed RNA polymerase embedded in an ER-derived membranous web (By similarity). Part of the viral assembly initiation complex composed of NS2, E1, E2, NS3, NS4A, NS5A and the mature core protein (By similarity). Homomultimer (By similarity). Interacts with non-structural protein NS5A (By similarity). Interacts with host PLA2G4C; this interaction likely initiates the recruitment of replication complexes to lipid droplets (By similarity). Interacts with host STING; this interaction disrupts the interaction between STING and TBK1 thereby suppressing the interferon signaling (By similarity). Part of the replication complex composed of NS2, NS3, NS4A, NS4B, NS5A and the RNA-directed RNA polymerase embedded in an ER-derived membranous web (By similarity). Monomer (By similarity). Homodimer; dimerization is required for RNA-binding (By similarity). Interacts with mature core protein (By similarity). Interacts (via N-terminus) with non-structural protein 4A (By similarity). Interacts with non-structural protein 4B (By similarity). Interacts with RNA-directed RNA polymerase (By similarity). Part of the viral assembly initiation complex composed of NS2, E1, E2, NS3, NS4A, NS5A and the mature core protein (By similarity). Part of the replication complex composed of NS2, NS3, NS4A, NS4B, NS5A and the RNA-directed RNA polymerase (By similarity). Interacts with host GRB2 (By similarity). Interacts with host BIN1 (By similarity). Interacts with host PIK3R1 (By similarity). Interacts with host SRCAP (By similarity). Interacts with host FKBP8 (By similarity). Interacts with host VAPB (By similarity). Interacts with host EIF2AK2/PKR; this interaction leads to disruption of EIF2AK2 dimerization by NS5A and probably allows the virus to evade the innate immune response (By similarity). Interacts (via N-terminus) with host PACSIN2 (via N-terminus); this interaction attenuates protein kinase C alpha-mediated phosphorylation of PACSIN2 by disrupting the interaction between PACSIN2 and PRKCA (By similarity). Interacts (via N-terminus) with host SRC kinase (via SH2 domain) (By similarity). Interacts with most Src-family kinases (By similarity). Interacts with host IFI27 and SKP2; promotes the ubiquitin-mediated proteasomal degradation of NS5A (By similarity). Interacts with host GPS2 (By similarity). Interacts with host TNFRSF21; this interaction allows the modulation by the virus of JNK, p38 MAPK, STAT3, and Akt signaling pathways in a DR6-dependent manner (By similarity). Interacts (via N-terminus) with host CIDEB (via N-terminus); this interaction seems to regulate the association of HCV particles with APOE (By similarity). Interacts with host CHKA/Choline Kinase-alpha; CHKA bridges host PI4KA and NS5A and potentiates NS5A-stimulated PI4KA activity, which then facilitates the targeting of the ternary complex to the ER for viral replication (By similarity). Interacts with host SPSB2 (via C-terminus); this interaction targets NS5A for ubiquitination and degradation (By similarity). Interacts with host RAB18; this interaction may promote the association of NS5A and other replicase components with lipid droplets (By similarity). Homooligomer (By similarity). Interacts with non-structural protein 5A (By similarity). Interacts with host VAPB (By similarity). Interacts with host PRK2/PKN2 (By similarity). Interacts with host HNRNPA1 and SEPT6; these interactions facilitate viral replication (By similarity). Part of the replication complex composed of NS2, NS3, NS4A, NS4B, NS5A and the RNA-directed RNA polymerase (By similarity). The C-terminal transmembrane domain of the core protein precursor contains an ER signal leading the nascent polyprotein to the ER membrane. Only a minor proportion of core protein is present in the nucleus (By similarity). Probably present on the surface of lipid droplets (By similarity). The C-terminal transmembrane domain acts as a signal sequence and forms a hairpin structure before cleavage by host signal peptidase (By similarity). After cleavage, the membrane sequence is retained at the C-terminus of the protein, serving as ER membrane anchor (By similarity). A reorientation of the second hydrophobic stretch occurs after cleavage producing a single reoriented transmembrane domain (By similarity). These events explain the final topology of the protein (By similarity). The C-terminal transmembrane domain acts as a signal sequence and forms a hairpin structure before cleavage by host signal peptidase (By similarity). After cleavage, the membrane sequence is retained at the C-terminus of the protein, serving as ER membrane anchor (By similarity). A reorientation of the second hydrophobic stretch occurs after cleavage producing a single reoriented transmembrane domain (By similarity). These events explain the final topology of the protein (By similarity). The C-terminus of p7 membrane domain acts as a signal sequence (By similarity). After cleavage by host signal peptidase, the membrane sequence is retained at the C-terminus of the protein, serving as ER membrane anchor (By similarity). ER retention of p7 is leaky and a small fraction reaches the plasma membrane (By similarity). Probably present on the surface of lipid droplets. NS3 is associated to the ER membrane through its binding to NS4A. Host membrane insertion occurs after processing by the NS3 protease. A reorientation of the N-terminus into the ER lumen occurs post-translationally. Host membrane insertion occurs after processing by the NS3 protease (By similarity). Localizes at the surface of lipid droplets (By similarity). Host membrane insertion occurs after processing by the NS3 protease. The transmembrane regions of envelope E1 and E2 glycoproteins are involved in heterodimer formation, ER localization, and assembly of these proteins. The transmembrane regions of envelope E1 and E2 glycoproteins are involved in heterodimer formation, ER localization, and assembly of these proteins (By similarity). Envelope E2 glycoprotein contain two highly variable regions called hypervariable region 1 and 2 (HVR1 and HVR2) (By similarity). E2 also contain two segments involved in CD81-binding (By similarity). HVR1 is implicated in the SCARB1-mediated cell entry and probably acts as a regulator of the association of particles with lipids (By similarity). The N-terminus of NS3 is required for the catalytic activity of protease NS2 (By similarity). The minimal catalytic region includes the C-terminus of NS2 and the N-terminus NS3 protease domain (active region NS2-3) (By similarity). The N-terminal one-third contains the protease activity (By similarity). This region contains a zinc atom that does not belong to the active site, but may play a structural rather than a catalytic role (By similarity). This region is essential for the activity of protease NS2, maybe by contributing to the folding of the latter (By similarity). The NTPase/helicase activity is located in the twothirds C-terminus of NS3, this domain contains the NTPase and RNA-binding regions (By similarity). Contains a glycine zipper region that critically contributes to the biogenesis of functional ER-derived replication organelles. The N-terminus of NS5A acts as membrane anchor (By similarity). The central part of NS5A contains a variable region called interferon sensitivity determining region (ISDR) and seems to be intrinsically disordered and interacts with NS5B and host EIF2AK2 (By similarity). The C-terminus of NS5A contains a variable region called variable region 3 (V3) (By similarity). ISDR and V3 may be involved in sensitivity and/or resistance to IFN-alpha therapy (By similarity). The C-terminus contains a nuclear localization signal (By similarity). The SH3-binding domain is involved in the interaction with host BIN1, GRB2 and Src-family kinases (By similarity). Specific enzymatic cleavages in vivo yield mature proteins (By similarity). The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases (By similarity). The core protein precursor is synthesized as a 23 kDa, which is retained in the ER membrane through the hydrophobic signal peptide (By similarity). Cleavage by the signal peptidase releases the 21 kDa mature core protein (By similarity). The cleavage of the core protein precursor occurs between aminoacids 176 and 188 but the exact cleavage site is not known (By similarity). Some degraded forms of the core protein appear as well during the course of infection (By similarity). The other proteins (p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (By similarity). Autoprocessing between NS2 and NS3 is mediated by the NS2 cysteine protease catalytic domain and regulated by the NS3 N-terminal domain (By similarity). Phosphorylated by host PKC and PKA. Ubiquitinated; mediated by UBE3A and leading to core protein subsequent proteasomal degradation. Highly N-glycosylated. Highly N-glycosylated. Palmitoylation is required for NS2/3 autoprocessing and E2 recruitment to membranes. Palmitoylated. This modification may play a role in its polymerization or in protein-protein interactions. Phosphorylated on serines in a basal form termed p56 (By similarity). p58 is a hyperphosphorylated form of p56 (By similarity). p56 and p58 coexist in the cell in roughly equivalent amounts (By similarity). Hyperphosphorylation is dependent on the presence of NS4A (By similarity). Host CSNK1A1/CKI-alpha or RPS6KB1 kinases may be responsible for NS5A phosphorylation (By similarity). Tyrosine phosphorylation is essential for the interaction with host SRC. The N-terminus is phosphorylated by host PRK2/PKN2. Viral particle assembly takes place at the surface of ER-derived membranes in close proximity to lipid droplets. NS2 associates with E1/E2 glycoproteins, NS3 and NS5A, which interacts with the viral RNA and core protein to promote genome encapsidation. The nucleocapsid buds at the ER membrane where E1/E2 glycoproteins are anchored and afterward associate with nascent lipid droplet to acquire APOE and APOC. Secretion of viral particles is probably regulated by viroporin p7. Cell culture adaptation of the virus leads to mutations in NS5A, reducing its inhibitory effect on replication. Exerts viral interference on hepatitis B virus when HCV and HBV coinfect the same cell, by suppressing HBV gene expression, RNA encapsidation and budding. Belongs to the hepacivirus polyprotein family. The core gene probably also codes for alternative reading frame proteins (ARFPs). Many functions depicted for the core protein might belong to the ARFPs. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +Confers cellular resistance to apoptosis induced by the non-steroidal anti-inflammatory drugs indomethacin and diclofenac. May act as an efflux pump (By similarity). Belongs to the major facilitator superfamily. +Belongs to the UPF0398 family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Zeins are major seed storage proteins. The alpha zeins of 19 kDa and 22 kDa account for 70% of the total zein fraction. They are encoded by a large multigene family. Structurally, 22K and 19K zeins are composed of nine adjacent, topologically antiparallel helices clustered within a distorted cylinder. Belongs to the zein family. Due to sequence microheterogeneity among zein messenger RNAs, this protein might be encoded by the same gene as AZS22-8 (AC P04699). +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Acts as essential component of the kinetochore MIND complex, which is required for the spindle checkpoint and kinetochore integrity. MIND plays a role in establishing a bipolar spindle-kinetochore interaction by joining kinetochore subunits contacting DNA to those contacting microtubules. NNF1 is required for a number of nuclear functions. Cells depleted of NNF11 or containing a temperature-sensitive NNF1 mutation have elongated microtubules and become bi- and multinucleate. They also have a fragmented nucleolus and accumulate poly(A)+ RNA inside the nucleus. Component of the MIND kinetochore complex, which is composed of at least MTW1, NNF1, NSL1 and DSN1. Associated with the kinetochore (PubMed:12455957, PubMed:14657030). Present with 2070 molecules/cell in log phase SD medium. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG. Homodimer. UreD, UreF and UreG form a complex that acts as a GTP-hydrolysis-dependent molecular chaperone, activating the urease apoprotein by helping to assemble the nickel containing metallocenter of UreC. The UreE protein probably delivers the nickel. Belongs to the SIMIBI class G3E GTPase family. UreG subfamily. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +(6S)-5,6,7,8-tetrahydrofolate + ATP + formate = (6S)-10-formyltetrahydrofolate + ADP + phosphate One-carbon metabolism; tetrahydrofolate interconversion. Belongs to the formate--tetrahydrofolate ligase family. +May negatively regulate the SNF1 kinase. Belongs to the SIP5 family. +Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 1 subfamily. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. Belongs to the FlgH family. +Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate from the periplasm across the membrane. Belongs to the dicarboxylate/amino acid:cation symporter (DAACS) (TC 2.A.23) family. +Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine (By similarity). Heterotetramer of two type I and two type II keratins. Associates with KRT8 (By similarity). Hyperphosphorylation at Ser-13 occurs during the early stages of apoptosis but becomes less prominent during the later stages. Phosphorylation at Ser-13 also increases in response to stress brought on by cell injury (By similarity). Proteolytically cleaved by caspases during apoptosis. Cleavage occurs at Asp-228 (By similarity). There are two types of cytoskeletal and microfibrillar keratin: I (acidic; 40-55 kDa) and II (neutral to basic; 56-70 kDa). Belongs to the intermediate filament family. +Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell. Homopentamer. Belongs to the MscL family. +Involved in oxygen transport from gills to the various peripheral tissues. Hb1 is a heterotetramer of two alpha chains and two beta chains. HbC is a heterotetramer of two alpha chains and two beta-C chains. Red blood cells. This fish has three hemoglobins: Hb1 (major) and two minor hemoglobins (about 1-2% of the total). Hb1 has a strong alkaline Bohr effect, and at low pH exhibits the reduced ligand affinity and cooperativity that comprise the Root effect. Belongs to the globin family. +(R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Belongs to the prokaryotic pantothenate kinase family. +Belongs to the UPF0312 family. Type 1 subfamily. +Catalyzes the hydrolysis of bioactive endogenous fatty acid amides to their corresponding acids (PubMed:16624618). The hydrolysis of endogenous amidated lipids terminates their participation as lipid mediators in various signaling systems (Probable). Converts a wide range of N-acylethanolamines (NAEs) to their corresponding free fatty acids and ethanolamine (PubMed:16624618). H2O + N-(9Z,12Z-octadecadienoyl)-ethanolamine = (9Z,12Z)-octadecadienoate + ethanolamine H2O + N-hexadecanoylethanolamine = ethanolamine + hexadecanoate H2O + N-dodecanoylethanolamine = dodecanoate + ethanolamine Inhibited by methyl arachidonyl fluorophosphonate (MAFP). Forms homodimers. Belongs to the amidase family. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. +Catalyzes the phosphorylation of D-glycero-D-manno-heptose 7-phosphate at the C-1 position to selectively form D-glycero-beta-D-manno-heptose-1,7-bisphosphate. Catalyzes the ADP transfer from ATP to D-glycero-beta-D-manno-heptose 1-phosphate, yielding ADP-D-glycero-beta-D-manno-heptose. ATP + D-glycero-beta-D-manno-heptose 7-phosphate = ADP + D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H(+) ATP + D-glycero-beta-D-manno-heptose 1-phosphate + H(+) = ADP-D-glycero-beta-D-manno-heptose + diphosphate Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate: step 1/4. Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate: step 3/4. Homodimer. In the N-terminal section; belongs to the carbohydrate kinase PfkB family. In the C-terminal section; belongs to the cytidylyltransferase family. +From analysis of the sizes of several other differentiated genes that hybridize to this one, the authors conclude that all of these V regions have rearranged to the same J segment, JH2. +Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA. a fatty acyl-[ACP] + phosphate = an acyl phosphate + holo-[ACP] Lipid metabolism; phospholipid metabolism. Homodimer. Probably interacts with PlsY. Associated with the membrane possibly through PlsY. Belongs to the PlsX family. +May form oligomeric structures. Binds to AKR2A (PubMed:21730198). Accumulates after heat shock. Belongs to the small heat shock protein (HSP20) family. +Globally modulates RNA abundance by binding to RNase E (Rne) and regulating its endonucleolytic activity. Can modulate Rne action in a substrate-dependent manner by altering the composition of the degradosome. Modulates RNA-binding and helicase activities of the degradosome. Homotrimer. Binds to both RNA-binding sites in the C-terminal region of Rne and to RhlB. Belongs to the RraA family. +As a component of IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), it is involved in ciliogenesis. Involved in retrograde ciliary transport along microtubules from the ciliary tip to the base. Component of the IFT complex A (IFT-A) complex. IFT-A complex is divided into a core subcomplex composed of IFT122:IFT140:WDR19 which is associated with TULP3 and a peripheral subcomplex composed of IFT43:WDR35:TTC21B. Interacts directy with IFT122, WDR35 and TTC21B. Associated with microtubules. Localized at the distal tip of the cilium. Belongs to the IFT43 family. +Required for gamma-tubulin complex recruitment to the microtubule organizing center (MTOC). Part of the gamma-tubulin complex. Belongs to the MOZART1 family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. A homomeric c-ring of probably 10 subunits is part of the complex rotary element. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Interacts with TMEM70 and TMEM242 (By similarity). Trimethylated by ATPSCKMT at Lys-110. Methylation is required for proper incorporation of the C subunit into the ATP synthase complex and mitochondrial respiration. This protein is the major protein stored in the storage bodies of animals or humans affected with ceroid lipofuscinosis (Batten disease). There are three genes which encode the mitochondrial ATP synthase proteolipid and they specify precursors with different import sequences but identical mature proteins. Belongs to the ATPase C chain family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. +Part of the Tol-Pal system, which plays a role in outer membrane invagination during cell division and is important for maintaining outer membrane integrity. The Tol-Pal system is composed of five core proteins: the inner membrane proteins TolA, TolQ and TolR, the periplasmic protein TolB and the outer membrane protein Pal. They form a network linking the inner and outer membranes and the peptidoglycan layer. Belongs to the TolB family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP = 7,8-dihydrofolate + dTMP Pyrimidine metabolism; dTTP biosynthesis. Homodimer. Belongs to the thymidylate synthase family. Bacterial-type ThyA subfamily. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Required for efficient N-glycosylation. Necessary for maintaining optimal levels of dolichol-linked oligosaccharides. Hydrolyzes dolichyl pyrophosphate at a very high rate and dolichyl monophosphate at a much lower rate. Does not act on phosphatidate (By similarity). a dolichyl diphosphate + H2O = a dolichyl phosphate + H(+) + phosphate Protein modification; protein glycosylation. Belongs to the dolichyldiphosphatase family. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +Prolyl 3,4-dihydroxylase that catalyzes 3,4-dihydroxylation of 'Pro-62' of small ribosomal subunit uS12 (rps23 and rps2302), thereby regulating protein translation termination efficiency. Negative regulator of the stability of the N-terminal transcription factor domain (Sre1N) of sre1 which is released from the membrane and enters the nucleus to activate hypoxic gene expression. 2-oxoglutarate + [ribosomal protein uS12]-L-proline + O2 = [ribosomal protein uS12]-(3S)-3-hydroxy-L-proline + CO2 + succinate 2-oxoglutarate + [ribosomal protein uS12]-(3S)-3-hydroxy-L-proline + O2 = [ribosomal protein uS12]-(3S)-3,4-dihydroxy-L-proline + CO2 + succinate Binds 1 Fe(2+) ion per subunit. Monomer and homodimer (By similarity). Interacts with nro1 (PubMed:19158663). Belongs to the TPA1 family. +G-protein coupled receptor for medium and long chain saturated and unsaturated fatty acids that plays an important role in glucose homeostasis. Fatty acid binding increases glucose-stimulated insulin secretion, and may also enhance the secretion of glucagon-like peptide 1 (GLP-1). May also play a role in bone homeostasis; receptor signaling activates pathways that inhibit osteoclast differentiation. Ligand binding leads to a conformation change that triggers signaling via G-proteins that activate phospholipase C, leading to an increase of the intracellular calcium concentration. Seems to act through a G(q) and G(i)-mediated pathway. Mediates the anti-inflammatory effects of omega-3 polyunsaturated fatty acids (PUFAs) via inhibition of NLRP3 inflammasome activation. Belongs to the G-protein coupled receptor 1 family. +Cytokine that in its homotrimeric form binds to TNFRSF1A/TNFR1, TNFRSF1B/TNFBR and TNFRSF14/HVEM (By similarity). In its heterotrimeric form with LTB binds to TNFRSF3/LTBR. Lymphotoxin is produced by lymphocytes and is cytotoxic for a wide range of tumor cells in vitro and in vivo. Homotrimer, and heterotrimer of either two LTB and one LTA subunits or (less prevalent) two LTA and one LTB subunits. Interacts with TNFRSF14. The homotrimer is secreted. The heterotrimer is membrane-associated. Belongs to the tumor necrosis factor family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Metalloglycoprotein, containing Ca, Mg, Mn, and Zn and the carbohydrates galactose, glucosamine, mannose, and fucose. It agglutinates erythrocytes of blood group A1. Homotetramer. Belongs to the leguminous lectin family. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis. ATP + beta-D-fructose 6-phosphate = ADP + beta-D-fructose 1,6-bisphosphate + H(+) Allosterically activated by ADP and other diphosphonucleosides, and allosterically inhibited by phosphoenolpyruvate. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 3/4. Homotetramer. Belongs to the phosphofructokinase type A (PFKA) family. ATP-dependent PFK group I subfamily. Prokaryotic clade 'B1' sub-subfamily. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. 2-oxoglutarate + O-phospho-L-serine = 3-phosphooxypyruvate + L-glutamate 2-oxoglutarate + 4-(phosphooxy)-L-threonine = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate Binds 1 pyridoxal phosphate per subunit. Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 2/3. Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 3/5. Homodimer. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. SerC subfamily. +Meiosis-specific telomere-associated protein involved in meiotic telomere attachment to the nucleus inner membrane, a crucial step for homologous pairing and synapsis. Component of the MAJIN-TERB1-TERB2 complex, which promotes telomere cap exchange by mediating attachment of telomeric DNA to the inner nuclear membrane and replacement of the protective cap of telomeric chromosomes: in early meiosis, the MAJIN-TERB1-TERB2 complex associates with telomeric DNA and the shelterin/telosome complex. During prophase, the complex matures and promotes release of the shelterin/telosome complex from telomeric DNA. In the MAJIN-TERB1-TERB2 complex, TERB1 probably mediates association with the shelterin/telosome complex via interaction with TERF1, promoting priming telomeric DNA attachment'. Promotes telomere association with the nuclear envelope and deposition of the SUN-KASH/LINC complex. Also recruits cohesin to telomeres to develop structural rigidity. Component of the MAJIN-TERB1-TERB2 complex, composed of MAJIN, TERB1 and TERB2. Interacts with TERF1, STAG3 and SUN1. Interacts (via Myb-like domain) with the cohesin complex; probably mediated via interaction with STAG3. Localizes to telomeres during meiotic prophase. In leptotene spermatocytes, localizes to telomeres that localize to the nucleus inner membrane. Phosphorylated by CDK. Phosphorylation by CDK takes place in late prophase when the cap exchange is prominent. is important for the stabilization of telomere attachment but dispenable for the cap exchange. The disease is caused by variants affecting the gene represented in this entry. Belongs to the TERB1 family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit (By similarity). 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +May cause loosening and extension of plant cell walls by disrupting non-covalent bonding between cellulose microfibrils and matrix glucans. No enzymatic activity has been found (By similarity). A number of isoforms are produced. According to EST sequences. Belongs to the expansin family. Expansin B subfamily. +Transcription factor that binds to the DNA sequence 5'-ACTCAT-3' in target gene promoters. Promotes POX1/PRODH1 expression in response to hypoosmolarity stress (PubMed:15047879). Positively regulates the expression of ASN1 and POX2/PRODH2 genes, which are involved in amino acid metabolism (PubMed:18088315). Regulates several metabolic pathways such as myo-inositol, raffinose and trehalose. Regulates several trehalose metabolism genes, including TRE1, TPP5 and TPP6 (PubMed:21534971). Mediates recruitment of the histone acetylation machinery to activate auxin-induced transcription. Interacts with ADA2B adapter protein to promote ADA2B-mediated recruitment of SAGA-like histone acetyltransferase complexes to specific auxin-responsive genes (PubMed:24861440). Forms heterodimers with BZIP1, BZIP9, BZIP10, BZIP25 and BZIP63 (PubMed:16709202). Interacts with ADA2B (PubMed:24861440). Highly expressed in stems and flowers (PubMed:9620274). Expressed in root tips, cotyledons, leaf vasculature, embryos, apical parts of siliques and funiculi (PubMed:9721683). By light (PubMed:9620274). Induced by hypoosmolarity (PubMed:15047879). Repressed by sucrose (at protein level) (PubMed:9721683, PubMed:15208401). A highly conserved upstream open reading frame (uORF) coding for 42 amino acids is essential for the BZIP11 sucrose-induced repression of translation (SIRT) (PubMed:15208401). Plants over-expressing BZIP11 show severe alterations of plant growth and development, reduced seed set and viability (PubMed:18088315). +Required for growth under high-pressure and low-temperature conditions. Belongs to the DLT1 family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II. PSII consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII forms dimeric complexes. Belongs to the PsbX family. Type 2 subfamily. +Belongs to the bacterial ribosomal protein bL32 family. +Plays a role in the inhibition of host type I interferon production within the host nucleus. Targets specifically the NF-kappa-B-mediated interferon-beta transcription. Found in the host nucleus but is excluded from the nucleoli. +Component of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum (ER) and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis, and function in nonvesicular lipid trafficking between the ER and mitochondria. The mdm12-mmm1 subcomplex functions in the major beta-barrel assembly pathway that is responsible for biogenesis of all outer membrane beta-barrel proteins, and acts in a late step after the SAM complex. The mdm10-mdm12-mmm1 subcomplex further acts in the TOM40-specific pathway after the action of the mdm12-mmm1 complex. Essential for establishing and maintaining the structure of mitochondria and maintenance of mtDNA nucleoids. Homodimer. Component of the ER-mitochondria encounter structure (ERMES) or MDM complex, composed of mmm1, mdm10, mdm12 and mdm34. A mmm1 homodimer associates with one molecule of mdm12 on each side in a pairwise head-to-tail manner, and the SMP-LTD domains of mmm1 and mdm12 generate a continuous hydrophobic tunnel for phospholipid trafficking. The ERMES/MDM complex localizes to a few discrete foci (around 10 per single cell), that represent mitochondria-endoplasmic reticulum junctions. These foci are often found next to mtDNA nucleoids. The SMP-LTD domain is a barrel-like domain that can bind various types of glycerophospholipids in its interior and mediate their transfer between two adjacent bilayers. Belongs to the MMM1 family. +Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Involved in the recycling pathway of the cell wall turnover product MurNAc-GlcNAc in S.aureus. Catalyzes the hydrolysis of MurNAc 6-phosphate-GlcNAc, the disaccharide product of MurP-uptake and phosphorylation, yielding MurNAc 6-phosphate and GlcNAc. 6-phospho-N-acetyl-beta-D-muramate-(1->4)-N-acetyl-D-glucosamine + H2O = N-acetyl-D-glucosamine + N-acetyl-D-muramate 6-phosphate Cell wall biogenesis; peptidoglycan recycling. Cells lacking this gene show a cytoplasmic accumulation of MurNAc 6-phosphate-GlcNAc, predominantly during stationary phase. This accumulation can be abolished by expressing MupG. Belongs to the glycosyl hydrolase 170 family. +This protein is one of many from the eggshell of the silk moth. Belongs to the chorion protein family. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel. Generally pentameric. This subunit coassembles with alpha-2, beta-1 and gamma-1. Belongs to the ligand-gated ion channel (TC 1.A.9) family. Gamma-aminobutyric acid receptor (TC 1.A.9.5) subfamily. GABRQ sub-subfamily. +O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway. a 3-demethylubiquinol + S-adenosyl-L-methionine = a ubiquinol + H(+) + S-adenosyl-L-homocysteine a 3-(all-trans-polyprenyl)benzene-1,2-diol + S-adenosyl-L-methionine = a 2-methoxy-6-(all-trans-polyprenyl)phenol + H(+) + S-adenosyl-L-homocysteine Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the methyltransferase superfamily. UbiG/COQ3 family. +Part of the ABC transporter complex MglABC involved in galactose/methyl galactoside import. Responsible for energy coupling to the transport system. ATP + D-galactose(out) + H2O = ADP + D-galactose(in) + H(+) + phosphate The complex is composed of two ATP-binding proteins (MglA), two transmembrane proteins (MglC) and a solute-binding protein (MglB). Belongs to the ABC transporter superfamily. Galactose/methyl galactoside importer (TC 3.A.1.2.3) family. +Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate. AH2 + GTP + S-adenosyl-L-methionine = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + A + H(+) + L-methionine Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate. Cofactor biosynthesis; molybdopterin biosynthesis. Belongs to the radical SAM superfamily. MoaA family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +Implicated in mitochondrial protein import and macromolecular assembly. May facilitate the correct folding of imported proteins. May also prevent misfolding and promote the refolding and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix. By heat shock. There are multiple isoforms that, with increasing temperature, shift in relative abundance from the more basic to the more acidic. Exists in at least five isoforms that are not related by a simple post-translational modification and may represent the products of different genes. Belongs to the chaperonin (HSP60) family. +Cleaves the alpha-chain at multiple sites and the beta-chain between 'Lys-53' and 'Lys-54' but not the gamma-chain of fibrinogen and therefore does not initiate the formation of the fibrin clot and does not cause the fibrinolysis directly. It does not cleave (activate) prothrombin and plasminogen but converts the inactive single chain urinary plasminogen activator (pro-urokinase) to the active two chain form. Activates coagulation factor VII (By similarity). Heterodimer; disulfide-linked. Heterodimer of a 50 kDa heavy and a 27 kDa light chain linked by a disulfide bond (By similarity). Secreted as an inactive single-chain precursor and is then activated to a heterodimeric form. Proteolytic cleavage at Gly-23 or Met-27 can give rise to the 50 kDa heavy chain and cleavage at Arg-311 or Lys-317 can give rise to the 27 kDa light chain. The heavy chain can undergo further proteolytic cleavage at Arg-168 or Arg-169 to give rise to two inactive 26 kDa fragments and the light chain can undergo further proteolytic cleavage at Arg-478 to give rise to inactive 17 kDa and 8 kDa fragments (By similarity). Belongs to the peptidase S1 family. +Transaminase; part of the gene clusters that mediate the biosynthesis of AM-toxins, host-selective toxins (HSTs) causing Alternaria blotch on apple, a worldwide distributed disease (Probable). AM-toxins are cyclic depsipeptides containing the 3 residues 2-hydroxy-isovaleric acid (2-HIV), dehydroalanine, L-alanine which are common for all 3 AM-toxins I to III. The fourth precursor is L-alpha-amino-methoxyphenyl-valeric acid (L-Amv) for AM-toxin I, L-alpha-amino-phenyl-valeric acid (L-Apv) for AM-toxin II, and L-alpha-amino-hydroxyphenyl-valeric acid (L-Ahv) for AM-toxin III (Probable). AM-toxins have two target sites for affecting susceptible apple cells; they cause invagination of the plasma membrane and electrolyte loss and chloroplast disorganization (PubMed:22846083). The non-ribosomal peptide synthetase AMT1 contains 4 catalytic modules and is responsible for activation of each residue in AM-toxin (PubMed:10875335). The aldo-keto reductase AMT2 catalyzes the conversion of 2-keto-isovaleric acid (2-KIV) to 2-hydroxy-isovaleric acid (2-HIV), one of the precursor residues incorporated by AMT1 during AM-toxin biosynthesis, by reduction of its ketone to an alcohol (PubMed:15066029). The cytochrome P450 monooxygenase AMT3 and the thioesterase AMT4 are also important for AM-toxin production, but their exact function within the AM-toxin biosynthesis are not known yet (PubMed:17990954). Up to 21 proteins (including AMT1 to AMT4) are predicted to be involved in AM-toxin biosynthesis since their expression is highly up-regulated in AM-toxin-producing cultures (PubMed:17990954). Mycotoxin biosynthesis. Expression is up-regulated more than 10 fold in toxin producing cultures. Gene clusters encoding host-selective toxins (HSTs) are localized on conditionally dispensable chromosomes (CDCs), also called supernumerary chromosomes, where they are present in multiple copies (PubMed:17990954). The CDCs are not essential for saprophytic growth but controls host-selective pathogenicity (PubMed:17990954). Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family. +May be involved in epidermal differentiation and inflammation and might therefore be important for the pathogenesis of psoriasis and other diseases. Overexpressed in psoriasis. Belongs to the S-100 family. +Binds 16S rRNA, required for the assembly of 30S particles. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS14 family. +Catalytic subunit of the periplasmic nitrate reductase complex NapAB. Receives electrons from NapB and catalyzes the reduction of nitrate to nitrite. 2 Fe(II)-[cytochrome] + 2 H(+) + nitrate = 2 Fe(III)-[cytochrome] + H2O + nitrite Binds 1 [4Fe-4S] cluster. Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit. Component of the periplasmic nitrate reductase NapAB complex composed of NapA and NapB. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/NapA/NarB subfamily. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation (By similarity). Required for trans-translation (PubMed:11395451). Probably required for sporulation; deletion of the gene for tmRNA impairs sporulation via its effect on trans-translation, and as smpB is required for trans-translation under non-stress conditions, it is also probably required during sporulation (PubMed:18673456). The tmRNA-SmpB complex associates with stalled 70S ribosomes. Constitutively expressed, part of a 5 gene operon with multiple promoters. Not ethanol-stress induced. Not essential for growth; loss of trans-translation (PubMed:11395451). Significantly decreased growth at 16 and 52 degrees Celsius (PubMed:17369301). Belongs to the SmpB family. +Product of a dubious CDS prediction. May be a non-coding RNA. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +Catalytic subunit of the essential mitochondrial processing protease (MPP), which cleaves the mitochondrial sequence off newly imported precursors proteins (PubMed:2007593, PubMed:9299349, PubMed:9654444). Preferentially, cleaves after an arginine at position P2 (By similarity). Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2. Binds 1 zinc ion per subunit. Binding to MAS2 is required for catalytic activity (PubMed:9654444, PubMed:9299349). Inhibited by high levels (> 1uM) of zinc (PubMed:9654444). Inhibited by metal chelators ethylenediaminetetraacetic acid (EDTA) and O-phenanthroline (PubMed:9654444). Heterodimer of MAS2 (alpha) and MAS1 (beta) subunits, forming the mitochondrial processing protease (MPP) in which MAS2 is involved in substrate recognition and binding and MAS1 is the catalytic subunit. Present with 1360 molecules/cell in log phase SD medium. Belongs to the peptidase M16 family. +Involved in the viral transport within, and between cells. Interacts with the capsid protein (CP). Part of a MP-CP-viral DNA complex (By similarity). Belongs to the mastrevirus movement protein family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 13 different subunits. Subunits NuoB, CD, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. 4-deoxy-4-formamido-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + H2O = 4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + formate Glycolipid biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate from UDP-4-deoxy-4-formamido-beta-L-arabinose and undecaprenyl phosphate: step 2/2. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the polysaccharide deacetylase family. ArnD deformylase subfamily. +Catalyzes the formation of N(4)-acetylcytidine (ac(4)C) at the wobble position of elongator tRNA(Met), using acetate and ATP as substrates. First activates an acetate ion to form acetyladenylate (Ac-AMP) and then transfers the acetyl group to tRNA to form ac(4)C34. acetate + ATP + cytidine(34) in elongator tRNA(Met) = AMP + diphosphate + N(4)-acetylcytidine(34) in elongator tRNA(Met) Belongs to the TmcAL family. +Myosin heavy chain that is required for the cell cycle-regulated transport of various organelles and proteins for their segregation. Functions by binding with its tail domain to receptor proteins on organelles and exerting force with its N-terminal motor domain against actin filaments, thereby transporting its cargo along polarized actin cables (By similarity). Involved in endocytosis via its action in endosomal trafficking. Homodimer. A number of isoforms are produced. According to EST sequences. IQ domain mediates interaction with calmodulin. Belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Myosin family. Plant myosin class VIII subfamily. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 4L family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +Truncated N-terminus. +Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+) Binds 1 dipyrromethane group covalently. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. Monomer. The porphobilinogen subunits are added to the dipyrromethane group. Belongs to the HMBS family. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +NDH-1 shuttles electrons from an unknown electron donor, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH-1 can be composed of about 15 different subunits; different subcomplexes with different compositions have been identified which probably have different functions. Belongs to the complex I subunit 3 family. +Belongs to the major facilitator superfamily. +ATP + uridine = ADP + H(+) + UMP ATP + cytidine = ADP + CMP + H(+) Pyrimidine metabolism; CTP biosynthesis via salvage pathway; CTP from cytidine: step 1/3. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uridine: step 1/1. Belongs to the uridine kinase family. +Catalyzes the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids. alpha-D-mannose 1-phosphate + GTP + H(+) = diphosphate + GDP-alpha-D-mannose Activated by Mn(2+). Nucleotide-sugar biosynthesis; GDP-alpha-D-mannose biosynthesis; GDP-alpha-D-mannose from alpha-D-mannose 1-phosphate (GTP route): step 1/1. Associates with GMPPA (in vivo). Expressed in the liver (at protein level). Belongs to the transferase hexapeptide repeat family. +Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit acts as a catalytic chaperone that increases the ATP-binding affinity of the ATP-hydrolyzing subunit KdpB by the formation of a transient KdpB/KdpC/ATP ternary complex. The system is composed of three essential subunits: KdpA, KdpB and KdpC. Belongs to the KdpC family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Catalyzes the ATP-dependent phosphorylation of L-homoserine to L-homoserine phosphate. ATP + L-homoserine = ADP + H(+) + O-phospho-L-homoserine Amino-acid biosynthesis; L-threonine biosynthesis; L-threonine from L-aspartate: step 4/5. Belongs to the GHMP kinase family. Homoserine kinase subfamily. +Downstream effector protein for Rho-type small GTPases that plays a role in cell polarity and directional migration (PubMed:27807006). Acts as an adapter protein, linking active Rho proteins to STK24 and STK26 kinases, and hence positively regulates Golgi reorientation in polarized cell migration upon Rho activation (PubMed:27807006). Involved in the subcellular relocation of STK26 from the Golgi to cytoplasm punctae in a Rho- and PDCD10-dependent manner upon serum stimulation (PubMed:27807006). Interacts (via N-terminus) with RHOA (GTP-bound form); this interaction links active RHOA to STK24 and STK26 kinases (PubMed:27807006). Interacts with RHOB (PubMed:27807006). Interacts with RHOC (PubMed:27807006). Interacts (via C-terminus) with PDCD10; this interaction occurs in a Rho-independent manner (PubMed:27807006). Interacts (via C-terminus) with STK24; this interaction occurs in a PDCD10-dependent and Rho-independent manner (PubMed:27807006). Interacts (via C-terminus) with STK26; this interaction occurs in a PDCD10-dependent and Rho-independent manner (PubMed:27807006). Interacts (via N-terminus) with 14-3-3 proteins; these interactions occur in a Rho-dependent manner (PubMed:27807006). Localizes to the podocyte major processes and cell body (By similarity). Colocalized with STK26 in the Golgi of serum-starved cells and relocated to cytoplasmic punctae, probably vesicular compartments, along with STK26 upon serum stimulation in a Rho- and PDCD10-dependent manner (PubMed:27807006). Belongs to the RIPOR family. Truncated C-terminus. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Plays an early essential role in mesoderm formation, as well as a later role in formation of somite-derived chondrogenic lineages. Efficient DNA binding requires dimerization with another bHLH protein. Dimerizes and binds the E-box consensus sequence with E12 (By similarity). +(S)-malate + NAD(+) = CO2 + NADH + pyruvate H(+) + oxaloacetate = CO2 + pyruvate Divalent metal cations. Prefers magnesium or manganese. Homotetramer. Belongs to the malic enzymes family. +Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif. L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-methionine = H(+) + N(5)-methyl-L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-homocysteine Belongs to the protein N5-glutamine methyltransferase family. PrmC subfamily. +Non-specific receptor for endothelin 1, 2, and 3. Mediates its action by association with G proteins that activate a phosphatidylinositol-calcium second messenger system. internalized after activation by endothelins. Belongs to the G-protein coupled receptor 1 family. Endothelin receptor subfamily. EDNRB sub-subfamily. +Belongs to the UPF0115 family. +Protease with a carboxypeptidase B-like function involved in the C-terminal processing of the lysine and arginine residues from protein precursors. Promotes cell fusion and is involved in the programmed cell death (By similarity). Preferential release of a C-terminal arginine or lysine residue. Belongs to the peptidase S10 family. +Belongs to the UPF0306 family. +May be involved in ulvan degradation (Probable). Ulvan is the main polysaccharide component of the Ulvales (green seaweed) cell wall. It is composed of disaccharide building blocks comprising 3-sulfated rhamnose (Rha3S) linked to D-glucuronic acid (GlcA), L-iduronic acid (IduA), or D-xylose (Xyl) (Probable). By ulvan and rhamnose. Truncated N-terminus. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS5 family. +This peptide hormone induces gall bladder contraction and the release of pancreatic enzymes in the gut. Its function in the brain is not clear. Binding to CCK-A receptors stimulates amylase release from the pancreas, binding to CCK-B receptors stimulates gastric acid secretion. Binds to CCK-A receptors in the pancreas and CCK-B receptors in the brain. The precursor is cleaved by proteases to produce a number of active cholecystokinins. The precursor is cleaved by ACE, which removes the Gly-Arg-Arg peptide at the C-terminus, leading to mature hormone. Belongs to the gastrin/cholecystokinin family. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked (PubMed:25041569, Ref.4). The disulfide link is formed within the large subunit homodimers (Ref.4). Interacts with assembly factor Raf1 which helps form the holoenzyme, most interaction (and folding) occurs in the cytoplasm (PubMed:25041569). The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. RuBisCO folding and assembly commences when the nascent large subunit folds with the help of chaperonin GroEL-GroES. Both RbcX and Raf1 help folded RbcL release from the chaperonin and dimerize (Probable). Dimeric Raf1 binds to RbcL(2) leading to an RbcL8-Raf1(8) complex. RbcS displaces Raf1, resulting in holoenzyme formation (By similarity). The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +Putative transcription factor. Homo- and heterodimer with other ZFHD proteins. The homeodomain differs form the typical one by having namely 4 instead of 3 extra amino acids inserted in the loop between helix 1 and helix 2. +Required for Fe(2+) ion low affinity uptake. By iron deprivation. Present with 573 molecules/cell in log phase SD medium. Belongs to the FET4 family. +Binds 1 Fe(2+) ion per subunit. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +Belongs to the universal ribosomal protein uL29 family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions. diphosphate + H2O = H(+) + 2 phosphate Homohexamer. Belongs to the PPase family. +Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit. S-adenosyl-L-methionine + uridine(2552) in 23S rRNA = 2'-O-methyluridine(2552) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase RlmE family. +Belongs to the asfivirus DP63R family. +Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP. Allosterically activated by GTP. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uracil: step 1/1. Belongs to the UPRTase family. +Binds 1 zinc ion per subunit. Belongs to the metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. Adenine deaminase type 2 subfamily. Although clearly a member of the adenine deaminase type 2 family, it lacks the conserved Glu active site residue in position 212 characteristic for this family. Its exact enzymatic activity is therefore unsure. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 1 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) In cyanobacteria the RNAP catalytic core is composed of 2 alpha, 1 beta, 1 beta', 1 gamma and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Catalyzes oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs. AH2 + O2 + uridine(34) in tRNA = 5-hydroxyuridine(34) in tRNA + A + H2O Belongs to the TrhO family. +Required for polarization of the embryonic, imaginal disk and follicular epithelia. Specifically restricts apical membrane determinants to the apical cell surface; acts to exclude crb from the basolateral domain and define adherens junction position. Regulates cellular growth and differentiation; acts as a tumor suppressor. Essential for odor guided behavior. Localized to epithelial septate junction at the boundary of the apical and basolateral cell surfaces. During germ band extension, expression of isoform A occurs predominantly in neuroblasts derived from the neuro-ectoderm and later is restricted to CNS neurons and pole cells. Isoform C is strongly expressed in PNS and a subset of CNS neurons. In the adult, expressed in third antennal segment and maxillary palps, major olfactory organs and in Johnstons organ in the second antennal segment. Expression is also observed in cortical regions of the brain. Isoforms expressed in epithelia are coexpressed with dlg1 throughout development. Expressed both zygotically and maternally in embryos. Isoform A and isoform C have high expression throughout embryonic development and very low expression in later developmental stages. In adults, isoform A is a male-specific isoform and isoform C a female specific. Flies exhibit aberrant cell shape and loss of the monolayer organization of embryonic epithelia creating a corrugated cuticular surface that is riddled with holes hence the gene name scribble. Misdistribution of apical proteins and adherens junctions to the basolateral cell surface is also exhibited. Belongs to the LAP (LRR and PDZ) protein family. Probable cloning artifact. +Transmembrane adapter protein which associates with KLRK1 to form an activation receptor KLRK1-HCST in lymphoid and myeloid cells; this receptor plays a major role in triggering cytotoxicity against target cells expressing cell surface ligands such as MHC class I chain-related MICA and MICB, and UL16-binding proteins (ULBPs); these ligands are up-regulated by stress conditions and pathological state such as viral infection and tumor transformation. Functions as docking site for PI3-kinase PIK3R1 and GRB2. Interaction of ULBPs with KLRK1-HCST triggers calcium mobilization and activation of the PIK3R1, MAP2K/ERK, and JAK2/STAT5 signaling pathways. Both PIK3R1 and GRB2 are required for full KLRK1-HCST-mediated activation and ultimate killing of target cells. In NK cells, KLRK1-HCST signaling directly induces cytotoxicity and enhances cytokine production initiated via DAP12/TYROBP-associated receptors. In T-cells, it provides primarily costimulation for TCR-induced signals. KLRK1-HCST receptor plays a role in immune surveillance against tumors and is required for cytolysis of tumors cells; indeed, melanoma cells that do not express KLRK1 ligands escape from immune surveillance mediated by NK cells. Homodimer; Disulfide-linked. Interacts with KLRK1 to form a stable complex, which results in surface expression of both proteins, whereas alone, it is minimally expressed. Interacts with PIK3R1 and GRB2. Interacts with CLEC5A (By similarity). Forms an CLEC5A/TYROBP/HCST trimolecular complex depending almost solely on TYROBP. Heterohexamer composed of four subunits of HCST/DAP10 and two subunits of KLRK1. Interacts (via transmembrane domain) with KLRK1 isoform 1 (via transmembrane domain); the interaction is required for KLRK1 cell surface expression on naive NK cells and activated CD8(+) T-cells, but is dispensable on activated TYROBP-expressing NK cells. Interacts (via transmembrane domain) with KLRK1 isoform 2 (via transmembrane domain); the interaction is required for KLRK1 NK cell surface expression and induces NK cell-mediated cytotoxicity. Interacts with CD300H (By similarity). Phosphorylated; PIK3R1 and GRB2 associate specifically with tyrosine-phosphorylated HCST. O-glycosylated. Mice exhibit low expression of KLRK1 in NK cells, but no expression in resting T-cells. KLRK1 expression is not induced upon T-cell activation, while it is up-regulated in activated NK cells; NK cells promote KLRK1-mediated tumor rejection due to substitution of HCST by DAP12/TYROBP. Mice lacking HCST exhibit antitumor phenotype; they show enhanced immunity against melanoma malignancies due to hyperactive functioning of a group of T-cells that share properties of both T-cells and NK cells (NKT cells). NKT cells exhibit increased cytokine production and cytotoxicity, leading to efficient killing of melanoma tumors. Upon activation, T regulatory cells (Tregs) maintain higher levels of IL2 and produced significantly lower amounts of IL10 and IFN-gamma cytokines. NKT cells activated by IL2 efficiently lyse B16-melanoma tumors in vitro in an KLRK1-independent way; The hyperactivity of NKT cells in these mice is not related to signaling of KLRK1. Immune reactivity to healthy cells that express KLRK1 ligands can happen under physiological conditions; NK cells are able to reject syngeneic bone marrow grafts when the bone marrow cells expressed sufficient KLRK1 ligand. Belongs to the DAP10 family. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. Binds 2 [4Fe-4S] clusters. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +(R)-amygdalin + H2O = (R)-prunasin + D-glucose Monomer. Absent from maturing black cherry fruits until 6 weeks after flowering. Then, concomitant with cotyledon development, the level of enzyme increases with specificity for embryonal tissues. Glycosylated. +Phosphorylated on some or all of the serine and threonine residues present in the C-terminal region. Belongs to the G-protein coupled receptor 1 family. Opsin subfamily. +Binds GTP and exhibits intrinsic GTPase activity. May activate NF-kappa-B-mediated gene transcription. Promotes signal transduction through MTOR, activates RPS6KB1, and is a downstream target of the small GTPase-activating proteins TSC1 and TSC2. Interacts with MTOR. Ubiquitously expressed. Expression increased at least 2-fold in several tumor cell lines. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the small GTPase superfamily. Rheb family. Wrong choice of CDS. +Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate + tRNA(n) Homohexameric ring arranged as a trimer of dimers. Belongs to the RNase PH family. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Tetramer of two alpha and two beta chains. Belongs to the leguminous lectin family. +H2O + L-glutamine = L-glutamate + NH4(+) Homotetramer. Belongs to the glutaminase family. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Required for insertion of 4Fe-4S clusters for at least IspG. Binds 1 iron-sulfur cluster per subunit. Homodimer. Belongs to the HesB/IscA family. +Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway. D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = beta-D-fructose 6-phosphate + D-erythrose 4-phosphate Carbohydrate degradation; pentose phosphate pathway; D-glyceraldehyde 3-phosphate and beta-D-fructose 6-phosphate from D-ribose 5-phosphate and D-xylulose 5-phosphate (non-oxidative stage): step 2/3. Belongs to the transaldolase family. Type 3B subfamily. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the eIF-3 subunit I family. +Light-harvesting photosynthetic bile pigment-protein from the phycobiliprotein complex (phycobilisome, PBS). Phycocyanin is the major phycobiliprotein in the PBS rod. Heterodimer of an alpha and a beta chain (PubMed:8168545). Dimers further assemble into trimers and the trimers into hexamers. The basic functional unit of phycobiliproteins is a ring-shaped hexamer formed from two back-to-back trimers contacting via the alpha chain subunits. The trimers are composed of alpha/beta subunit heterodimers arranged around a three-fold axis of symmetry. The phycoerythrins also contain a gamma subunit which is located in the center of the hexamer (By similarity). Part of the phycobilisome rod. Contains two covalently linked bilin chromophores. Belongs to the phycobiliprotein family. +Acts as a pathogen alarming molecule by acting on host neutrophil chemotactic factors FPR2. Plays a role of chemoattractant and induces degranulation and oxidative burst in neutrophils. Interacts with host FPR2; this interaction promotes neutrophil chemotaxis. Belongs to the staphylococcal/streptococcal toxin family. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Substrate recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. Mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome. In the presence of PML, HIPK2 ubiquitination still occurs, but degradation is prevented. PML, HIPK2 and FBXO3 may act synergically to activate p53/TP53-dependent transactivation. Part of a SCF (SKP1-cullin-F-box) protein ligase complex consisting of FBXO3, SKP1, CUL1 and RBX1. Interacts with PML, interaction is direct and takes place either alone or within the SCF complex. (Microbial infection) Isoform 1 and 2 interact with Rift valley fever virus NSs; this interaction is important for GT2H1 degradation. Colocalizes with PML at the peripheries of nuclear bodies. +Secreted metalloproteinase that allows assimilation of proteinaceous substrates. Belongs to the peptidase M43B family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) Binds 1 zinc ion per subunit. Homotetramer. Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. Belongs to the class-II aminoacyl-tRNA synthetase family. +May play a role during germination or early tube growth. Expressed in anthers and pollen. Belongs to the Ole e I family. +Catalytic subunit of the periplasmic nitrate reductase complex NapAB. Receives electrons from NapB and catalyzes the reduction of nitrate to nitrite. 2 Fe(II)-[cytochrome] + 2 H(+) + nitrate = 2 Fe(III)-[cytochrome] + H2O + nitrite Binds 1 [4Fe-4S] cluster. Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit. Component of the periplasmic nitrate reductase NapAB complex composed of NapA and NapB. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/NapA/NarB subfamily. +Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. adenosine + H(+) + H2O = inosine + NH4(+) 2'-deoxyadenosine + H(+) + H2O = 2'-deoxyinosine + NH4(+) Binds 1 zinc ion per subunit. Belongs to the metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. Adenosine deaminase subfamily. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Repressed under conditions of excess protein secretion capacity and derepressed when protein secretion becomes limiting. This is regulated by SecM. Belongs to the SecA family. +Catalyzes the cleavage of 5-oxoproline to form L-glutamate coupled to the hydrolysis of ATP to ADP and inorganic phosphate. 5-oxo-L-proline + ATP + 2 H2O = ADP + H(+) + L-glutamate + phosphate Forms a complex composed of PxpA, PxpB and PxpC. Belongs to the LamB/PxpA family. +Produced by third-instar larvae. +Component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Forms part of the TOM (translocase of outer membrane) complex. Outer membrane-anchored. Belongs to the Tom5 family. +Catalyzes the NAD-dependent reduction of succinylglutamate semialdehyde into succinylglutamate. H2O + N-succinyl-L-glutamate 5-semialdehyde + NAD(+) = 2 H(+) + N-succinyl-L-glutamate + NADH Amino-acid degradation; L-arginine degradation via AST pathway; L-glutamate and succinate from L-arginine: step 4/5. Belongs to the aldehyde dehydrogenase family. AstD subfamily. +Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate. (S)-dihydroorotate + H2O = H(+) + N-carbamoyl-L-aspartate Binds 2 Zn(2+) ions per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 3/3. Homodimer. Belongs to the metallo-dependent hydrolases superfamily. DHOase family. Class II DHOase subfamily. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. Interacts with UvrB in an incision complex. Belongs to the UvrC family. +Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis. (R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) A monovalent cation. Ammonium or potassium. Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Homodimer. Belongs to the type III pantothenate kinase family. +Belongs to the universal ribosomal protein uL29 family. +Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene). 5-methylsulfanyl-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate Binds 1 Mg(2+) ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 3/6. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 4/6. Monomer. Belongs to the HAD-like hydrolase superfamily. MasA/MtnC family. +Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit acts as a catalytic chaperone that increases the ATP-binding affinity of the ATP-hydrolyzing subunit KdpB by the formation of a transient KdpB/KdpC/ATP ternary complex. The system is composed of three essential subunits: KdpA, KdpB and KdpC. Belongs to the KdpC family. +Required for nuclear import of FGF1. Interacts with SGO1. Localization in the nuclear envelope depends upon the nuclear import machinery. +Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine. H(+) + L-aspartate = beta-alanine + CO2 Binds 1 pyruvoyl group covalently per subunit. Cofactor biosynthesis; (R)-pantothenate biosynthesis; beta-alanine from L-aspartate: step 1/1. Heterooctamer of four alpha and four beta subunits. Is synthesized initially as an inactive proenzyme, which is activated by self-cleavage at a specific serine bond to produce a beta-subunit with a hydroxyl group at its C-terminus and an alpha-subunit with a pyruvoyl group at its N-terminus. Belongs to the PanD family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 5 family. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +Plays an essential role in homologous recombination (HR) which is a major pathway for repairing DNA double-strand breaks (DSBs), single-stranded DNA (ssDNA) gaps, and stalled or collapsed replication forks (PubMed:12453424). Acts as a molecular motor during the homology search and guides RAD51 ssDNA along a donor dsDNA thereby changing the homology search from the diffusion-based mechanism to a motor-guided mechanism (PubMed:32502392). Also plays an essential role in RAD51-mediated synaptic complex formation which consists of three strands encased in a protein filament formed once homology is recognized (PubMed:31492866). Once DNA strand exchange occured, dissociates RAD51 from nucleoprotein filaments formed on dsDNA (PubMed:12453424). ATP + H2O = ADP + H(+) + phosphate Homohexamer (By similarity). Interacts with RAD51; RAD51-ssDNA filaments do not interact autonomously with dsDNA but do so robustly in the presence of RAD54 (PubMed:9590697, PubMed:31492866). Expression increases in late G1 phase compared to other phases of the cell cycle. Belongs to the SNF2/RAD54 helicase family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP = 7,8-dihydrofolate + dTMP Pyrimidine metabolism; dTTP biosynthesis. Homodimer. Belongs to the thymidylate synthase family. Bacterial-type ThyA subfamily. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34. 5-aminomethyl-2-thiouridine(34) in tRNA + S-adenosyl-L-methionine = 5-methylaminomethyl-2-thiouridine(34) in tRNA + H(+) + S-adenosyl-L-homocysteine In the N-terminal section; belongs to the methyltransferase superfamily. tRNA (mnm(5)s(2)U34)-methyltransferase family. In the C-terminal section; belongs to the DAO family. +Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Belongs to the Nudix hydrolase family. RppH subfamily. +Endothelins are endothelium-derived vasoconstrictor peptides (By similarity). Probable ligand for G-protein coupled receptors EDNRA and EDNRB which activates PTK2B, BCAR1, BCAR3 and, GTPases RAP1 and RHOA cascade in glomerular mesangial cells (PubMed:19086031). Also binds the DEAR/FBXW7-AS1 receptor (PubMed:17446437). Expressed in lung, placental stem villi vessels and in cultured placental vascular smooth muscle cells. EDN1 genetic variants may influence high density lipoprotein cholesterol (HDLC) levels in some populations and in a sex-specific manner, defining the high density lipoprotein cholesterol level quantitative trait locus 7 (HDLCQ7) [MIM:618979]. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the endothelin/sarafotoxin family. Endothelin entry +Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 4L family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Catalyzes the transfer of sulfate to the C2-position of selected hexuronic acid residues within the maturing heparan sulfate (HS). Involved in cell adhesion and guidance by specifically modifying proteoglycans in the extracellular matrix and on the cell surface that are essential for axon migrations. Homotrimer. Present in the hypodermis, muscle, distal tip cells (DTCs) and in neurons (at protein level). Worms are viable but display axonal and cellular guidance defects in specific neuron classes. Belongs to the sulfotransferase 3 family. +Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. May govern uptake and detoxification of both endogenous compounds and xenobiotics at the testis and brain blood barriers. glutathione + RX = a halide anion + an S-substituted glutathione + H(+) Homodimer. Testis and brain. The N-terminus is blocked. Belongs to the GST superfamily. Mu family. +Can convert Man(9)GlcNAc(2) and Man(8)GlcNAc(2) into N-glycans with a terminal alpha-1,6-linked Man residue in the C-branch. Functions in the formation of unique N-glycan structures that are specifically recognized by components of the endoplasmic reticulum-associated degradation (ERAD) machinery, which leads to the degradation of misfolded glycoproteins. Most likely generates N-glycan signal on misfolded glycoproteins that is subsequently recognized by OS9. Required for ERAD of the heavily glycosylated and misfolded BRI1 variants BRI1-5 and BRI1-9. Does not seem to play role in N-glycan processing of correctly folded proteins destined for secretion. Protein modification; protein glycosylation. Belongs to the glycosyl hydrolase 47 family. +Involved in pre-mRNA splicing as component of the activated spliceosome. Part of the activated spliceosome B/catalytic step 1 spliceosome, one of the forms of the spliceosome which has a well-formed active site but still cannot catalyze the branching reaction and is composed of at least 52 proteins, the U2, U5 and U6 snRNAs and the pre-mRNA. Belongs to the IST3 family. +By cadmium. To B.subtilis YqcK. +Extracellular dipeptidyl-peptidase which removes N-terminal dipeptides sequentially from polypeptides having unsubstituted N-termini. Contributes to pathogenicity (By similarity). Belongs to the peptidase S9C family. +E3 ubiquitin ligase that plays an essential role in the organization of autophagic response and ubiquitination upon lysosomal and phagosomal damages. Plays a role in the stress-induced biogenesis and degradation of protein aggresomes by regulating the p62-KEAP1-NRF2 signaling and particularly by modulating the ubiquitination levels and thus stability of NRF2. Acts as a scaffold protein and facilitates autophagic degradation of protein aggregates by interacting with p62/SQSTM, ATG16L1 and LC3B/MAP1LC3B. In turn, protects the cell against oxidative stress-induced cell death as a consequence of endomembrane damage. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Homodimerizes via its coiled-coil domain. Heterodimerizes with MID1, TRIM24 and PML. Interacts with Galectin-3/LGALS3 in a ULK1-dependent manner; this interaction mediates autophagy of damage endomembranes. Interacts with BECN1. Interacts with ATG16L1. Interacts with p62/SQSTM and LC3B/MAP1LC3B. Widely expressed. Expressed in basal keratinocytes. Phosphorylated by ULK1. Auto-ubiquitinates via its B-Boxes. Belongs to the TRIM/RBCC family. +Accessory subunit that is involved in the functional assembly of the mitochondrial respiratory chain complex I. Complex I has an NADH dehydrogenase activity with ubiquinone as an immediate electron acceptor and mediates the transfer of electrons from NADH to the respiratory chain. Complex I is composed of 45 different subunits. Interacts with CHCHD4. Belongs to the complex I NDUFB10 subunit family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. It is uncertain whether Met-1 or Met-5 is the initiator. +Belongs to the UPF0283 family. +Involved in the biosynthesis of the osmoprotectant glycine betaine. Catalyzes the irreversible oxidation of betaine aldehyde to the corresponding acid. betaine aldehyde + H2O + NAD(+) = glycine betaine + 2 H(+) + NADH Binds 2 potassium ions per subunit. Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway; betaine from betaine aldehyde: step 1/1. Dimer of dimers. Belongs to the aldehyde dehydrogenase family. +Catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates. Cleaves off the terminal sialic acids on the glycosylated HA during virus budding to facilitate virus release. Additionally helps virus spread through the circulation by further removing sialic acids from the cell surface. These cleavages prevent self-aggregation and ensure the efficient spread of the progeny virus from cell to cell. Otherwise, infection would be limited to one round of replication. Described as a receptor-destroying enzyme because it cleaves a terminal sialic acid from the cellular receptors. May facilitate viral invasion of the upper airways by cleaving the sialic acid moieties on the mucin of the airway epithelial cells. Likely to plays a role in the budding process through its association with lipid rafts during intracellular transport. May additionally display a raft-association independent effect on budding. Plays a role in the determination of host range restriction on replication and virulence. Sialidase activity in late endosome/lysosome traffic seems to enhance virus replication. Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates. Inhibited by the neuraminidase inhibitors zanamivir (Relenza) and oseltamivir (Tamiflu). These drugs interfere with the release of progeny virus from infected cells and are effective against all influenza strains. Resistance to neuraminidase inhibitors is quite rare. Homotetramer. Preferentially accumulates at the apical plasma membrane in infected polarized epithelial cells, which is the virus assembly site. Uses lipid rafts for cell surface transport and apical sorting. In the virion, forms a mushroom-shaped spike on the surface of the membrane. Intact N-terminus is essential for virion morphogenesis. Possesses two apical sorting signals, one in the ectodomain, which is likely to be a glycan, and the other in the transmembrane domain. The transmembrane domain also plays a role in lipid raft association. N-glycosylated. The influenza A genome consist of 8 RNA segments. Genetic variation of hemagglutinin and/or neuraminidase genes results in the emergence of new influenza strains. The mechanism of variation can be the result of point mutations or the result of genetic reassortment between segments of two different strains. Belongs to the glycosyl hydrolase 34 family. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Protamines substitute for histones in the chromatin of sperm during the haploid phase of spermatogenesis. They compact sperm DNA into a highly condensed, stable and inactive complex. Testis. +Involved in vitamin D transport and storage, scavenging of extracellular G-actin, enhancement of the chemotactic activity of C5 alpha for neutrophils in inflammation and macrophage activation. Associates with membrane-bound immunoglobulin on the surface of B-lymphocytes and with IgG Fc receptor on the membranes of T-lymphocytes. Interacts with LRP2; the interaction is required for renal uptake of GC in complex with 25-hydroxyvitamin D3. Belongs to the ALB/AFP/VDB family. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. A methylated and unmethylated form are thought to exist. For unmethylated form. For methylated form. Belongs to the universal ribosomal protein uL24 family. +Belongs to the universal ribosomal protein uL29 family. +Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA. cytidine(32) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(32) in tRNA + H(+) + S-adenosyl-L-homocysteine S-adenosyl-L-methionine + uridine(32) in tRNA = 2'-O-methyluridine(32) in tRNA + H(+) + S-adenosyl-L-homocysteine Homodimer. Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway. a 3-demethylubiquinol + S-adenosyl-L-methionine = a ubiquinol + H(+) + S-adenosyl-L-homocysteine a 3-(all-trans-polyprenyl)benzene-1,2-diol + S-adenosyl-L-methionine = a 2-methoxy-6-(all-trans-polyprenyl)phenol + H(+) + S-adenosyl-L-homocysteine Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the methyltransferase superfamily. UbiG/COQ3 family. +Belongs to the UPF0756 family. +Affects the expression of the receptor, named binding substance, that mediates mating aggregate formation. Could be a regulatory protein that suppresses the function or expression of ebsA and/or ebsMB. Belongs to the prolyl-tRNA editing family. YbaK/EbsC subfamily. +1-(5-phospho-beta-D-ribosyl)-ATP + H2O = 1-(5-phospho-beta-D-ribosyl)-5'-AMP + diphosphate + H(+) 1-(5-phospho-beta-D-ribosyl)-5'-AMP + H2O = 1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 2/9. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 3/9. In the N-terminal section; belongs to the PRA-CH family. In the C-terminal section; belongs to the PRA-PH family. +Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). Component of the Mediator complex. Belongs to the Mediator complex subunit 22 family. +Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides. Belongs to the RlpA family. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Histone H3-like nucleosomal protein that is specifically found in centromeric nucleosomes. Replaces conventional H3 in the nucleosome core of centromeric chromatin at the inner plate of the kinetochore. The presence of CENPA subtly modifies the nucleosome structure and the way DNA is wrapped around the nucleosome and gives rise to protruding DNA ends that are less well-ordered and rigid compared to nucleosomes containing histone H3. May serve as an epigenetic mark that propagates centromere identity through replication and cell division (By similarity). Required for recruitment and assembly of kinetochore proteins, and as a consequence required for progress through mitosis, chromosome segregation and cytokinesis (PubMed:27499292). Component of centromeric nucleosomes, where DNA is wrapped around a histone octamer core. The octamer contains two molecules each of H2A, H2B, CENPA and H4 assembled in one CENPA-H4 heterotetramer and two H2A-H2B heterodimers. CENPA modulates the DNA-binding characteristics of nucleosomes so that protruding DNA ends have higher flexibility than in nucleosomes containing conventional histone H3. Inhibits binding of histone H1 to nucleosomes, since histone H1 binds preferentially to rigid DNA linkers that protrude from nucleosomes. Nucleosomes containing CENPA also contain histone H2A variants such as MACROH2A and H2A.Z/H2AZ1. The CENPA-H4 heterotetramer is more compact and structurally more rigid than corresponding H3-H4 heterotetramers. Can assemble into nucleosomes that contain both CENPA and histone H3.3; these nucleosomes interact with a single CENPC chain. Heterotrimer composed of HJURP, CENPA and histone H4, where HJURP interacts with the dimer formed by CENPA and histone H4 and prevents tetramerization of CENPA and H4. Component of the CENPA-NAC complex, at least composed of CENPA, CENPC, CENPH, CENPM, CENPN, CENPT and CENPU. Interacts (via CATD domain) with HJURP; the interaction is direct and is required for its localization to centromeres. Interacts with CENPC, CENPN and CENPT; interaction is direct. Part of a centromere complex consisting of CENPA, CENPT and CENPW. Identified in centromere complexes containing histones H2A, H2B and H4, and at least CENPA, CENPB, CENPC, CENPT, CENPN, HJURP, SUPT16H, SSRP1 and RSF1. Can self-associate. The CENPA-H4 heterotetramer can bind DNA by itself (in vitro). Interacts with CDK1, PPP1CA and RBBP7. Localizes exclusively in the kinetochore domain of centromeres. Occupies a compact domain at the inner kinetochore plate stretching across 2 thirds of the length of the constriction but encompassing only one third of the constriction width and height. Phosphorylation at Ser-62 during early mitosis abolishes association with chromatin and centromeres and results in dispersed nuclear location. The CATD (CENPA targeting domain) region is responsible for the more compact structure of nucleosomes containing CENPA. It is necessary and sufficient to mediate the localization into centromeres. Poly-ADP-ribosylated by PARP1. Trimethylated by NTMT1 at the N-terminal glycine after cleavage of Met-1. Methylation is low before incorporation into nucleosomes and increases with cell cycle progression, with the highest levels in mitotic nucleosomes. Phosphorylated by CDK1 at Ser-62 during early mitosis; this abolishes association with chromatin and centromeres, prevents interaction with HJURP and thereby prevents premature assembly of CENPA into centromeres. Dephosphorylated at Ser-62 by PPP1CA during late mitosis. Belongs to the histone H3 family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Contained within a telomeric X element core sequence. Belongs to the UPF0320 family. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +This protein is involved in regulating the plasmid copy-number. Increasing the level of this protein results in a higher plasmid copy-number. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. ATP + CoA + succinate = ADP + phosphate + succinyl-CoA Binds 1 Mg(2+) ion per subunit. Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. Heterotetramer of two alpha and two beta subunits. Belongs to the succinate/malate CoA ligase beta subunit family. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP = 7,8-dihydrofolate + dTMP Pyrimidine metabolism; dTTP biosynthesis. Homodimer. Belongs to the thymidylate synthase family. Bacterial-type ThyA subfamily. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiC family. +Belongs to the universal ribosomal protein uS2 family. +Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP). (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate Cofactor biosynthesis; molybdopterin biosynthesis. Homohexamer; trimer of dimers. Belongs to the MoaC family. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +Component of chylomicrons, very low-density lipoproteins (VLDL), low-density lipoproteins (LDL), and high-density lipoproteins (HDL) in plasma. Plays an important role in lipoprotein metabolism as an activator of lipoprotein lipase. Both proapolipoprotein C-II and apolipoprotein C-II can activate lipoprotein lipase. Proapolipoprotein C-II is synthesized as a sialic acid containing glycoprotein which is subsequently desialylated prior to its proteolytic processing. Proapolipoprotein C-II, the major form found in plasma undergoes proteolytic cleavage of its N-terminal hexapeptide to generate apolipoprotein C-II, which occurs as the minor form in plasma. Belongs to the apolipoprotein C2 family. +Involved in the endoplasmic reticulum-associated degradation (ERAD) pathway that targets misfolded glycoproteins for degradation in an N-glycan-dependent manner (PubMed:15537790, PubMed:25092655). May initiate ERAD by promoting the first mannose trimming step of ERAD substrates, from Man9GlcNAc2 to Man8GlcNAc2 (PubMed:25092655). Seems to recognize and bind to exposed hydrophobic regions in target proteins (By similarity). Expressed ubiquitously in all tissues tested with slightly higher levels detected in small intestine and peripheral blood leukocytes and weakest levels in brain and skeletal muscle. N-glycosylated. Belongs to the glycosyl hydrolase 47 family. Has similarity to alpha 1,2-mannosidases, but the catalytic activity of this protein is controversial (PubMed:15537790, PubMed:25092655). One study shows that it is important for a specific oligosaccharide trimming step from Man9GlcNAc2 to Man8GlcNAc2, suggesting activity as a mannosidase (PubMed:25092655). However, another study reports that this protein has no mannosidase activity (PubMed:15537790). +TRAPP plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. Part of the multisubunit TRAPP (transport protein particle) complex composed of bet3, bet5, trs20, trs23, trs31, trs33, trs65, trs85, trs120 and trs130. Belongs to the TRAPP small subunits family. BET3 subfamily. +Exhibits chaperone activity toward chloroplast outer envelope membrane, mitochondrion outer membrane, endoplasmic reticulum membrane and peroxisomal proteins, by recruiting specific proteins containing a single transmembrane associated with an AKR2A-binding sequence (ABS) and subsequently binding glycolipids (e.g. monogalactosyldiacylglycerol (MGDG) and phosphatidylglycerol (PG)) present in the membrane of the target organelle. Binds to chloroplast outer envelope membrane (OEM) protein targeting signals, as well as to chloroplasts. Binds specifically to two chloroplast glycolipids, monogalactosyldiacylglycerol (MGDG) and phosphatidylglycerol (PG) (By similarity). Interacts with APX3, APX5 and TOC34 (PubMed:20215589). The ankyrin repeats (ANK) mediate interactions with hexoses-containing lipids present in organellar membranes (e.g. chloroplast), such as monogalactosyldiacylglycerol (MGDG) and phosphatidylglycerol (PG). +RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs. Homohexamer. Belongs to the Hfq family. +Responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs. uridine(13) in tRNA = pseudouridine(13) in tRNA Belongs to the pseudouridine synthase TruD family. +May only reduce GSH-thiol disulfides, but not protein disulfides. Belongs to the glutaredoxin family. CGFS subfamily. +Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12. [sulfur carrier]-SH + AH2 + L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 2 S-adenosyl-L-methionine = 3-methylsulfanyl-L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Belongs to the methylthiotransferase family. RimO subfamily. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. Belongs to the phosphatidylserine decarboxylase family. PSD-A subfamily. +Catalyzes the NAD(+)-dependent oxidation of the hydroxyl group at C3 of D-gulosides leading to 3-dehydro-D-gulosides. Probably functions in a metabolic pathway that transforms D-gulosides to D-glucosides. Is also able to catalyze the reverse reactions, i.e. the NADH-dependent reduction of the oxo group at C3 of 3-dehydro-D-gulosides leading to D-gulosides. In vitro, can oxidize D-gulose and methyl beta-D-guloside, and reduce methyl alpha-3-dehydro-D-guloside and methyl beta-3-dehydro-D-guloside. However, the actual specific physiological substrates for this metabolic pathway are unknown. a D-guloside + NAD(+) = a 3-dehydro-D-guloside + H(+) + NADH Binds 1 Zn(2+) ions per subunit. kcat is 0.18 sec(-1) for the NAD(+)-dependent oxidation of D-gulose (at pH 8.0 and 30 degrees Celsius). kcat is 0.23 sec(-1) for the NAD(+)-dependent oxidation of D-gulose (at pH 9.0 and 30 degrees Celsius). kcat is 0.35 sec(-1) for the NAD(+)-dependent oxidation of methyl beta-D-guloside (at pH 8.0 and 30 degrees Celsius). kcat is 1.2 sec(-1) for the NAD(+)-dependent oxidation of methyl beta-D-guloside (at pH 9.0 and 30 degrees Celsius). kcat is 18.5 sec(-1) for the NADH-dependent reduction of methyl alpha-3-dehydro-D-guloside (at pH 7.0 and 30 degrees Celsius). kcat is 3.8 sec(-1) for the NADH-dependent reduction of methyl alpha-3-dehydro-D-guloside (at pH 8.0 and 30 degrees Celsius). kcat is 7.0 sec(-1) for the NADH-dependent reduction of methyl beta-3-dehydro-D-guloside (at pH 7.0 and 30 degrees Celsius). kcat is 9.7 sec(-1) for the NADH-dependent reduction of methyl beta-3-dehydro-D-guloside (at pH 8.0 and 30 degrees Celsius). Belongs to the zinc-containing alcohol dehydrogenase family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity. adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue. Belongs to the radical SAM superfamily. RlmN family. +Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles. Belongs to the globin family. +Possible increased expression of this protein (due to mutations upstream of the start codon) is proposed to be responsible for resistance to 3-hydroxypropionic acid (3-HP). Mutagenesis of the start codon from ATG to TTG, which should decrease protein expression, results in loss of 3-HP resistance. Encoded by the 21 C-terminal amino acids of the HcaR transcriptional activator, it is suggested to be produced by an independent promoter within the hcaR gene. However the peptide's existence has not been proven, nor has mutagenesis of HcaR itself rather than overexpression of IroK been ruled out as the cause of 3-HP resistance. +Cytosolic enzyme that catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the first and rate-limiting step of de novo fatty acid biosynthesis. This is a 2 steps reaction starting with the ATP-dependent carboxylation of the biotin carried by the biotin carboxyl carrier (BCC) domain followed by the transfer of the carboxyl group from carboxylated biotin to acetyl-CoA. acetyl-CoA + ATP + hydrogencarbonate = ADP + H(+) + malonyl-CoA + phosphate Binds 2 magnesium or manganese ions per subunit. Inhibited by phosphorylation (By similarity). Citrate promotes oligomerization of the protein into filaments that correspond to the most active form of the carboxylase (By similarity). Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Monomer, homodimer, and homotetramer. Can form filamentous polymers. Interacts in its inactive phosphorylated form with the BRCT domains of BRCA1 which prevents ACACA dephosphorylation and inhibits lipid synthesis. Interacts with MID1IP1; interaction with MID1IP1 promotes oligomerization and increases its activity. Consists of an N-terminal biotin carboxylation/carboxylase (BC) domain that catalyzes the ATP-dependent transient carboxylation of the biotin covalently attached to the central biotinyl-binding/biotin carboxyl carrier (BCC) domain. The C-terminal carboxyl transferase (CT) domain catalyzes the transfer of the carboxyl group from carboxylated biotin to acetyl-CoA to produce malonyl-CoA. The N-terminus is blocked. Phosphorylation on Ser-1262 is required for interaction with BRCA1. Phosphorylation at Ser-79 by AMPK inactivates enzyme activity. Phosphorylated in vitro at Ser-1200 and Ser-1215 by AMPK; the relevance of phosphorylation of these sites in vivo is however unclear. The biotin cofactor is covalently attached to the central biotinyl-binding domain and is required for the catalytic activity. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Binds to 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL23 family. +Catalyzes two subsequent steps in gluconeogenesis: the aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GA3P) to fructose-1,6-bisphosphate (FBP), and the dephosphorylation of FBP to fructose-6-phosphate (F6P). beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate Can also use Zn(2+) or Mn(2+) in vitro, although with much less efficiency than Mg(2+). kcat is 2.5 sec(-1) for the FBPase activity (at 80 degrees Celsius) (PubMed:15274916). kcat is 0.62 sec(-1) for the FBPase activity (at 48 degrees Celsius). kcat is 0.91 sec(-1) for the FBP aldolase activity in the anabolic direction (at 48 degrees Celsius). kcat is 0.027 sec(-1) for the FBP aldolase activity in the catabolic direction (at 48 degrees Celsius) (PubMed:21983966). Optimum pH is 8.0. Optimum temperature is over 100 degrees Celsius. Carbohydrate biosynthesis; gluconeogenesis. Homooctamer; dimer of tetramers. Consists of a single catalytic domain, but remodels its active-site architecture via a large structural change to exhibit dual activities. Belongs to the FBP aldolase/phosphatase family. +Binds 16S rRNA, required for the assembly of 30S particles. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS14 family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Belongs to the eukaryotic ribosomal protein eL21 family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the demethylesterification of homogalacturonan components of pectin. May be involved in pollen tube development (By similarity). [(1->4)-alpha-D-galacturonosyl methyl ester](n) + n H2O = [(1->4)-alpha-D-galacturonosyl](n) + n H(+) + n methanol Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-gluconate from pectin: step 1/5. Expressed in pollen. Glycosylated. Several isoforms of the allergen exist due to polymorphism. Causes an allergic reaction in human. Allergen from olive pollen. Important in Mediterranean countries and California. Its prevalence is related to the geographic area. Belongs to the pectinesterase family. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids. acetyl-CoA + H(+) + malonyl-[ACP] = 3-oxobutanoyl-[ACP] + CO2 + CoA Lipid metabolism; fatty acid biosynthesis. Homodimer. The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH. Belongs to the thiolase-like superfamily. FabH family. +Belongs to the TMEM104 family. +Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX. (6R)-NADHX = (6S)-NADHX (6R)-NADPHX = (6S)-NADPHX Binds 1 potassium ion per subunit. Belongs to the NnrE/AIBP family. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. Required to maintain the reduced state of SoxR. Binds 3 [4Fe-4S] clusters. The complex is composed of six subunits: RsxA, RsxB, RsxC, RsxD, RsxE and RsxG. Belongs to the 4Fe4S bacterial-type ferredoxin family. RnfB subfamily. +Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. Homodimer. Belongs to the transketolase family. DXPS subfamily. +May be involved in the facilitation of anaphase progression in mitosis. Monomer. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. The TIM22 complex forms a twin-pore translocase that uses the membrane potential as the external driving force. Required for the stability of the TIM22 complex and functions in the assembly of the TIMM22 protein into the TIM22 complex. May facilitate cooperation between TIM22 and TOM complexes by interacting with TOMM40. Component of the TIM22 complex, which core is composed of TIMM22, associated with TIMM10 (TIMM10A and/or TIMM10B), TIMM9, AGK and TIMM29. Interacts with TIMM10B; the interaction is direct. Interacts with TOMM40; linking the TIM22 complex to the TOM complex. Interacts with TIMM22 (when oxidized); the interaction is direct. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. [sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Monomer. Belongs to the methylthiotransferase family. MiaB subfamily. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +Catalyzes the oxidative deamination and cyclization of 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid (ADH) to yield 3-dehydroquinate (DHQ), which is fed into the canonical shikimic pathway of aromatic amino acid biosynthesis. 2-amino-2,3,7-trideoxy-D-lyxo-hept-6-ulosonate + H2O + NAD(+) = 3-dehydroquinate + H(+) + NADH + NH4(+) Belongs to the archaeal-type DHQ synthase family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +May act as an transcriptional repressor for PCK1 gene expression, in turn may participate in the hepatic gluconeogenesis regulation through the activated AMPK signaling pathway. Ubiquitous (PubMed:17097062). Highly expressed in brain, thymus and spleen (PubMed:17097062). Phosphorylation at Ser-470 results in loss of DNA-binding activity. Belongs to the krueppel C2H2-type zinc-finger protein family. +Ketoamine kinase that phosphorylates ketoamines, such as erythruloselysine, erythrulosecadaverine, ribuloselysine and ribulosecadaverine, on the third carbon of the sugar moiety to generate ketoamine 3-phosphate (PubMed:17681011). Has higher activity on free lysine (erythruloselysine and ribuloselysine), than on ribuloselysine and erythruloselysine residues on glycated proteins (PubMed:17681011). ATP + N(6)-(D-ribulosyl)-L-lysine = ADP + H(+) + N(6)-(3-O-phospho-D-ribulosyl)-L-lysine ATP + N-(D-ribulosyl)-cadaverine = ADP + H(+) + N-(3-O-phospho-D-ribulosyl)-cadaverine ATP + N(6)-(D-erythrulosyl)-L-lysine = ADP + H(+) + N(6)-(3-O-phospho-D-erythrulosyl)-L-lysine ATP + N-(D-erythrulosyl)-cadaverine = ADP + H(+) + N-(3-O-phospho-D-erythrulosyl)-cadaverine ATP + N(6)-D-ribulosyl-L-lysyl-[protein] = ADP + H(+) + N(6)-(3-O-phospho-D-ribulosyl)-L-lysyl-[protein] ATP + N(6)-(D-erythrulosyl)-L-lysyl-[protein] = ADP + H(+) + N(6)-(3-O-phospho-D-erythrulosyl)-L-lysyl-[protein] Belongs to the fructosamine kinase family. +Interacts with CbpA and inhibits both the DnaJ-like co-chaperone activity and the DNA binding activity of CbpA. Together with CbpA, modulates the activity of the DnaK chaperone system. Does not inhibit the co-chaperone activity of DnaJ. Belongs to the CbpM family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Converts GTP to 7,8-dihydroneopterin triphosphate. GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Belongs to the GTP cyclohydrolase IV family. +Belongs to the UPF0253 family. +May function in the formation of membrane-bound replication complexes or in the assembly of the virus. Belongs to the coronaviruses ns7/ns7a protein family. +Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain. Dimer of alpha and beta chains. A typical microtubule is a hollow water-filled tube with an outer diameter of 25 nm and an inner diameter of 15 nM. Alpha-beta heterodimers associate head-to-tail to form protofilaments running lengthwise along the microtubule wall with the beta-tubulin subunit facing the microtubule plus end conferring a structural polarity. Microtubules usually have 13 protofilaments but different protofilament numbers can be found in some organisms and specialized cells. Undergoes a tyrosination/detyrosination cycle, the cyclic removal and re-addition of a C-terminal tyrosine residue by the enzymes tubulin tyrosine carboxypeptidase (TTCP) and tubulin tyrosine ligase (TTL), respectively. Acetylation of alpha chains at Lys-40 stabilizes microtubules and affects affinity and processivity of microtubule motors. This modification has a role in multiple cellular functions, ranging from cell motility, cell cycle progression or cell differentiation to intracellular trafficking and signaling (By similarity). Belongs to the tubulin family. +Specifically methylates the 50S ribosomal protein L3 on a specific glutamine residue. L-glutaminyl-[ribosomal protein uL3] + S-adenosyl-L-methionine = H(+) + N(5)-methyl-L-glutaminyl-[ribosomal protein uL3] + S-adenosyl-L-homocysteine Belongs to the protein N5-glutamine methyltransferase family. PrmB subfamily. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +ATP + thymidine = ADP + dTMP + H(+) Homotetramer. Belongs to the thymidine kinase family. +Belongs to the bacterial ribosomal protein bL27 family. +Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA. a fatty acyl-[ACP] + phosphate = an acyl phosphate + holo-[ACP] Lipid metabolism; phospholipid metabolism. Homodimer. Probably interacts with PlsY. Associated with the membrane possibly through PlsY. Belongs to the PlsX family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA. Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule. Binds 2 Zn(2+) ions. Homodimer. Belongs to the RNase Z family. +May catalyze a purine salvage reaction, the substrate is unknown. Belongs to the purine/pyrimidine phosphoribosyltransferase family. Archaeal HPRT subfamily. +Induces apoptosis in cooperation with SIAH1A. Acts as a mediator between p53/TP53 and BAX in a neuronal death pathway that is activated by DNA damage. Acts synergistically with TRAF2 and inhibits TNF induced apoptosis through activation of NF-kappa-B. Plays a role in regulating maternal behavior and offspring growth. Homodimer. Interacts with SIAH1A and SIAH2. Interacts with TRAF2. Brain, glial cells, neurons, skeletal muscle, uterus and placenta. In the placenta it found in all trophoblast cells. Strongly expressed upon gastrulation and subsequently becomes restricted to skeletal muscle and subregions of the CNS. At 9.5 dpc, expressed in the branchial arches, somites and gut but little in the heart and neural tissues. At 12.5 dpc strongly expressed in the cranial skeleton, tongue, vertebral cartilage, pituitary and the luminal epithelium. Induced during p53/TP53 mediated apoptosis. Up-regulated by DNA damage in cortical neurons in the presence of p53/TP53. The SCAN domain enables PEG3 homo- or heterodimerization to control gene expression in a combinatorial fashion. Belongs to the krueppel C2H2-type zinc-finger protein family. +Required for corrinoid utilization. Probably part of the ABC transporter complex BtuCDF involved in cobalamin (vitamin B12) import. Probably responsible for energy coupling to the transport system. an R-cob(III)alamin(out) + ATP + H2O = ADP + an R-cob(III)alamin(in) + H(+) + phosphate The complex is composed of two ATP-binding proteins (BtuD), two transmembrane proteins (BtuC) and a solute-binding protein (BtuF). Belongs to the ABC transporter superfamily. Truncated N-terminus. +Probable serine protease. Belongs to the peptidase S1C family. +Both substrate-binding domains (SBD1 and SBD2) are involved in the substrate recognition, and are sufficient to confer the substrate specificity. Belongs to the ATP-dependent AMP-binding enzyme family. +Inhibits the expression or activity of extracellular murein hydrolases by interacting, possibly with LrgA, with the holin-like protein CidA. The LrgAB and CidA proteins may affect the proton motive force of the membrane. May be involved in programmed cell death (PCD), possibly triggering PCD in response to antibiotics and environmental stresses. Belongs to the CidB/LrgB family. LrgB subfamily. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +To M.tuberculosis Rv1815. +The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. Binds 4 bacteriochlorophylls per trimer. Binds 2 bacteriopheophytins per trimer. Binds 1 Fe cation per trimer. Binds 4 Mg(2+) ions per trimer. Binds 1 menaquinone per trimer. Binds 1 ubiquinone per trimer. Heterotrimer composed of subunits L, M, and H. Belongs to the reaction center PuhA family. +Belongs to the UPF0602 family. +Gap class segmentation protein that controls development of head structures. Belongs to the hunchback C2H2-type zinc-finger protein family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +By desiccation (leaves) and by abscisic acid (ABA) (leaves and callus). Belongs to the LEA type 2 family. +2 ATP + H2O + hydrogencarbonate + L-glutamine = 2 ADP + carbamoyl phosphate + 2 H(+) + L-glutamate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 1/3. Composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate. Belongs to the CarA family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +H(+) + hydrogencarbonate = CO2 + H2O Binds 1 zinc ion per subunit. Homodimer. Belongs to the beta-class carbonic anhydrase family. +Probable ligand of isoforms a and b of the calcitonin receptor-like protein, pdfr-1, a G-protein coupled receptor (PubMed:18390545). May not signal through isoform c of pdfr-1 (PubMed:18390545). Involved in locomotion; may play a role in circadian rhythms of locomotor activity (PubMed:18390545, PubMed:22579613, PubMed:26113231). Modulator of egg-laying (PubMed:22579613). Expressed in the interneurons BDUL/R, AVG, AIML/R, RIS, AVD and PVT, the chemosensory neuron pairs PHA and PHB, the motor neurons RID and RIML/R, the sensory neurons AQR and PQR, and in the PVPL/R interneurons (PubMed:19686386). Also expressed in rectal gland cells rectD and rectVL/R, the intestino-rectal valve cells virL/R and three posterior arcade cells in the head (PubMed:19686386). Delay in the timing of the reproductive peak of egg-laying. +Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)). 7-carboxy-7-deazaguanine + ATP + NH4(+) = 7-cyano-7-deazaguanine + ADP + H(+) + H2O + phosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. Belongs to the QueC family. +Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. Homodimer. Belongs to the transketolase family. DXPS subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Forms part of the preprotein translocase complex of the outer mitochondrial membrane (TOM complex) which consists of at least 7 different proteins (TOMM5, TOMM6, TOMM7, TOMM20, TOMM22, TOMM40 and TOMM70). Belongs to the Tom5 family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate. ATP + L-glutamate = ADP + L-glutamyl 5-phosphate Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 1/2. Belongs to the glutamate 5-kinase family. +Belongs to the orthopoxvirus C6 protein family. +Required for the post-translational delivery of tail-anchored (TA) proteins to the endoplasmic reticulum. Together with GET2, acts as a membrane receptor for soluble GET3, which recognizes and selectively binds the transmembrane domain of TA proteins in the cytosol. The GET complex cooperates with the HDEL receptor ERD2 to mediate the ATP-dependent retrieval of resident ER proteins that contain a C-terminal H-D-E-L retention signal from the Golgi to the ER. Component of the Golgi to ER traffic (GET) complex, which is composed of GET1, GET2 and GET3. Within the complex, GET1 and GET2 form a heterotetramer which is stabilized by phosphatidylinositol binding and which binds to the GET3 homodimer. Belongs to the WRB/GET1 family. +The predicted gene At2g24650 has been split into 2 genes: At2g24645 and At2g24650. +Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins. Absence of FtsH leads to increased sigma-32 levels, which suggests, in analogy to E.coli, that sigma-32 is a substrate for FtsH. May play a role in the general stress response, as overexpression leads to improved resistance to salt stress. Binds 1 zinc ion per subunit. Homohexamer. By heat shock at 40 degrees Celsius. Cells lacking this gene grow more slowly than wild-type, are filamentous and under high-phosphate defective in stalk biogenesis. They are hypersensitive to a range of antibiotics. Cells do not grow at 37 degrees Celsius, or in 50 mM NaCl. Required for stationary phase survival. Depletion leads to increased levels of sigma-32. In the central section; belongs to the AAA ATPase family. In the C-terminal section; belongs to the peptidase M41 family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the PetN family. +Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Interacts with nop5. Component of box C/D small ribonucleoprotein (sRNP) particles that contain rpl7ae, FlpA and nop5, plus a guide RNA. Belongs to the methyltransferase superfamily. Fibrillarin family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Required for 20S pre-rRNA processing. Belongs to the TSR2 family. +This is one of the 2 subunits of the biotin-dependent propionyl-CoA carboxylase (PCC), a mitochondrial enzyme involved in the catabolism of odd chain fatty acids, branched-chain amino acids isoleucine, threonine, methionine, and valine and other metabolites. Propionyl-CoA carboxylase catalyzes the carboxylation of propionyl-CoA/propanoyl-CoA to D-methylmalonyl-CoA/(S)-methylmalonyl-CoA (By similarity). Within the holoenzyme, the alpha subunit catalyzes the ATP-dependent carboxylation of the biotin carried by the biotin carboxyl carrier (BCC) domain, while the beta subunit then transfers the carboxyl group from carboxylated biotin to propionyl-CoA (By similarity). Propionyl-CoA carboxylase also significantly acts on butyryl-CoA/butanoyl-CoA, which is converted to ethylmalonyl-CoA/(2S)-ethylmalonyl-CoA (By similarity). Other alternative minor substrates include (2E)-butenoyl-CoA/crotonoyl-CoA (By similarity). ATP + hydrogencarbonate + propanoyl-CoA = (S)-methylmalonyl-CoA + ADP + H(+) + phosphate ATP + butanoyl-CoA + hydrogencarbonate = (2S)-ethylmalonyl-CoA + ADP + H(+) + phosphate Binds 2 magnesium or manganese ions per subunit. Metabolic intermediate metabolism; propanoyl-CoA degradation; succinyl-CoA from propanoyl-CoA: step 1/3. The holoenzyme is a dodecamer composed of 6 alpha subunits and 6 beta subunits (By similarity). Interacts with sir-2.2 and sir-2.3 (PubMed:23438705). Consists of an N-terminal biotin carboxylation/carboxylase (BC) domain that catalyzes the transient carboxylation of the biotin covalently attached to the C-terminal biotinyl-binding/biotin carboxyl carrier (BCC) domain. The biotin cofactor is covalently attached to the C-terminal biotinyl-binding domain and is required for the catalytic activity. +Probable neurotoxin. Expressed by the venom duct. The cysteine framework is XXVIII (C-C-C-CC-C-C-C-C-C). Contains 5 disulfide bonds. Belongs to the conotoxin D superfamily. +Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel. Component of the large ribosomal subunit. RNAi-mediated knockdown results in few viable embryos and as a result few live progeny and defective growth. There's a functional difference between the two L11-encoding proteins in C.briggsae. rpl-11.1 plays a role in the germline whereas rpl-11.2 has a somatic function. Belongs to the universal ribosomal protein uL5 family. +Activator of LATS1/2 in the Hippo signaling pathway which plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein STK3/MST2 and STK4/MST1, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Phosphorylation of YAP1 by LATS1/2 inhibits its translocation into the nucleus to regulate cellular genes important for cell proliferation, cell death, and cell migration. Stimulates the kinase activity of STK38 and STK38L. Acts cooperatively with STK3/MST2 to activate STK38 (By similarity). Binds STK38 and STK38L. Interacts with LATS1 and LATS2 (By similarity). Forms a tripartite complex with STK38 and STK3/MST2 (By similarity). Phosphorylated by STK3/MST2 and STK4/MST1 and this phosphorylation enhances its binding to LATS1. Belongs to the MOB1/phocein family. +Microtubule-associated force-producing protein involved in producing microtubule bundles and able to bind and hydrolyze GTP. Most probably involved in vesicular trafficking processes. Involved in receptor-mediated endocytosis. GTP + H2O = GDP + H(+) + phosphate Interacts with CAV1 and SH3GLB1. Binds SH3GL1, SH3GL2 and SH3GL3 (By similarity). Interacts with PHOCN. Interacts with PACSIN1, PACSIN2 and PACSIN3 (By similarity). Interacts with SNX9. Interacts with MYO1E (via SH3 domain). Interacts with SNX33 (via SH3 domain). Interacts with UNC119; leading to a decrease of DNM1 GTPase activity (By similarity). Interacts with DIAPH1 (PubMed:23325789). Interacts with AMPH, BIN1 AND SYNJ1 (By similarity). Microtubule-associated. The disease is caused by variants affecting the gene represented in this entry. Belongs to the TRAFAC class dynamin-like GTPase superfamily. Dynamin/Fzo/YdjA family. Probable cloning artifact. +Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR). 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + H(+) = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate from 5-amino-1-(5-phospho-D-ribosyl)imidazole (N5-CAIR route): step 2/2. Belongs to the AIR carboxylase family. Class I subfamily. +Catalyzes the decarboxylation of L-tyrosine to produce tyramine for methanofuran biosynthesis (PubMed:15715981). Can also catalyze the decarboxylation of L-aspartate to produce beta-alanine for coenzyme A (CoA) biosynthesis (PubMed:24891443). H(+) + L-tyrosine = CO2 + tyramine H(+) + L-aspartate = beta-alanine + CO2 Inhibited by hydroxylamine and O-methylhydroxylamine. Optimum pH is 7.5-8.5 for tyrosine decarboxylase activity. Thermostable. Retains full tyrosine decarboxylase activity after heating at 100 degrees Celsius for 10 minutes and 42% of its activity after 10 minutes at 110 degrees Celsius. Inactive after 10 minutes at 121 degrees Celsius. Cofactor biosynthesis; methanofuran biosynthesis. Cofactor biosynthesis; coenzyme A biosynthesis. Homodimer. Belongs to the group II decarboxylase family. MfnA subfamily. +Binds to the IL-1 type I receptor following IL-1 engagement, triggering intracellular signaling cascades leading to transcriptional up-regulation and mRNA stabilization. Interacts with MYD88. IL-1 stimulation leads to the formation of a signaling complex which dissociates from the IL-1 receptor following the binding of PELI1 (By similarity). The protein kinase domain is predicted to be catalytically inactive. Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. Pelle subfamily. Asn-335 is present instead of the conserved Asp which is expected to be an active site residue. +Necessary for the introduction of cis unsaturation into fatty acids. Catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to E-(2)-decenoyl-ACP and then its isomerization to Z-(3)-decenoyl-ACP. Can catalyze the dehydratase reaction for beta-hydroxyacyl-ACPs with saturated chain lengths up to 16:0, being most active on intermediate chain length. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O (3R)-hydroxydecanoyl-[ACP] = (2E)-decenoyl-[ACP] + H2O (2E)-decenoyl-[ACP] = (3Z)-decenoyl-[ACP] Lipid metabolism; fatty acid biosynthesis. Homodimer. Belongs to the thioester dehydratase family. FabA subfamily. +Probable exonuclease required for enuclation of sieve elements. Accumulates in the nuclei prior to enuclation. Expressed in the sieve elements and phloem pole pericycle cells. Regulated by the transcription factors NAC045 and NAC086. Shorter root phenotype and impaired phloem function. +carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Was identified as a high-confidence drug target. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD. Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides. Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding. Belongs to the RecD family. +Defense against chitin-containing fungal and bacterial pathogens. Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins. Constitutively expressed at low levels. Belongs to the glycosyl hydrolase 19 family. Chitinase class I subfamily. +Belongs to the bacterial ribosomal protein bS16 family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis. Belongs to the YciB family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the LeuD family. LeuD type 1 subfamily. +RNA-dependent RNA polymerase that plays an essential role in the virus replication. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Readthrough of the terminator UAG occurs at position 297. Belongs to the tombusviridae RNA polymerase family. Amino acid integrated instead of terminator codon missing. +Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules (By similarity). The COPII coat is composed of at least 5 proteins: the sec23/24 complex, the sec13/31 complex, and the protein sar1A or sar1B. sec13 and sec31 make a 2:2 tetramer that forms the edge element of the COPII outer coat. The tetramer self-assembles in multiple copies to form the complete polyhedral cage. Interacts (via WD 8) with sec13 (By similarity). Belongs to the WD repeat SEC31 family. +Forms oligomers. Belongs to the MraZ family. +Negative regulator of replication initiation, which contributes to regulation of DNA replication and ensures that replication initiation occurs exactly once per chromosome per cell cycle. Binds to pairs of hemimethylated GATC sequences in the oriC region, thus preventing assembly of replication proteins and re-initiation at newly replicated origins. Repression is relieved when the region becomes fully methylated. Homodimer. Polymerizes to form helical filaments. Belongs to the SeqA family. +Seems to be involved in non-photochemical quenching, a process maintains the balance between dissipation and utilization of light energy to minimize generation of oxidizing molecules, thereby protecting the plant against photo-oxidative damage. Belongs to the ELIP/psbS family. +Monomer. Expressed by the venom gland. Belongs to the peptidase S1 family. Snake venom subfamily. Ala-206 is present instead of the conserved Ser which is expected to be an active site residue. +Vacuolar effluxer which mediate the efflux of amino acids resulting from autophagic degradation. The release of autophagic amino acids allows the maintenance of protein synthesis and viability during nitrogen starvation (By similarity). Vacuole and punctate structures. Belongs to the ATG22 family. +Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate. (S)-dihydroorotate + H2O = H(+) + N-carbamoyl-L-aspartate Binds 2 Zn(2+) ions per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 3/3. Homodimer. Belongs to the metallo-dependent hydrolases superfamily. DHOase family. Class II DHOase subfamily. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +Necessary for formate dehydrogenase activity. Belongs to the FdhE family. +Seems to play a role in the dimerization of PSII. Belongs to the PsbT family. +The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-amino acid + H(+) Monomer. Belongs to the PTH family. +Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. 2 D-sedoheptulose 7-phosphate = D-glycero-alpha-D-manno-heptose 7-phosphate + D-glycero-beta-D-manno-heptose 7-phosphate Binds 1 zinc ion per subunit. Carbohydrate biosynthesis; D-glycero-D-manno-heptose 7-phosphate biosynthesis; D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate from sedoheptulose 7-phosphate: step 1/1. Homotetramer. The reaction produces a racemic mixture of D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate. Belongs to the SIS family. GmhA subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +Mainly expressed in leaves. Expressed at the flowering stage. Up-regulated early after infection with P.syringae carrying avrRpt2 (PubMed:8742710). Up-regulated by brassinolide, cold treatment, syringolin, P.infestans infection and, at a lower level, by salicylic acid (PubMed:17723251). Down-regulated by 2-aminoethoxyvinylglycine (AVG), high CO(2), isoxaben, and propiconazole treatments (PubMed:17723251). Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. AIG1/Toc34/Toc159-like paraseptin GTPase family. IAN subfamily. +Component of the tagatose-1,6-bisphosphate aldolase KbaYZ that is required for full activity and stability of the Y subunit. Could have a chaperone-like function for the proper and stable folding of KbaY. When expressed alone, KbaZ does not show any aldolase activity. Is involved in the catabolism of N-acetylgalactosamine and D-galactosamine. Carbohydrate metabolism; D-tagatose 6-phosphate degradation; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-tagatose 6-phosphate: step 2/2. Forms a complex with KbaY. Belongs to the GatZ/KbaZ family. KbaZ subfamily. +Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression. Purine metabolism; purine nucleotide biosynthesis [regulation]. Homodimer. Consists of two structural and functional domains: an N-terminal DNA-binding domain, approximately the first 60 residues, and a larger C-terminal domain, approximately 280 residues, which imparts the function of corepressor binding and oligomerization. +Probably part of a periplasmic ABC transporter complex futA1A2BC (TC 3.A.1.10.2) involved in Fe(3+) ion import (ferric iron). This protein and futA1 (slr1295) are subunit proteins that have redundant or overlapping substrate-binding functions (Probable). The differing subcellular locations of futA1 (predominantly thylakoid lumen) and futA2 (predominantly periplasmic) suggest they may fulfill different roles. Plays an important role in protecting the acceptor side of photosystem II (PSII) against oxidative damage, especially under iron-limiting growth conditions. Plays an undefined role in copper supply to thylakoid proteins. Binds Fe(3+) in the periplasm. Transcript levels increase when cells are grown in the absence of iron. Periplasmic levels increase when cells are grown in high NaCl or in the absence of iron. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Cells grow normally in the absence of iron; double knockouts of this gene and futA1 (slr1295) grow very poorly in the absence of iron and have a marked reduction in their ability to take up Fe(3+). Belongs to the bacterial solute-binding protein 1 family. There is some controversy as to whether this protein preferentially binds Fe(2+) or Fe(3+). +Catalyzes the rearrangement of 1-deoxy-D-xylulose 5-phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S. 1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + [sulfur-carrier protein ThiS]-C-terminal Gly-Gly + 2 H(+) + 2 H2O Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homotetramer. Forms heterodimers with either ThiH or ThiS. Belongs to the ThiG family. +Inactive tyrosine kinase involved in Wnt signaling pathway. Component of both the non-canonical (also known as the Wnt/planar cell polarity signaling) and the canonical Wnt signaling pathway. Functions in cell adhesion, cell migration, cell polarity, proliferation, actin cytoskeleton reorganization and apoptosis. Has a role in embryogenesis, epithelial tissue organization and angiogenesis. Interacts with CTNNB1. Colocalizes with MMP14 at cell junctions. Also localizes at the leading edge of migrating cells. Expressed at high levels in lung and un-pregnant uterus among adult tissues, and in the tail, limbs, somites, gut and craniofacial regions among embryonic tissues. The protein kinase domain is predicted to be catalytically inactive. MMP14 cleaves PTK7 between Pro-613 and Leu-614 generating an N-terminal soluble (70 kDa) fragment and a membrane C-terminal (50 kDa) fragment. Proteolysis by MMP14 regulates PTK7 function in non-canonical Wnt signaling pathway. Mice die perinatally and display craniorachischisis, a severe form of neural tube defect in which the neural tube fails to close from the midbrain hindbrain boundary to the base of the spine. Chuzhoi mutants also display disruption of planar cell polarity in the inner ear, and defective heart and lung development. Belongs to the protein kinase superfamily. Tyr protein kinase family. Insulin receptor subfamily. +Homeotic protein that acts downstream of Arm in the Wg cascade during embryogenesis to determine segment identity throughout the entire trunk. Acts cooperatively with other trunk homeotic proteins to repress head homeotic genes and therefore repress head segmental identity. Necessary, in combination with Scr, for the formation of the prothoracic segment. Promotes eye development in the dorsal region of the eye disk and suppresses eye development in the ventral region in combination with Wg-signaling and several early dorso-ventral eye patterning genes. Required for proper development of proximal leg segments. Has differential functions along the dorso-ventral axs of the antennal and leg disks. May play a role in wing hinge development. Possible involvement in chromatin structure for modulation of transcription. Binds DNA and can act as both a transcriptional repressor and activator. Positively regulates its own expression as well as that of Dll. Negatively regulates the expression of mod. Required for Wg-mediated transcriptional repression of Ubx in the midgut. Also represses transcription of lab in the midgut and is necessary for the proper formation of anterior and central midgut structures. Tiptop (tio) and teashirt (tsh) have, on the whole, common activities. Tio and tsh repress each other's expression and tsh has a crucial role for trunk patterning that is in part masked by ectopic expression of tiptop. Both genes share a common activity required for the activation of Ser and svb and the maintenance of en and wg. Binds arm. Initially localized in the cytoplasm soon after the blastoderm stage, and becomes nuclear by stage 9. Shows a dynamic expression pattern during embryogenesis. Expressed in the embryonic trunk region (PS 3-13) with expression strongest in the thoracic segments. Expressed in a small group of cells corresponding to the anal tuft from stage 14. Strongly expressed in the embryonic ventral nerve cord. Also expressed in the proximal domain of the leg imaginal disk and in the region of the wing disk that will give rise to the proximal wing hinge. Expressed at high levels in the anterior and central embryonic midgut mesoderm and in the embryonic midgut endoderm. Expressed at a low level in more posterior visceral mesoderm of the gut. From stage 12 onwards, tsh and tio are colocalized in some cells of the CNS, trunk epidermis, hindgut and Malpighian tubules. Expressed throughout embryonic, larval and adult development. Not maternally expressed. The tsh tio gene pair seems to have arisen from a recent duplication event: tsh has the dominant role compared to tio. Belongs to the teashirt C2H2-type zinc-finger protein family. +Belongs to the dGTPase family. Type 2 subfamily. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Homodimer. Belongs to the DXR family. +ATP-binding (A) component of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). Belongs to the ABC transporter superfamily. Energy-coupling factor EcfA family. +Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. Binds to the N-terminal domain of the chaperone ClpA. Belongs to the ClpS family. +Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine. putrescine + S-adenosyl 3-(methylsulfanyl)propylamine = H(+) + S-methyl-5'-thioadenosine + spermidine Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1. Homodimer or homotetramer. Belongs to the spermidine/spermine synthase family. +Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin derivatives with an aromatic side chains at the 5'-position. Has no activity on dihydropyrimidines. The physiological function is unknown. D-5-phenylhydantoin + H2O = H(+) + N-carbamoyl-D-phenylglycine Binds 2 divalent metal cations per subunit. Homotetramer. Carboxylation allows a single lysine to coordinate two divalent metal cations. Belongs to the metallo-dependent hydrolases superfamily. Hydantoinase/dihydropyrimidinase family. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. The rod consists of about 26 subunits of FlgG in the distal portion, and FlgB, FlgC and FlgF are thought to build up the proximal portion of the rod with about 6 subunits each (By similarity). Belongs to the flagella basal body rod proteins family. +Belongs to the staphylococcal tandem lipoprotein family. +Might function as an inhibitor of Lys-specific proteases. Might influence the maturation of megakaryocytes via its action as a serpin (By similarity). Belongs to the serpin family. Ov-serpin subfamily. +Alpha toxins bind voltage-independently at site-3 of sodium channels (Nav) and inhibit the inactivation of the activated channels, thereby blocking neuronal transmission. This toxin is active against insects and mammals. Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). LD(50) is 10.4 ug/kg by intracerebroventricular injection into mice and is 4.7 ug/g to cockroaches. Belongs to the long (4 C-C) scorpion toxin superfamily. Sodium channel inhibitor family. Alpha subfamily. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +Ketocytochalasin monooxygenase; part of the gene cluster that mediates the biosynthesis of a family of the mycotoxins cytochalasins E and K (PubMed:21983160). The hybrid PKS-NRPS synthetase ccsA and the enoyl reductase ccsC are responsible for fusion of phenylalanine with an octaketide backbone and subsequent release of the stable tetramic acid precursor (PubMed:21983160, PubMed:27551732). The polyketide synthase module (PKS) of the PKS-NRPS ccsA is responsible for the synthesis of the octaketide backbone (PubMed:21983160). The downstream nonribosomal peptide synthetase (NRPS) amidates the carboxyl end of the octaketide with a phenylalanine (PubMed:21983160). A reductase-like domain (R) at the C-terminus catalyzes the reductive release of the polyketide-amino acid intermediate (PubMed:21983160). Because ccsA lacks a designated enoylreductase (ER) domain, the required activity is provided the enoyl reductase ccsC (PubMed:21983160, PubMed:27551732). Upon formation of the 11-membered carbocycle-fused perhydroisoindolone intermediate, a number of oxidative steps are required to afford the final cytochalasin E and K, including two hydroxylations at C17 and C18, one alcohol oxidation at C17, one epoxidation at C6 and C7 and two Baeyer-Villiger oxidations (PubMed:21983160). The oxidative modification at C17, C18 and the C6-C7 epoxidation are likely to be catalyzed by the two cytochrome P450 oxygenases ccsD and ccsG (PubMed:21983160). CcsD may be responsible for the epoxidation of the C6-C7 double bond (PubMed:21983160). CcsG may be responsible for the successive oxidative modifications at C17 and C18 (PubMed:21983160). The double Baeyer-Villiger oxidations of ketocytochalasin to precytochalasin and cytochalasin Z(16) are among the final steps leading to cytochalasin E and K and are catalyzed by ccsB (PubMed:21983160, PubMed:24838010). The first oxygen insertion step follows that of the classic BVMO mechanism, generating the ester precytochalasin (PubMed:24838010). Release of precytochalasin into an aqueous environment can generate the shunt product iso-precytochalasin through spontaneous isomerization (PubMed:24838010). Alternatively, precytochalasin can undergo further oxidation by ccsB to yield the in-line carbonate-containing cytochalasin Z(16) (PubMed:24838010). Cytochalasin Z(16) is a precursor to cytochalasin E and cytochalasin K, whereas iso-precytochalasin is a precursor to cytochalasin Z(17) and rosellichalasin (PubMed:21983160, PubMed:24838010). The hydrolyase ccsE may catalyze hydrolysis of epoxide bond in cytochalasin E to afford cytochalasin K (PubMed:21983160). The function of ccsF has not been assigned but it may play a role in post-PKS-NRPS biosynthetic step, resistance or transport of cytochalasins and related PKS-NRPS products (PubMed:21983160). H(+) + ketocytochalasin + NADPH + O2 = H2O + iso-precytochalasin + NADP(+) H(+) + iso-precytochalasin + NADPH + O2 = cytochalasin Z16 + H2O + NADP(+) Binds 1 FAD per subunit. Mycotoxin biosynthesis. Belongs to the FAD-binding monooxygenase family. +Involved in pyrimidine catabolism. May facilitate the hydrolysis of carbamate, a reaction that can also occur spontaneously. carbamate + 2 H(+) = CO2 + NH4(+) Belongs to the AB hydrolase superfamily. Hydrolase RutD family. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity). a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +This is a receptor for bradykinin. Could be a factor in chronic pain and inflammation. Belongs to the G-protein coupled receptor 1 family. Bradykinin receptor subfamily. BDKRB1 sub-subfamily. +Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system). L-serine(in) + Na(+)(in) = L-serine(out) + Na(+)(out) L-threonine(in) + Na(+)(in) = L-threonine(out) + Na(+)(out) Belongs to the dicarboxylate/amino acid:cation symporter (DAACS) (TC 2.A.23) family. +Catalyzes the irreversible NADPH-dependent deamination of GMP to IMP. It functions in the conversion of nucleobase, nucleoside and nucleotide derivatives of G to A nucleotides, and in maintaining the intracellular balance of A and G nucleotides. IMP + NADP(+) + NH4(+) = GMP + 2 H(+) + NADPH Belongs to the IMPDH/GMPR family. GuaC type 2 subfamily. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the eIF-3 subunit C family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Transcriptional repressor which negatively regulates transcription of FYV5 by binding to the promoter on the sense strand. Encoded by the antisense strand of the FYV5 gene. Belongs to the ADF1 family. +Adds the second glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. Transfers glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Glc(1)Man(9)GlcNAc(2)-PP-Dol (By similarity). a dolichyl beta-D-glucosyl phosphate + alpha-D-Glc-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphosphodolichol = a dolichyl phosphate + alpha-D-Glc-(1->3)-alpha-D-Glc-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphosphodolichol + H(+) Protein modification; protein glycosylation. Belongs to the ALG6/ALG8 glucosyltransferase family. +Highly reducing polyketide synthase (HR-PKS); part of the gene cluster that mediates the biosynthesis of citreoviridin, an inhibitor of the of F1-ATPase beta-subunit (PubMed:26954888). The HR-PKS ctvA accepts acetyl-CoA as the starter unit and catalyzes eight iterations of malonyl-CoA extension and four iterations of SAM-dependent methylation at C4, C12, C14, and C16 (PubMed:26954888). The KR and DH domains selectively act on the first six iterations to generate the hexaene chain (PubMed:26954888). In the last three iterations, the KR and DH domains terminate their functions to yield a beta,delta-diketo ester moiety, which then undergoes intramolecular cyclization to yield an alpha-pyrone intermediate (PubMed:26954888). Subsequently, ctvB methylates the alpha-pyrone hydroxyl group to generate citreomontanin (PubMed:26954888). In order to form the tetrahydrofuran ring with the correct stereochemistry, the terminal alkenes of citreomontanin need to undergo isomerization to yield a (17Z)-hexaene, a step that could be catalyzed by ctvC (PubMed:26954888). The (17Z)-hexaene then undergoes bisepoxidation by ctvC to form a (17R,16R,15S,14R)-bisepoxide moiety (PubMed:26954888). Lastly, ctvD acts as a regioselective hydrolase to form the tetrahydrofuran ring with the substituents in the correct absolute configuration, completing the biosynthesis of citreoviridin (PubMed:26954888). Binds 1 phosphopantetheine covalently. Mycotoxin biosynthesis. Citreoviridin inhibits mitochondrial oxidative phosphorylation by binding to the beta-subunit of F1-ATPase (PubMed:2523213). Ectopic mitochondrial ATP synthase is a factor that mediates HIV-1 transfer between antigen-presenting cells (APCs) and CD4+ target cells, and citreoviridin can completely block antigen-presenting cell (APC)-mediated transfer of HIV-1 at the APC-target cells (PubMed:22753871). Inhibition of Ectopic mitochondrial ATP synthase by citreoviridin can also lead to suppression of cancer growth by activating the unfolded protein response (PubMed:22822083). +Secreted subtilisin-like serine endopeptidase (PubMed:25944934). Mediates the degradation of collagen, the major structural protein in the mammalian host. Degrades the nonhelical regions of collagen that function in the cross-linking of the helical components (By similarity). May function as virulence factor involved in epidermal wing necrosis observed in white nose syndrome (WNS) in bats (By similarity). Belongs to the peptidase S8 family. +Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P). S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 1/6. Belongs to the eIF-2B alpha/beta/delta subunits family. MtnA subfamily. +This gene belongs to a multigene family expressed in a large variety of tumors whereas in normal tissues, expression is restricted to germ cells. These genes organized in clustered repeats, have a high degree of predicted sequence identity, but differ by scattered single nucleotide substitution. Their sequences contain either the antigenic peptide YYWPRPRRY or YRPRPRRY which is recognized by cytotoxic T-cells. Belongs to the GAGE family. The first GAGE nomenclature was based on identified mRNA sequences, but the high identity of the GAGE members made impossible to separate products of paralogous genes from polymorph products. PubMed:18179644 presented a new GAGE gene nomenclature based on the identified genes and their products. +Acts as a radical domain for damaged PFL and possibly other radical proteins. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)). 7-carboxy-7-deazaguanine + ATP + NH4(+) = 7-cyano-7-deazaguanine + ADP + H(+) + H2O + phosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. Belongs to the QueC family. +Non-reducing polyketide synthase; part of the gene cluster that mediates the biosynthesis of diterpenoid pyrones (PubMed:32286350). The first step of the pathway is the synthesis of the alpha-pyrone moiety by the polyketide synthase dpfgA via condensation of one acetyl-CoA starter unit with 3 malonyl-CoA units and 2 methylations (Probable). The alpha-pyrone is then combined with geranylgeranyl pyrophosphate (GGPP) formed by the GGPP synthase dpfgD through the action of the prenyltransferase dpfgC to yield a linear alpha-pyrone diterpenoid (Probable). Subsequent steps in the diterpenoid pyrone biosynthetic pathway involve the decalin core formation, which is initiated by the epoxidation of the C10-C11 olefin by the FAD-dependent oxidoreductase dpfgE, and is followed by a cyclization cascade catalyzed by the terpene cyclase dpfgB (Probable). The short chain dehydrogenase/reductase dpfgG then oxidizes the 8S hydroxy group to a ketone and the short chain dehydrogenase/reductase dpfgH reduces the ketone to the 8R hydroxy group to yield higginsianin B (PubMed:32286350). Higginsianin B is further methylated by the methyltransferase dpfgI to produce the intermediate named FDDP B (PubMed:32286350). The cytochrome P450 monooxygenase dfgpJ then catalyzes a three-step oxidation at C-27 to generate a carboxylic acid as well as C-26 hydroxylation (PubMed:32286350). Finally, methyltransferase dpfgK methylates the carboxylic acid generated by dpfgJ, yielding the final diterpenoid pyrones from the pathway which were named FDDP D and FDDP E (PubMed:32286350). Secondary metabolite biosynthesis; terpenoid biosynthesis. Multidomain protein; including a starter unit:ACP transacylase (SAT) that selects the starter unit; a ketosynthase (KS) that catalyzes repeated decarboxylative condensation to elongate the polyketide backbone; a malonyl-CoA:ACP transacylase (MAT) that selects and transfers the extender unit malonyl-CoA; a product template (PT) domain that controls the immediate cyclization regioselectivity of the reactive polyketide backbone; a methyltransferase (CMeT) domain responsible for methylations; and an acyl-carrier protein (ACP) that serves as the tether of the growing and completed polyketide via its phosphopantetheinyl arm. Diterpenoid pyrones display various biological activities and FDDP E shows anti-HIV activity (PubMed:32286350). FDDP D and FDDP E show also inhibitory activity of 42-mer-amyloid beta aggregation that is involved in the pathogenesis of Alzheimer's disease (PubMed:32286350). +Chemotactic-signal transducers respond to changes in the concentration of attractants and repellents in the environment, transduce a signal from the outside to the inside of the cell, and facilitate sensory adaptation through the variation of the level of methylation. Attractants increase the level of methylation while repellents decrease the level of methylation (By similarity). Belongs to the methyl-accepting chemotaxis (MCP) protein family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP). diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 1/2. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrE subfamily. +Belongs to the UPF0304 family. +Gamma subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. CTDK-I phosphorylates 'Ser-5' if the CTD substrate is not phosphorylated at 'Ser-5', but will phosphorylate 'Ser-2' of a CTD substrate if 'Ser-5' is already phosphorylated. CTDK-I is also more reactive toward substrates that are prephosphorylated at 'Ser-2' or 'Ser-5' compared with an unphosphorylated CTD substrate, therefore efficiently creating doubly phosphorylated CTD repeats. Involved in RNA polymerase I transcription and RNA polymerase II transcriptional elongation, and as part of the CTDK-I complex, pre-mRNA 3'-end processing and SET2 mediated H3K36 methylation. Together with CTK2, required for CTK1 CTD kinase activation. Required for DNA damage induced transcription. Involved in the adaptation to alternative carbon sources, including galactose, glycerol and ethanol, but not raffinose. Required for the integrity of the rDNA locus. CTDK-I consists of three subunits, CTK1, CTK2 and CTK3 (also called alpha, beta and gamma). Interacts with CTK1. Heterodimerization with CTK2 is required to protect this subunit from degradation. Ubiquitinated. Ubiquitination leads to degradation by the 26S proteasome pathway. Null mutants are viable, but grow more slowly than wild-type cells at 30 degrees Celsius. They are cold-sensitive, failing to grow at 12 degrees Celsius. They display flocculent growth in liquid media and they show abnormal cell morphologies, for example, a significant fraction of the cells are greatly enlarged. Deletion mutant is sensitive to the DNA synthesis inhibitor hydroxyurea (HU) and UV irradiation. Present with 2640 molecules/cell in log phase SD medium. Belongs to the CTK3 family. +Lectin that specifically binds to L-fucose (PubMed:2193930, PubMed:2666154, PubMed:7397108, PubMed:18493851, PubMed:21945439, PubMed:27650323, PubMed:28800497, PubMed:14503859, PubMed:12732625). Has strongest preference for the alpha-1,6-fucosylated chain (core fucose) on glycoproteins among alpha-1,2-, alpha-1,3-, alpha-1,4-, and alpha-1,6-fucosylated chains (PubMed:17383961, PubMed:19109923, PubMed:20798114, PubMed:22226468). Might play a role in the differentiation of the fruiting body (PubMed:2193930). Exhibits antifungal activity against Mucor racemosus and thus could act as an antifungal protein in natural ecosystems (PubMed:22738968). Forms homodimers (PubMed:2193930, PubMed:7397108, PubMed:20798114, PubMed:12732625). The two AAL monomers are associated via interactions between N-terminal and C-terminal peptides (PubMed:12732625). Tyr-7 interacts via aromatic ring stacking with its counterpart on the other monomer, whereas Ser-284 interacts via hydrogen bonding with Asp-264 on the other monomer (PubMed:12732625). AAL is detected in fruiting bodies but not in mycelia (PubMed:2193930). AAL adopts the six-bladed beta-propeller fold and contains 5 binding sites per monomer, each located between two adjacent blades (PubMed:14503859, PubMed:12732625). Residues conserved at 5 of the 6 sites, are located on the surface of the AAL and directly contribute to fucose recognition (PubMed:14503859). Because the corresponding residues forming site 6 are not conserved, this site cannot be considered to accommodate fucose molecules (PubMed:14503859). The 5 binding sites that are non-equivalent, and owing to minor differences in amino-acid composition they exhibit a marked difference in specific ligand recognition (PubMed:18493851, PubMed:12732625). AAL's binding activity could be used to identify secreted fucosylated glycoproteins that may represent candidate biomarkers for cancer since fucosylation of N-linked glycans has been associated with several types of cancer such as liver cancer (PubMed:22789673, PubMed:24027776, PubMed:27650323). Identified as one of the several suitable fluorescently labeled lectins that can be used in a combination for the visualization and quantification of extracellular glycoconjugates in dental supragingival biofilms grown for 48 hours in situ in the absence of dietary carbohydrates (PubMed:28748044). Belongs to the fungal fucose-specific lectin family. +Central regulator of manganese homeostasis. DNA binding is strongly activated by Mn(2+). Homodimer. Belongs to the DtxR/MntR family. +Involved in phosphonate degradation. (2-aminoethyl)phosphonate + pyruvate = L-alanine + phosphonoacetaldehyde Homodimer. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. PhnW subfamily. +May play a role in cell growth. Belongs to the TMEM184 family. +Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. ATP + CoA + succinate = ADP + phosphate + succinyl-CoA Binds 1 Mg(2+) ion per subunit. Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. Heterotetramer of two alpha and two beta subunits. Belongs to the succinate/malate CoA ligase beta subunit family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Transient kinetochore component required for chromosome and spindle pole alignment and chromosome segregation during mitosis (PubMed:18765790, PubMed:18936247). Functions downstream of the RZZ complex to mediate kinetochore-microtubule attachments and nuclear envelope breakdown during cell division (PubMed:18765790, PubMed:18936247, PubMed:24231804). Required for kinetochore assembly and localizes the checkpoint proteins mdf-1 and mdf-2, dynein and dynactin to unattached kinetochores (PubMed:18765790, PubMed:18936247, PubMed:24231804). Dynein is believed to control the initial lateral interaction between the kinetochore and spindle microtubules and to facilitate the subsequent formation of end-on kinetochore-microtubule attachments mediated by the NDC80 complex (PubMed:24231804). Required for embryonic development (PubMed:18765790, PubMed:18936247). Interacts with Zwilch homolog zwl-1, a component of the RZZ complex (PubMed:18765790). Interacts with mdf-1 and mdf-2 (PubMed:18936247). Localizes to microtubules during mitosis (PubMed:18936247). Recruited to the kinetochore by the RZZ complex (PubMed:18765790, PubMed:18936247). Localization to the kinetochore is also dependent on the NDC80 complex and bub-1 (PubMed:18765790). Localizes to the kinetochore during nuclear envelope breakdown and remains there until the metaphase-anaphase transition (PubMed:18765790, PubMed:18936247). Recessive embryonic lethality (PubMed:18936247). Hemizygous mutants are viable and survive through embryogenesis, but are either lethal at the larval stage of development or sterile (PubMed:18936247). The oocytes of sterile mutants have extra chromosomes and prematurely exit the prophase stage of meiosis which results in endomitosis (PubMed:18936247). RNAi-mediated knockdown results in embryonic lethality (PubMed:18765790, PubMed:18936247). RNA-mediated knockdown results in defective cell division characterized by irregular chromosome alignment and segregation, longer spindles during chromatid separation, premature spindle pole separation, defective formation of kinetochore-microtubule attachments and chromatin bridge formation during the anaphase stage of mitosis (PubMed:18765790, PubMed:18936247, PubMed:24231804). +Transports the calcitonin gene-related peptide type 1 receptor (CALCRL) to the plasma membrane. Acts as a receptor for calcitonin-gene-related peptide (CGRP) together with CALCRL. Heterodimer of CALCRL and RAMP1. Expressed predominantly in the thymus, skeletal muscle, embryonic and adult brain, embryonic and adult lung, and colon. Belongs to the RAMP family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Belongs to the NDK family. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Hydrolyzes nucleoside diphosphates with a preference for GDP, IDP and UDP compared to ADP and CDP (By similarity). In the lumen of the endoplasmic reticulum, hydrolyzes UDP that acts as an end-product feedback inhibitor of the UDP-Glc:glycoprotein glucosyltransferases. UMP can be transported back by an UDP-sugar antiporter to the cytosol where it is consumed to regenerate UDP-glucose. Therefore, it positively regulates protein reglucosylation by clearing UDP from the ER lumen and by promoting the regeneration of UDP-glucose. Protein reglucosylation is essential to proper glycoprotein folding and quality control in the ER (By similarity). a ribonucleoside 5'-diphosphate + H2O = a ribonucleoside 5'-phosphate + H(+) + phosphate GDP + H2O = GMP + H(+) + phosphate H2O + UDP = H(+) + phosphate + UMP H2O + IDP = H(+) + IMP + phosphate CDP + H2O = CMP + H(+) + phosphate ADP + H2O = AMP + H(+) + phosphate Protein modification; protein glycosylation. Monomer; active form. Homodimer; disulfide-linked. Homodimers are enzymatically inactive. N-glycosylated; high-mannose type. Belongs to the GDA1/CD39 NTPase family. +Release of an N-terminal amino acid, Xaa-|-Yaa- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action). When a terminal hydrophobic residue is followed by a prolyl residue, the two may be released as an intact Xaa-Pro dipeptide. Binds 1 zinc ion per subunit. Belongs to the peptidase M1 family. +Rhomboid-type serine protease that catalyzes intramembrane proteolysis. Cleaves type-1 transmembrane domains using a catalytic dyad composed of serine and histidine that are contributed by different transmembrane domains. Belongs to the peptidase S54 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +Catalyzes the transfer of a N-acetyl-glucosamine moiety to 1D-myo-inositol 3-phosphate to produce 1D-myo-inositol 2-acetamido-2-deoxy-glucopyranoside 3-phosphate in the mycothiol biosynthesis pathway. 1D-myo-inositol 3-phosphate + UDP-N-acetyl-alpha-D-glucosamine = 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside 3-phosphate + H(+) + UDP Homodimer. Belongs to the glycosyltransferase group 1 family. MshA subfamily. +Beta toxins bind voltage-independently at site-4 of sodium channels (Nav) and shift the voltage of activation toward more negative potentials thereby affecting sodium channel activation and promoting spontaneous and repetitive firing. Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). Belongs to the long (4 C-C) scorpion toxin superfamily. Sodium channel inhibitor family. Beta subfamily. +Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY. Part of the signal recognition particle protein translocation system, which is composed of SRP and FtsY. The SRP-RNC complex is targeted to the cytoplasmic membrane. Composed of three domains: the N-terminal N domain, which is responsible for interactions with the ribosome, the central G domain, which binds GTP, and the C-terminal M domain, which binds the RNA and the signal sequence of the RNC. Belongs to the GTP-binding SRP family. SRP54 subfamily. +Product of a dubious CDS prediction. +Catalyzes the hydrolysis of UDP-3-O-myristoyl-N-acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate, the committed step in lipid A biosynthesis. a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 2/6. Belongs to the LpxC family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Sarcotoxins, which are potent bactericidal proteins, are produced in response to injury. They are cytotoxic to both Gram-positive and Gram-negative bacteria. Belongs to the cecropin family. +A methylase that recognizes the double-stranded sequence 5'-GAATTC-3', methylates A-3 on both strands, and protects the DNA from cleavage by the EcoRI endonuclease. a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an N(6)-methyl-2'-deoxyadenosine in DNA + H(+) + S-adenosyl-L-homocysteine Monomer. Belongs to the N(4)/N(6)-methyltransferase family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +D-serine = NH4(+) + pyruvate Belongs to the serine/threonine dehydratase family. DsdA subfamily. +Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NAD(+) (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADPH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NADP(+) Belongs to the MnmG family. TrmFO subfamily. +May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Protein modification; protein ubiquitination. The BTB/POZ domain mediates the interaction with some component of ubiquitin ligase complexes. Belongs to the NPH3 family. +Catalyzes the introduction of a C-5 double bond in the B ring of ergosterol. May contribute to the regulation of ergosterol biosynthesis. a Delta(7)-sterol + 2 Fe(II)-[cytochrome b5] + 2 H(+) + O2 = a Delta(5),Delta(7)-sterol + 2 Fe(III)-[cytochrome b5] + 2 H2O Steroid metabolism; ergosterol biosynthesis; ergosterol from zymosterol: step 3/5. The histidine box domains may contain the active site and/or be involved in metal ion binding. Belongs to the sterol desaturase family. +Probable transcription factor. Belongs to the HD-ZIP homeobox family. Class IV subfamily. +Component of some SCF (SKP1-cullin-F-box) protein ligase complex that plays a central role in iron homeostasis by promoting the ubiquitination and subsequent degradation of ireb2/irp2. Upon high iron and oxygen level, it specifically recognizes and binds ireb2/irp2, promoting its ubiquitination and degradation by the proteasome (By similarity). Protein modification; protein ubiquitination. Part of a SCF (SKP1-cullin-F-box) protein ligase complex. The hemerythrin-like region acts as an oxygen and iron sensor by binding oxygen through a diiron metal-center. In absence of oxygen and iron, the protein is ubiquitinated and degraded (By similarity). Ubiquitinated upon iron and oxygen depletion, leading to its degradation by the proteasome. Ubiquitination is regulated by the hemerythrin-like region that acts as an oxygen and iron sensor (By similarity). +Affects actin polymerization through interaction with the actin-binding protein CAP32/34 (acpA/acpB). Acts as a chaperone by stimulating the refolding of denaturated acpA and acpB, but neither stimulates nor inhibits the capping activity of native CAP32/34. Interacts with the heterodimeric F-actin-capping protein CAP32/34 (acpA/acpB). Binds via its C-terminal tail and interaction is ATP-dependent. Found in F-actin-rich regions of the cell cortex and cell protrusions. Heat shock cognate proteins are expressed constitutively during normal development. Up-regulated in aspidocytes, a resistant cell type induced from amoebae by a range of toxins including heavy metals and antibiotics. Belongs to the heat shock protein 70 family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +May help in the organization of the PsaE and PsaF subunits. Belongs to the PsaJ family. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 1 family. +Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Capsid protein VP1 mainly forms the vertices of the capsid (By similarity). Capsid protein VP1 interacts with host CXADR to provide virion attachment to target host cells (Probable). This attachment induces virion internalization (By similarity). Tyrosine kinases are probably involved in the entry process (By similarity). After binding to its receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP1 N-terminus (that contains an amphipathic alpha-helix) and capsid protein VP4 are externalized (By similarity). Together, they shape a pore in the host membrane through which viral genome is translocated to host cell cytoplasm (By similarity). Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Lies on the inner surface of the capsid shell (By similarity). After binding to the host receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP4 is released, Capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm (By similarity). Component of immature procapsids, which is cleaved into capsid proteins VP4 and VP2 after maturation (By similarity). Allows the capsid to remain inactive before the maturation step (By similarity). Cysteine protease that cleaves viral polyprotein and specific host proteins (By similarity). It is responsible for the autocatalytic cleavage between the P1 and P2 regions, which is the first cleavage occurring in the polyprotein (By similarity). Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation (By similarity). Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores (By similarity). Counteracts stress granule formation probably by antagonizing its assembly or promoting its dissassembly (By similarity). Cleaves and inhibits host IFIH1/MDA5, thereby inhibiting the type-I IFN production and the establishment of the antiviral state (By similarity). Cleaves and inhibits host MAVS, thereby inhibiting the type-I IFN production and the establishment of the antiviral state (By similarity). Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host reticulum endoplasmic and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cytoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication. Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3. Localizes the viral replication complex to the surface of membranous vesicles. Together with protein 3CD binds the Cis-Active RNA Element (CRE) which is involved in RNA synthesis initiation. Acts as a cofactor to stimulate the activity of 3D polymerase, maybe through a nucleid acid chaperone activity. Localizes the viral replication complex to the surface of membranous vesicles (By similarity). It inhibits host cell endoplasmic reticulum-to-Golgi apparatus transport and causes the disassembly of the Golgi complex, possibly through GBF1 interaction (By similarity). This would result in depletion of MHC, trail receptors and IFN receptors at the host cell surface (By similarity). Plays an essential role in viral RNA replication by recruiting ACBD3 and PI4KB at the viral replication sites, thereby allowing the formation of the rearranged membranous structures where viral replication takes place (By similarity). Acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU (By similarity). The oriI viral genomic sequence may act as a template for this. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome (By similarity). Following genome release from the infecting virion in the cytoplasm, the VPg-RNA linkage is probably removed by host TDP2 (By similarity). During the late stage of the replication cycle, host TDP2 is excluded from sites of viral RNA synthesis and encapsidation, allowing for the generation of progeny virions (By similarity). Involved in the viral replication complex and viral polypeptide maturation. It exhibits protease activity with a specificity and catalytic efficiency that is different from protease 3C. Protein 3CD lacks polymerase activity. Protein 3CD binds to the 5'UTR of the viral genome. Replicates the viral genomic RNA on the surface of intracellular membranes. May form linear arrays of subunits that propagate along a strong head-to-tail interaction called interface-I. Covalently attaches UMP to a tyrosine of VPg, which is used to prime RNA synthesis. The positive stranded RNA genome is first replicated at virus induced membranous vesicles, creating a dsRNA genomic replication form. This dsRNA is then used as template to synthesize positive stranded RNA genomes. ss(+)RNA genomes are either translated, replicated or encapsidated. Major viral protease that mediates proteolytic processing of the polyprotein (By similarity). Cleaves host EIF5B, contributing to host translation shutoff (By similarity). Cleaves also host PABPC1, contributing to host translation shutoff (By similarity). Cleaves host NLRP1, triggers host N-glycine-mediated degradation of the autoinhibitory NLRP1 N-terminal fragment (By similarity). a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. Binds 2 magnesium ions that constitute a dinuclear catalytic metal center (By similarity). The magnesium ions are not prebound but only present for catalysis (By similarity). Requires the presence of 3CDpro or 3CPro (By similarity). Replication or transcription is subject to high level of random mutations by the nucleotide analog ribavirin. Interacts with capsid protein VP1 and capsid protein VP3 to form heterotrimeric protomers. Interacts with capsid protein VP0, and capsid protein VP3 to form heterotrimeric protomers (By similarity). Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid (By similarity). Interacts with capsid protein VP2, capsid protein VP3 and capsid protein VP4 following cleavage of capsid protein VP0 (By similarity). Interacts with host CXADR (PubMed:10814575). Interacts with capsid protein VP1 and capsid protein VP3 in the mature capsid. Interacts with capsid protein VP0 and capsid protein VP1 to form heterotrimeric protomers (By similarity). Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid (By similarity). Interacts with capsid protein VP4 in the mature capsid (By similarity). Interacts with protein 2C; this interaction may be important for virion morphogenesis (By similarity). Interacts with capsid protein VP1 and capsid protein VP3. Homodimer. Homohexamer; forms a hexameric ring structure with 6-fold symmetry characteristic of AAA+ ATPases (By similarity). Interacts (via N-terminus) with host RTN3 (via reticulon domain); this interaction is important for viral replication (By similarity). Interacts with capsid protein VP3; this interaction may be important for virion morphogenesis (By similarity). Interacts with protein 3CD. Homodimer (By similarity). Interacts with host GBF1 (By similarity). Interacts (via GOLD domain) with host ACBD3 (via GOLD domain); this interaction allows the formation of a viral protein 3A/ACBD3 heterotetramer with a 2:2 stoichiometry, which will stimulate the recruitment of host PI4KB in order to synthesize PI4P at the viral RNA replication sites (By similarity). Interacts with RNA-directed RNA polymerase. Interacts with protein 3AB and with RNA-directed RNA polymerase. Interacts with Viral protein genome-linked and with protein 3CD. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. The N-terminus has membrane-binding (By similarity). The N-terminus also displays RNA-binding properties (By similarity). The N-terminus is involved in oligomerization (By similarity). The central part contains an ATPase domain and a degenerate C4-type zinc-finger with only 3 cysteines (By similarity). The C-terminus is involved in RNA-binding (By similarity). The extreme C-terminus contains a region involved in oligomerization (By similarity). Specific enzymatic cleavages in vivo by the viral proteases yield processing intermediates and the mature proteins. Myristoylation is required for the formation of pentamers during virus assembly. Further assembly of 12 pentamers and a molecule of genomic RNA generates the provirion. During virion maturation, immature virions are rendered infectious following cleavage of VP0 into VP4 and VP2. This maturation seems to be an autocatalytic event triggered by the presence of RNA in the capsid and it is followed by a conformational change infectious virion. Myristoylation is required during RNA encapsidation and formation of the mature virus particle. VPg is uridylylated by the polymerase into VPg-pUpU. This acts as a nucleotide-peptide primer for the genomic RNA replication. Belongs to the picornaviruses polyprotein family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type B subfamily. +Requires at least three xylose residues for catalytic activity. Does not have activity against xylobiose. Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans. Belongs to the glycosyl hydrolase 10 (cellulase F) family. +Structural component of the T=16 icosahedral capsid. The capsid is composed of pentamers and hexamers of major capsid protein/MCP, which are linked together by heterotrimers called triplexes. These triplexes are formed by a single molecule of triplex protein 1/TRX1 and two copies of triplex protein 2/TRX2. Additionally, TRX1 is required for efficient transport of TRX2 to the nucleus, which is the site of capsid assembly. Interacts with TRX1 and major capisd protein/MCP. Belongs to the herpesviridae TRX2 protein family. +Membrane-bound UDP-glucosyltransferase (UGT) which catalyzes the C-glucosylation of kermesate and flavokermesate to produce carminate and flavokermesate 7-C-beta-D-glucoside (dcll) respectively (PubMed:29215010). Carminate is used as a deterrent against insect predators (PubMed:29215010). kermesate + UDP-alpha-D-glucose = carminate + 2 H(+) + UDP flavokermesate + UDP-alpha-D-glucose = flavokermesate 7-C-beta-D-glucoside + 2 H(+) + UDP Localization to the endoplasmic reticulum membrane is critical for its activity. Expressed in adult female. Glycosylated. Carminate, also known as cochineal dye, is used as a fabric and cosmetics dye and as a natural food coloring. Belongs to the UDP-glycosyltransferase family. +Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity). Ubiquitin is encoded by 16 different genes. Ubiquitin is generally synthesized as a polyubiquitin precursor with tandem head to tail repeats. Often, there is one to three additional amino acids after the last repeat, removed in the mature protein. Alternatively, ubiquitin extension protein is synthesized as a single copy of ubiquitin fused to a ribosomal protein (either L40 or S27A) or to a ubiquitin-related protein (either RUB1 or RUB2). Following translation, extension protein is cleaved from ubiquitin. Belongs to the ubiquitin family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +Adds the first galactose to the lacto-N-tetraose chain in lipooligosaccharide (LOS). Glycan metabolism; lacto-N-neotetraose biosynthesis. Bacterial outer membrane biogenesis; lipooligosaccharide biosynthesis. Belongs to the glycosyltransferase 25 family. +ATP + H2O = ADP + H(+) + phosphate Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type V subfamily. Truncated N-terminus. Unlikely isoform. Cloning artifact. +Involved in phosphonate degradation. (2-aminoethyl)phosphonate + pyruvate = L-alanine + phosphonoacetaldehyde Homodimer. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. PhnW subfamily. +A P subtype restriction enzyme that recognizes the double-stranded sequence 5'-CCN(7)GG-3' and cleaves after N-7. Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Binds 1 zinc ion per subunit. Is one of the thermostable restriction enzymes that remain active after 20 to 30 cycles of thermal PCR cycling. Heterotetramer of two alpha and two beta subunits. The alpha subunit is believed to be responsible for DNA recognition, while the beta subunit is thought to mediate cleavage. Could be used to screen carcinogenic mutations in a restriction endonuclease-mediated selective PCR (or REMS-PCR) assay. In particular, could be used to detect the vast majority of mutations that occur at codons 12 or 13 of the Ras oncogenes that encode glycine (codons GGN) at those positions. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreB releases sequences of up to 9 nucleotides in length. Belongs to the GreA/GreB family. GreB subfamily. +Deposition-and-exchange histone chaperone specific for H2AZ1, specifically chaperones H2AZ1 and deposits it into nucleosomes. As component of the SRCAP complex, mediates the ATP-dependent exchange of histone H2AZ1/H2B dimers for nucleosomal H2A/H2B, leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the NuA4 histone acetyltransferase complex which contains the catalytic subunit KAT5/TIP60 and the subunits EP400, TRRAP/PAF400, BRD8/SMAP, EPC1, DMAP1/DNMAP1, RUVBL1/TIP49, RUVBL2, ING3, actin, ACTL6A/BAF53A, MORF4L1/MRG15, MORF4L2/MRGX, MRGBP, YEATS4/GAS41 and VPS72/YL1. Component of a NuA4-related complex which contains EP400, TRRAP/PAF400, SRCAP, BRD8/SMAP, EPC1, DMAP1/DNMAP1, RUVBL1/TIP49, RUVBL2, actin, ACTL6A/BAF53A, VPS72 and YEATS4/GAS41. Also part of a multiprotein complex which contains SRCAP and which binds to H2AZ1/H2AZ. Interacts (via N-terminal domain) with H2AZ1. Belongs to the VPS72/YL1 family. +Serine endoprotease that processes various proproteins by cleavage at paired basic amino acids, recognizing the RXXX[KR]R consensus motif. Likely functions in the constitutive secretory pathway, with unique restricted distribution in both neuroendocrine and non-neuroendocrine tissues. The PACE4A-I precursor protein seems to exist in the reticulum endoplasmic as both a monomer and a dimer-sized complex whereas mature PACE4A-I exists only as a monomer, suggesting that propeptide cleavage affects its tertiary or quaternary structure. Interacts (immature form including the propeptide) with RCN3; probably involved in the maturation and the secretion of PCSK6 (PubMed:16433634). Not secreted, remains probably in zymogen form in endoplasmic reticulum. Not secreted, remains probably in zymogen form in endoplasmic reticulum. Retained intracellularly probably through a hydrophobic cluster in their C-terminus. Retained intracellularly probably through a hydrophobic cluster in their C-terminus. Each PACE4 isoform exhibits a unique restricted distribution. Isoform PACE4A-I is expressed in heart, brain, placenta, lung, skeletal muscle, kidney, pancreas, but at comparatively higher levels in the liver. Isoform PACE4A-II is at least expressed in placenta. Isoform PACE4B was only found in the embryonic kidney cell line from which it was isolated. Isoform PACE4C and isoform PACE4D are expressed in placenta. Isoform PACE4E-I is expressed in cerebellum, placenta and pituitary. Isoform PACE4E-II is at least present in cerebellum. The propeptide domain acts as an intramolecular chaperone assisting the folding of the zymogen within the endoplasmic reticulum. Isoform PACE4D lacks the propeptide domain. Probably enzymatically inactive. Probably enzymatically inactive. Probably enzymatically inactive. Probably enzymatically inactive. Belongs to the peptidase S8 family. +Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ). 5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphooxyethyl)-thiazole + ADP + H(+) Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-methyl-5-(2-phosphoethyl)-thiazole from 5-(2-hydroxyethyl)-4-methylthiazole: step 1/1. Belongs to the Thz kinase family. +Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides. May be an antioxidant enzyme particularly in the developing shoot and photosynthesizing leaf. [thioredoxin]-dithiol + a hydroperoxide = [thioredoxin]-disulfide + an alcohol + H2O Homodimer; disulfide-linked, upon oxidation. On the 2D-gel the determined pI of this protein is: 5.7, its MW is: 22.8 kDa. The active site is a conserved redox-active cysteine residue, the peroxidatic cysteine (C(P)), which makes the nucleophilic attack on the peroxide substrate. The peroxide oxidizes the C(P)-SH to cysteine sulfenic acid (C(P)-SOH), which then reacts with another cysteine residue, the resolving cysteine (C(R)), to form a disulfide bridge. The disulfide is subsequently reduced by an appropriate electron donor to complete the catalytic cycle. In this typical 2-Cys peroxiredoxin, C(R) is provided by the other dimeric subunit to form an intersubunit disulfide. The disulfide is subsequently reduced by thioredoxin. Belongs to the peroxiredoxin family. AhpC/Prx1 subfamily. The order of the peptides shown is unknown. +Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine (By similarity). Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. This function is generally fulfilled by the C-terminal part of HisG, which is missing in some bacteria such as this one. Belongs to the class-II aminoacyl-tRNA synthetase family. HisZ subfamily. +The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently. Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits. The heterotrimers can form oligomers, although 1 heterotrimer is thought to be able to translocate proteins. Interacts with the ribosome. Interacts with SecDF, and other proteins may be involved. Interacts with SecA. Belongs to the SecY/SEC61-alpha family. +Catalyzes the ligation of CoA on butanoate to produce butanoyl-CoA (PubMed:23300257). Can also use hexanoate, pentanoate and 4-methylpentanoate as substrates with a lower efficiency (PubMed:23300257). ATP + butanoate + CoA = AMP + butanoyl-CoA + diphosphate ATP + CoA + hexanoate = AMP + diphosphate + hexanoyl-CoA ATP + CoA + pentanoate = AMP + diphosphate + pentanoyl-CoA 4-methylpentanoate + ATP + CoA = 4-methylpentanoyl-CoA + AMP + diphosphate A number of isoforms are produced. According to EST sequences. Expressed in roots, leaves, stems, flowers and developing seeds. Belongs to the ATP-dependent AMP-binding enzyme family. +Involved in the biosynthesis of the thiazole moiety of thiamine. Catalyzes the conversion of NAD and glycine to adenosine diphosphate 5-(2-hydroxyethyl)-4-methylthiazole-2-carboxylate (ADT), an adenylated thiazole intermediate, using free sulfide as a source of sulfur. glycine + hydrogen sulfide + NAD(+) = ADP-5-ethyl-4-methylthiazole-2-carboxylate + H(+) + 3 H2O + nicotinamide Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homooctamer; tetramer of dimers. Belongs to the THI4 family. +Belongs to the PsaM family. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +ATP-binding (A) component of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). Belongs to the ABC transporter superfamily. Energy-coupling factor EcfA family. +Belongs to the protein kinase superfamily. ADCK protein kinase family. +Belongs to the bacterial ribosomal protein bL36 family. +Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids. Forms a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD. Belongs to the 'phage' integrase family. XerC subfamily. +Calcium-binding protein that acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium. Together with PDCD6, acts as calcium-dependent adapter for the BCR(KLHL12) complex, a complex involved in endoplasmic reticulum (ER)-Golgi transport by regulating the size of COPII coats. In response to cytosolic calcium increase, the heterodimer formed with PDCD6 interacts with, and bridges together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export, which is required for neural crest specification. Its role in the heterodimer formed with PDCD6 is however unclear: some evidence shows that PEF1 and PDCD6 work together and promote association between PDCD6 and SEC31 in presence of calcium. Other reports show that PEF1 dissociates from PDCD6 in presence of calcium, and may act as a negative regulator of PDCD6 (By similarity). Also acts as a negative regulator of ER-Golgi transport; possibly by inhibiting interaction between PDCD6 and SEC31 (By similarity). Heterodimer; heterodimerizes (via the EF-hand 5) with PDCD6. Dissociates from PDCD6 in presence of calcium. Membrane-associated in the presence of Ca(2+) (By similarity). Localizes to endoplasmic reticulum exit site (ERES) (By similarity). Ubiquitinated by the BCR(KLHL12) E3 ubiquitin ligase complex. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Binds 1 zinc ion per subunit. Belongs to the universal ribosomal protein uS14 family. +Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) Binds 1 zinc ion per subunit. Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. Belongs to the class-II aminoacyl-tRNA synthetase family. +Cell wall lytic enzyme. Hydrolyzes the link between L-alanine and D-glutamate residues in certain bacterial cell-wall glycopeptides. Expressed at about 20 minutes after infection. Belongs to the peptidase M15C family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella. Phosphorylated on tyrosine residue(s). Flagellin from strain 5939 but not from strain 170018 is glycosylated. Belongs to the bacterial flagellin family. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Member of the two-component regulatory system PhoQ/PhoP which regulates the expression of genes involved in virulence and resistance to host defense antimicrobial peptides. Phosphorylated by PhoQ. +Glycosyltransferase that initiates the elongation of O-linked fucose residues attached to EGF-like repeats in the extracellular domain of Notch molecules. Modulates NOTCH1 activity by modifying O-fucose residues at specific EGF-like domains resulting in inhibition of NOTCH1 activation by JAG1 and enhancement of NOTCH1 activation by DLL1 via an increase in its binding to DLL1 (By similarity). Decreases the binding of JAG1 to NOTCH2 but not that of DLL1 (PubMed:11346656). Essential mediator of somite segmentation and patterning (By similarity). 3-O-(alpha-L-fucosyl)-L-threonyl-[EGF-like domain protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-(N-acetyl-beta-D-glucosaminyl-(1->3)-alpha-L-fucosyl)-L-threonyl-[EGF-like domain protein] + H(+) + UDP 3-O-(alpha-L-fucosyl)-L-seryl-[EGF-like domain protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-(N-acetyl-beta-D-glucosaminyl-(1->3)-alpha-L-fucosyl)-L-seryl-[EGF-like domain protein] + H(+) + UDP Experimental confirmation may be lacking for some isoforms. A soluble form may be derived from the membrane form by proteolytic processing. The disease is caused by variants affecting the gene represented in this entry. Belongs to the glycosyltransferase 31 family. Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe +Involved in DNA repair and RecF pathway recombination. Belongs to the RecO family. +L-homoserine + NADP(+) = H(+) + L-aspartate 4-semialdehyde + NADPH L-homoserine + NAD(+) = H(+) + L-aspartate 4-semialdehyde + NADH Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-homoserine from L-aspartate: step 3/3. Amino-acid biosynthesis; L-threonine biosynthesis; L-threonine from L-aspartate: step 3/5. Belongs to the homoserine dehydrogenase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Effector protein that plays different roles depending on the species and plant cultivars that interact with the pathogen. Acts as a virulence determinant by enhancing the development of disease symptoms and bacterial growth. Acts as an avirulence factor by eliciting hypersensitive response (HR) and plant resistance. Secreted via type III secretion system (TTSS). Transcriptionally induced by HrpL. Belongs to the HopAB family. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Shows particularly broad specificity; although bonds involving phenylalanine and leucine are preferred, many others are also cleaved to some extent. Preferential cleavage: hydrophobic, preferably aromatic, residues in P1 and P1' positions. Cleaves 1-Phe-|-Val-2, 4-Gln-|-His-5, 13-Glu-|-Ala-14, 14-Ala-|-Leu-15, 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17, 23-Gly-|-Phe-24, 24-Phe-|-Phe-25 and 25-Phe-|-Tyr-26 bonds in the B chain of insulin. Belongs to the peptidase A1 family. +Transcriptional activator which binds to the enhancer of the T-cell receptor alpha and delta genes. Binds to the consensus sequence 5'-AGATAG-3'. Required for the T-helper 2 (Th2) differentiation process following immune and inflammatory responses. Positively regulates ASB2 expression (PubMed:31175139). Interacts with TBX21 ('Tyr-525' phosphorylated form). T-cell specific. Binds DNA via the 2 GATA-type zinc fingers. Each zinc finger may bind either adjacent sites in a palindromic motif, or a different DNA molecule allowing looping and long-range gene regulation (By similarity). The YxKxHxxxRP motif is critical for DNA-binding and function. +Inhibits both peak current and fast inactivation of voltage-gated sodium channels (Nav) channels. Inhibits the inactivation of Nav on DRG neurons (EC(50)=1.77 uM) and peak current of cardiac myocytes (IC(50)=0.90 uM). Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Monoisotopic mass. Belongs to the neurotoxin 10 (Hwtx-1) family. 37 (Jztx-31) subfamily. +Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo-MPT) cofactor (Moco or molybdenum cofactor) to form Mo-molybdopterin guanine dinucleotide (Mo-MGD) cofactor. GTP + H(+) + Mo-molybdopterin = diphosphate + Mo-molybdopterin guanine dinucleotide Monomer. The N-terminal domain determines nucleotide recognition and specific binding, while the C-terminal domain determines the specific binding to the target protein. Belongs to the MobA family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Endoribonuclease that initiates mRNA decay. Belongs to the RNase Y family. +Belongs to the UPF0145 family. +Belongs to the UPF0208 family. +Calmodulin mediates the control of a large number of enzymes, ion channels and other proteins by Ca(2+). Among the enzymes to be stimulated by the calmodulin-Ca(2+) complex are a number of protein kinases and phosphatases. This protein has four functional calcium-binding sites. Belongs to the calmodulin family. +Required for the assembly of cytochrome c oxidase. Belongs to the COX23 family. +Belongs to the SspH family. +Part of an ABC transporter complex involved in carbohydrate import. Could be involved in ribose, galactose and/or methyl galactoside import. Responsible for energy coupling to the transport system. ATP + D-ribose(out) + H2O = ADP + D-ribose(in) + H(+) + phosphate ATP + D-galactose(out) + H2O = ADP + D-galactose(in) + H(+) + phosphate Belongs to the ABC transporter superfamily. Carbohydrate importer 2 (CUT2) (TC 3.A.1.2) family. +Involved in control of cellular proliferation. Onconcogenic modifier contributing to the tumor suppressor function of DNMT3B (By similarity). Phosphorylation sites are present in the extracellular medium. +Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP. an acyl phosphate + sn-glycerol 3-phosphate = a 1-acyl-sn-glycero-3-phosphate + phosphate Lipid metabolism; phospholipid metabolism. Probably interacts with PlsX. Belongs to the PlsY family. +Belongs to the universal ribosomal protein uS2 family. +Involved in both the histidine and tryptophan biosynthetic pathways. 1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 3/5. Belongs to the HisA/HisF family. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homodimer. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 2 subfamily. +Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is transferred onto alpha-ketoisovalerate to form ketopantoate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = (6S)-5,6,7,8-tetrahydrofolate + 2-dehydropantoate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantoate from 3-methyl-2-oxobutanoate: step 1/2. Homodecamer; pentamer of dimers. Belongs to the PanB family. +Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-aspartyl-tRNA(Asx) Binds 3 Mg(2+) cations per subunit. The strongest magnesium site (Mg1) is bound to the beta- and gamma-phosphates of ATP and four water molecules complete its coordination sphere. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 2 subfamily. +Homodimer and heterodimers. Belongs to the Casparian strip membrane proteins (CASP) family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Belongs to the V-ATPase E subunit family. +Belongs to the tellurite-resistance/dicarboxylate transporter (TDT) family. +Methylates ribosomal protein L11. L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. PrmA family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome. Belongs to the 'phage' integrase family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +D-arabinose 5-phosphate + H2O + phosphoenolpyruvate = 3-deoxy-alpha-D-manno-2-octulosonate-8-phosphate + phosphate Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate: step 2/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsA family. +Involved in lipopolysaccharide (LPS) biosynthesis. Translocates lipid A-core from the inner to the outer leaflet of the inner membrane. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation. ATP + H2O + lipid A-core oligosaccharideSide 1 = ADP + phosphate + lipid A-core oligosaccharideSide 2. Homodimer. In MsbA the ATP-binding domain (NBD) and the transmembrane domain (TMD) are fused. Belongs to the ABC transporter superfamily. Lipid exporter (TC 3.A.1.106) family. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Probable inactive heme oxygenase. Binds protoporphyrin IX, a precursor for both heme and chlorophyll biosynthesis. Plays a minor role in phytochrome assembly and photomorphogenesis. A number of isoforms are produced. According to EST sequences. Widely expressed at low levels. Slight reduction in plant size and chlorophyll content, and early flowering. Belongs to the heme oxygenase family. Lacks the conserved His residue involved in heme iron binding and essential for heme oxygenase activity. Its enzyme activity is therefore unsure. +Involved in the degradation of chitin. ChbG is essential for growth on the acetylated chitooligosaccharides chitobiose and chitotriose but is dispensable for growth on cellobiose and chitosan dimer, the deacetylated form of chitobiose. Deacetylation of chitobiose-6-P and chitotriose-6-P is necessary for both the activation of the chb promoter by the regulatory protein ChbR and the hydrolysis of phosphorylated beta-glucosides by the phospho-beta-glucosidase ChbF. Catalyzes the removal of only one acetyl group from chitobiose-6-P to yield monoacetylchitobiose-6-P, the inducer of ChbR and the substrate of ChbF. H2O + N,N'-diacetylchitobiose = acetate + N-acetyl-beta-D-glucosaminyl-(1->4)-D-glucosamine diacetylchitobiose-6'-phosphate + H2O = acetate + N'-monoacetylchitobiose-6'-phosphate Glycan degradation; chitin degradation. Homodimer. Belongs to the YdjC deacetylase family. ChbG subfamily. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Methylated by PrmB. Belongs to the universal ribosomal protein uL3 family. +Transcription factor (By similarity). Regulates myogenesis, in cooperation with transcription factors hlh-1 and hnd-1 (PubMed:15892873, PubMed:17142668). Required for maintenance of muscle in adulthood (PubMed:29314608). Expressed in muscle, varying with age, decreasing twofold during the first week of adulthood. Mutants usually hatch and appear normal in early L1, but become progressively paralyzed later during L1 (PubMed:17142668). Complete larval lethal, typically at late L1 or early L2 (PubMed:17142668). Abnormal bodywall and egg-laying muscle in hermaphrodites, but with no obvious abnormality of pharyngeal muscle or other cell types (PubMed:17142668). Five percent of the progeny from hlh-1, unc-120 double heterozygous parents exhibit partial absence of bodywall muscle and reduced expression of myosin myo-3 (PubMed:17142668). RNAi-mediated knockdown causes a low frequency of embryonic lethality, with embryos arresting paralyzed at the two-fold stage; increases in frequency significantly on an hlh-1 or hnd-1 mutant background (PubMed:15892873). RNAi-mediated knockdown causes those embryos that survive to hatching to become uncoordinated, dumpy larvae (PubMed:15892873). RNAi-mediated knockdown causes abnormalities in muscle, including: altered mitochondrial morphology at day 6 of adulthood, two-fold to five-fold down-regulation of transcript levels at day 7 and significant increase in the number of autophagic vesicles (PubMed:29314608). RNAi-mediated knockdown causes a reduction in average lifespan by 16% (PubMed:29314608). RNAi-mediated knockdown on a daf-2 mutant background causes a dramatic decrease in physical performance at day 18 (PubMed:29314608). +In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated protein (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins. Interacts with hair keratins. Restricted to hair root, not detected in any other tissues. Belongs to the KRTAP type 5 family. +Small GTPase which cycles between an active GTP-bound and an inactive GDP-bound state (By similarity). Involved in protein transport. Plays a role in vesicular traffic. Mediates VEGFR2 endosomal trafficking to enhance VEGFR2 signaling (By similarity). Acts as a regulator of platelet alpha-granule release during activation and aggregation of platelets (By similarity). GTP + H2O = GDP + H(+) + phosphate Interacts with RAB11FIP1, RABEP1, ZFYVE20 and RUFY1. Interacts with SGSM1, SGSM2 and SGSM3. Interacts (membrane-bound form) with NDRG1; the interaction involves NDRG1 in vesicular recycling of E-cadherin. Interacts (in GTP-bound form) with GRIPAP1. Interacts with RABEP1 and RBSN (By similarity). Does not interact with HPS4 (By similarity). Generally associated with membranes. Cytoplasmic when phosphorylated by CDK1. Serotonylation of Gln-72 by TGM2 during activation and aggregation of platelets leads to constitutive activation of GTPase activity. Phosphorylated by CDK1 kinase during mitosis. Belongs to the small GTPase superfamily. Rab family. It is uncertain whether Met-1 or Met-6 is the initiator. +Promotes efficient viral genome replication by accelerating both G1 and S phase progression of the cell cycle. Inhibits host PP2A by binding to the A subunit, thereby displacing lower affinity regulatory B subunit. Inactivation of PP2A in turn results in the transactivation of cyclin A and cyclin D1 promoters. Late during the infection cycle, ST may induce dephosphorylation of host eIF4E-binding protein EIF4EBP1 leading to the inhibition of cap-dependent translation. May establish and maintain high levels of viral genomes during persistent infection in cell culture. Interacts with host PPP2R1A; the interaction inhibits PP2A activity. The common region of SV40 ST, 17kT and LT proteins comprises the J domain. This domain is essential for multiple viral activities, including virion assembly, viral DNA replication, transformation and transcriptional activation. This domain is also required for cyclin A-transactivating activity of ST. Produced by alternative splicing. +PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) Binds 1 Ca(2+) ion. Belongs to the phospholipase A2 family. Group II subfamily. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form the product. After dissociation, two additional enzymatic reactions on the tRNA convert PreQ1 to queuine (Q), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine). 7-aminomethyl-7-carbaguanine + guanosine(34) in tRNA = 7-aminomethyl-7-carbaguanosine(34) in tRNA + guanine Binds 1 zinc ion per subunit. tRNA modification; tRNA-queuosine biosynthesis. Homodimer. Within each dimer, one monomer is responsible for RNA recognition and catalysis, while the other monomer binds to the replacement base PreQ1. Belongs to the queuine tRNA-ribosyltransferase family. +Essential cell division protein that stabilizes the FtsZ protofilaments by cross-linking them and that serves as a cytoplasmic membrane anchor for the Z ring. Also required for the recruitment to the septal ring of downstream cell division proteins. Interacts with FtsZ via their C-terminal domains. Localizes to the Z ring in an FtsZ-dependent manner. Belongs to the ZipA family. +Catalyzes the formation of N(4)-acetylcytidine (ac(4)C) at the wobble position of elongator tRNA(Met), using acetate and ATP as substrates. First activates an acetate ion to form acetyladenylate (Ac-AMP) and then transfers the acetyl group to tRNA to form ac(4)C34. acetate + ATP + cytidine(34) in elongator tRNA(Met) = AMP + diphosphate + N(4)-acetylcytidine(34) in elongator tRNA(Met) Belongs to the TmcAL family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a, b, b' and c. Belongs to the ATPase A chain family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL2 family. There is 1 gene for this protein in each of the chloroplast inverted repeats; while they are usually identical, in this organism they are not. The other copy is AC A0A398. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbJ family. +Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of the pseudouridine corresponding to position 914 in M.jannaschii 16S rRNA. a pseudouridine in 16S/18S rRNA + S-adenosyl-L-methionine = an N(1)-methylpseudouridine in 16S/18S rRNA + H(+) + S-adenosyl-L-homocysteine Homodimer. Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase NEP1 family. +Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III. 4 H(+) + uroporphyrinogen III = 4 CO2 + coproporphyrinogen III Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 4/4. Homodimer. Belongs to the uroporphyrinogen decarboxylase family. +Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type B subfamily. +Belongs to the universal ribosomal protein uL29 family. +Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. AH2 + H2O2 = A + 2 H2O 2 H2O2 = 2 H2O + O2 Binds 1 heme b (iron(II)-protoporphyrin IX) group per dimer. Homodimer or homotetramer. Formation of the three residue Trp-Tyr-Met cross-link is important for the catalase, but not the peroxidase activity of the enzyme. Belongs to the peroxidase family. Peroxidase/catalase subfamily. +Probable mitochondrial acylpyruvase which is able to hydrolyze acetylpyruvate and fumarylpyruvate in vitro. Also has oxaloacetate decarboxylase activity. a 3-acylpyruvate + H2O = a carboxylate + H(+) + pyruvate H(+) + oxaloacetate = CO2 + pyruvate Homodimer. Belongs to the FAH family. +The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination. The AddA nuclease domain is required for chi fragment generation; this subunit has the helicase and 3' -> 5' nuclease activities. ATP + H2O = ADP + H(+) + phosphate Heterodimer of AddA and AddB/RexB. Belongs to the helicase family. AddA subfamily. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Probable regulator of sister chromatid cohesion in mitosis which may stabilize cohesin complex association with chromatin. May couple sister chromatid cohesion during mitosis to DNA replication. Cohesion ensures that chromosome partitioning is accurate in both meiotic and mitotic cells and plays an important role in DNA repair (By similarity). Interacts with the cohesin complex. Interacts with WAPL (via FGF motifs) or CDCA5 (via the FGF motif); the interaction is direct, cohesin-dependent and competitive. Interacts with SMC3. Interacts with TP63 (By similarity). Associated with chromatin through most of the cell cycle. Dissociates from chromatin in late prophase, reassociates during late telophase (By similarity). Belongs to the PDS5 family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 1 family. +Part of the ABC transporter complex CysAWTP (TC 3.A.1.6.1) involved in sulfate/thiosulfate import. Probably responsible for the translocation of the substrate across the membrane (By similarity). The complex is composed of two ATP-binding proteins (CysA), two transmembrane proteins (CysT and CysW) and a solute-binding protein (CysP). Belongs to the binding-protein-dependent transport system permease family. CysTW subfamily. +Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide. 2 H2O2 = 2 H2O + O2 Belongs to the catalase family. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis. (R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) A monovalent cation. Ammonium or potassium. Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Homodimer. Belongs to the type III pantothenate kinase family. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +Catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose via an epimerization at carbon 6 of the heptose. ADP-D-glycero-beta-D-manno-heptose = ADP-L-glycero-beta-D-manno-heptose Binds 1 NADP(+) per subunit. Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate: step 4/4. Homopentamer. Contains a large N-terminal NADP-binding domain, and a smaller C-terminal substrate-binding domain. Belongs to the NAD(P)-dependent epimerase/dehydratase family. HldD subfamily. +Ion channel inhibitor. Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 10 (Hwtx-1) family. 12 (Hntx-12) subfamily. +ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. ATP + L-cysteine + L-glutamate = ADP + gamma-L-glutamyl-L-cysteine + H(+) + phosphate Belongs to the glutamate--cysteine ligase type 2 family. YbdK subfamily. +CAHS proteins are cytosolic heat soluble proteins that seem to contribute to the anhydrobiosis in tardigrades, but their specific mechanisms are yet to be identified (PubMed:22937162, PubMed:33545053). It is possible that protection during anhydrobiosis might occur via the stabilization of vitrifying small molecules such as sugars, but not via the direct glass transition of CAHS proteins themselves (Probable). CAHS proteins contain 2 repeats of 19-mer peptides designated as CAHS-motifs that comprise each two octapeptides connected by a tripeptide (PubMed:27649274). Trehalose, a disaccharide essential for several organisms to survive drying, is detected at low levels or not at all in some tardigrade species, indicating that tardigrades possess potentially novel mechanisms for surviving desiccation involving tardigrade-specific intrinsically disordered proteins (TDPs) (By similarity). Belongs to the Cytosolic-abundant heat soluble protein (CAHS) family. +Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. Specifically modifies U47 in cytoplasmic tRNAs (By similarity). Catalyzes the synthesis of dihydrouridine in some mRNAs, thereby affecting their translation (By similarity). 5,6-dihydrouridine(47) in tRNA + NAD(+) = H(+) + NADH + uridine(47) in tRNA 5,6-dihydrouridine(47) in tRNA + NADP(+) = H(+) + NADPH + uridine(47) in tRNA a 5,6-dihydrouridine in mRNA + NAD(+) = a uridine in mRNA + H(+) + NADH a 5,6-dihydrouridine in mRNA + NADP(+) = a uridine in mRNA + H(+) + NADPH Belongs to the Dus family. Dus3 subfamily. +Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Could be involved in hydrogenase-linked redox processes. Binds 1 Fe(3+) ion per subunit. Belongs to the rubredoxin family. +Responsible for the transport of C4-dicarboxylates during anaerobic growth. Belongs to the DcuC/DcuD transporter (TC 2.A.61) family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Plant type III polyketide synthases (PKSs) that catalyzes the condensation of malonyl-CoA units with various CoA ester starter molecules to generate a diverse array of natural products including long-chain alkyl alpha-pyrones. Secondary metabolite biosynthesis; flavonoid biosynthesis. Homodimer. Belongs to the thiolase-like superfamily. Chalcone/stilbene synthases family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Plays a role in DNA damage repair as component of the ASCC complex. Part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. May also play a role in the development of neuromuscular junction. Identified in the ASCC complex that contains ASCC1, ASCC2 and ASCC3. Interacts directly with ASCC3. The ASCC complex interacts with ALKBH3. Part of the ASC-1 complex, that contains TRIP4, ASCC1, ASCC2 and ASCC3. Interacts with CSRP1. Interacts with ZCCHC4 (By similarity). Colocalizes with PRPF8 in nuclear speckles in the absence of DNA damage. Expressed in the spinal cord, brain, paraspinal ganglia, thyroid, and submandibular glands. Expressed in 17.5-day-old embryos. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Belongs to the SMAP family. +Belongs to the PsaM family. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). 3-methyl-2-oxobutanoate + acetyl-CoA + H2O = (2S)-2-isopropylmalate + CoA + H(+) Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 1/4. Homotetramer. Belongs to the alpha-IPM synthase/homocitrate synthase family. LeuA type 2 subfamily. +Involved in abscisic acid (ABA) signaling during seed germination and abiotic stress response. Acts as positive regulator of ABA-mediated inhibition of seed germination, and tolerance to drought and cold stresses (PubMed:26362328). Together with PP2C50 and SAPK10, may form an ABA signaling module involved in stress response (PubMed:28827170). Inhibits the protein phosphatases PP2C06 and PP2C09 when activated by abscisic acid (ABA) (PubMed:24743650). Monomer (PubMed:24743650). Interacts with PP2C50. Binding to PP2C50 is dependent on the presence of abscisic acid (ABA) (PubMed:28827170). Interacts with PP2C30 and PP2C53 (PubMed:26362328). Repressed by abscisic acid (ABA). Plants overexpressing PYL3 exhibit abscisic acid (ABA) hypersensitive phenotype during seed germination. Plants overexpressing PYL3 exhibit tolerance to cold and drought stresses. Belongs to the PYR/PYL/RCAR abscisic acid intracellular receptor family. +beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 4/4. Belongs to the class I fructose-bisphosphate aldolase family. +Catalyzes the coenzyme A-dependent oxidative decarboxylation of different 2-oxoacids such as pyruvate, 2-oxobutyrate, glyoxylate and 2-oxoglutarate to form their CoA derivatives. a 2-oxocarboxylate + CoA + 2 oxidized [2Fe-2S]-[ferredoxin] = an acyl-CoA + CO2 + H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Optimum pH is 8.5. Optimum temperature is over 110 degrees Celsius. Heterodimer composed of an alpha and a beta subunit. The Tyr-Pro-Ile-Thr-Pro (YPITP) motif is important for the turnover of the reaction, presumably through its flexibility and mobility. +Prenyltransferase that mediates the formation of menaquinone-4 (MK-4) and coenzyme Q10. MK-4 is a vitamin K2 isoform required for endothelial cell development. Mediates the conversion of phylloquinone (PK) into MK-4, probably by cleaving the side chain of phylloquinone (PK) to release 2-methyl-1,4-naphthoquinone (menadione; K3) and then prenylating it with geranylgeranyl pyrophosphate (GGPP) to form MK-4. Also plays a role in cardiovascular development independently of MK-4 biosynthesis, by acting as a coenzyme Q10 biosynthetic enzyme: coenzyme Q10, also named ubiquinone, plays an important antioxidant role in the cardiovascular system. Mediates biosynthesis of coenzyme Q10 in the Golgi membrane, leading to protect cardiovascular tissues from nos3/eNOS-dependent oxidative stress (By similarity). Quinol/quinone metabolism; menaquinone biosynthesis. Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the UbiA prenyltransferase family. +Belongs to the UPF0102 family. +Dermonecrotic toxins cleave the phosphodiester linkage between the phosphate and headgroup of certain phospholipids (sphingolipid and lysolipid substrates), forming an alcohol (often choline) and a cyclic phosphate (By similarity). This toxin acts on sphingomyelin (SM) (By similarity). It may also act on ceramide phosphoethanolamine (CPE), lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE), but not on lysophosphatidylserine (LPS), and lysophosphatidylglycerol (LPG) (By similarity). It acts by transphosphatidylation, releasing exclusively cyclic phosphate products as second products (By similarity). Induces dermonecrosis, hemolysis, increased vascular permeability, edema, inflammatory response, and platelet aggregation (By similarity). an N-(acyl)-sphingosylphosphocholine = an N-(acyl)-sphingosyl-1,3-cyclic phosphate + choline an N-(acyl)-sphingosylphosphoethanolamine = an N-(acyl)-sphingosyl-1,3-cyclic phosphate + ethanolamine a 1-acyl-sn-glycero-3-phosphocholine = a 1-acyl-sn-glycero-2,3-cyclic phosphate + choline a 1-acyl-sn-glycero-3-phosphoethanolamine = a 1-acyl-sn-glycero-2,3-cyclic phosphate + ethanolamine Binds 1 Mg(2+) ion per subunit. Expressed by the venom gland. Belongs to the arthropod phospholipase D family. Class II subfamily. The most common activity assay for dermonecrotic toxins detects enzymatic activity by monitoring choline release from substrate. Liberation of choline from sphingomyelin (SM) or lysophosphatidylcholine (LPC) is commonly assumed to result from substrate hydrolysis, giving either ceramide-1-phosphate (C1P) or lysophosphatidic acid (LPA), respectively, as a second product. However, two studies from Lajoie and colleagues (2013 and 2015) report the observation of exclusive formation of cyclic phosphate products as second products, resulting from intramolecular transphosphatidylation. Cyclic phosphates have vastly different biological properties from their monoester counterparts, and they may be relevant to the pathology of brown spider envenomation. +H(+) + 2 pyruvate = (2S)-2-acetolactate + CO2 Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 1/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 1/4. Dimer of large and small chains. Belongs to the acetolactate synthase small subunit family. +Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides. a hydroperoxide + 2 glutathione = an alcohol + glutathione disulfide + H2O Optimum pH is 7.8. Homotetramer; interconnecting Prx and Grx domains of different monomers. The active site is a conserved redox-active cysteine residue, the peroxidatic cysteine (C(P)), which makes the nucleophilic attack on the peroxide substrate. The peroxide oxidizes the C(P)-SH to cysteine sulfenic acid (C(P)-SOH), which then reacts with another cysteine residue, the resolving cysteine (C(R)), to form a disulfide bridge. The disulfide is subsequently reduced by an appropriate electron donor to complete the catalytic cycle. In the hybrid peroxiredoxin hyPrx5, no C(R) is present and C(P) instead is reduced directly by the redox-active site in the Grx-domain of another monomer, regenerating peroxidase activity of the enzyme. The oxidized glutaredoxin is reduced by reduced glutathione (GSH) (Probable). C(P) may also be reactivated by glutathionylation and subsequent reduction by the Grx-domain (Probable). In the N-terminal section; belongs to the peroxiredoxin family. Prx5 subfamily. In the C-terminal section; belongs to the glutaredoxin family. +Involved in the biosynthesis of the arabinogalactan (AG) region of the mycolylarabinogalactan-peptidoglycan (mAGP) complex, an essential component of the mycobacterial cell wall. Catalyzes the transfer of the first two galactofuranosyl (Galf) units from UDP-galactofuranose (UDP-Galf) onto the rhamnosyl-GlcNAc-diphospho-decaprenol (Rha-GlcNAc-PP-C50) acceptor, yielding galactofuranosyl-galactofuranosyl-rhamnosyl-GlcNAc-diphospho-decaprenol (Galf-Galf-Rha-GlcNAc-PP-C50). Thus, GlfT1 is the initiator of galactan synthesis, while GlfT2 continues with the subsequent polymerization events. alpha-L-rhamnosyl-(1->3)-N-acetyl-alpha-D-glucosaminyl-diphospho-trans,octa-cis-decaprenol + 2 UDP-alpha-D-galactofuranose = beta-D-galactofuranosyl-(1->5)-beta-D-galactofuranosyl-(1->4)-alpha-L-rhamnosyl-(1->3)-N-acetyl-alpha-D-glucosaminyl-diphospho-trans,octa-cis-decaprenol + 2 H(+) + 2 UDP Cell wall biogenesis; cell wall polysaccharide biosynthesis. Interacts with Rv3789. Is thus probably part of an AG biosynthetic complex. Was identified as a high-confidence drug target. Belongs to the glycosyltransferase 2 family. +Steroid hormone receptors are ligand-activated transcription factors that regulate eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues (PubMed:19022849). Transcription factor activity is modulated by bound coactivator and corepressor proteins like ZBTB7A that recruits NCOR1 and NCOR2 to the androgen response elements/ARE on target genes, negatively regulating androgen receptor signaling and androgen-induced cell proliferation (PubMed:20812024). Transcription activation is also down-regulated by NR0B2. Activated, but not phosphorylated, by HIPK3 and ZIPK/DAPK3. Lacks the C-terminal ligand-binding domain and may therefore constitutively activate the transcription of a specific set of genes independently of steroid hormones. Lacks the C-terminal ligand-binding domain and may therefore constitutively activate the transcription of a specific set of genes independently of steroid hormones. AIM-100 (4-amino-5,6-biaryl-furo[2,3-d]pyrimidine) suppresses TNK2-mediated phosphorylation at Tyr-269. Inhibits the binding of the Tyr-269 phosphorylated form to androgen-responsive enhancers (AREs) and its transcriptional activity. Binds DNA as a homodimer. Part of a ternary complex containing AR, EFCAB6/DJBP and PARK7. Interacts with HIPK3 and NR0B2 in the presence of androgen. The ligand binding domain interacts with KAT7/HBO1 in the presence of dihydrotestosterone. Interacts with EFCAB6/DJBP, PQBP1, RANBP9, RBAK, SPDEF, SRA1, TGFB1I1 and RREB1. Interacts with ZMIZ1/ZIMP10 and ZMIZ2/ZMIP7 which both enhance its transactivation activity. Interacts with SLC30A9 and RAD54L2/ARIP4. Interacts with MACROD1 (via macro domain) (PubMed:19022849). Interacts via the ligand-binding domain with LXXLL and FXXLF motifs from NCOA1, NCOA2, NCOA3, NCOA4 and MAGEA11. The AR N-terminal poly-Gln region binds Ran resulting in enhancement of AR-mediated transactivation. Ran-binding decreases as the poly-Gln length increases. Interacts with HIP1 (via coiled coil domain). Interacts (via ligand-binding domain) with TRIM68. Interacts with TNK2. Interacts with USP26. Interacts with RNF6. Interacts (regulated by RNF6 probably through polyubiquitination) with RNF14; regulates AR transcriptional activity. Interacts with PRMT2 and TRIM24. Interacts with RACK1. Interacts with RANBP10; this interaction enhances dihydrotestosterone-induced AR transcriptional activity. Interacts with PRPF6 in a hormone-independent way; this interaction enhances dihydrotestosterone-induced AR transcriptional activity. Interacts with STK4/MST1. Interacts with ZIPK/DAPK3. Interacts with LPXN. Interacts with MAK. Part of a complex containing AR, MAK and NCOA3. Interacts with CRY1. Interacts with CCAR1 and GATA2. Interacts with ZNF318 (By similarity). Interacts with BUD31 (PubMed:25091737). Interacts with ARID4A (PubMed:23487765). Interacts with ARID4B (By similarity). Interacts (via NR LBD domain) with ZBTB7A; the interaction is direct and androgen-dependent (PubMed:20812024). Interacts with NCOR1 (PubMed:20812024). Interacts with NCOR2 (PubMed:20812024). Interacts with CRY2 in a ligand-dependent manner (By similarity). Detected at the promoter of target genes (PubMed:25091737). Predominantly cytoplasmic in unligated form but translocates to the nucleus upon ligand-binding. Can also translocate to the nucleus in unligated form in the presence of RACK1. Mainly expressed in heart and skeletal muscle. Expressed in basal and stromal cells of the prostate (at protein level). Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain. In the presence of bound steroid the ligand-binding domain interacts with the N-terminal modulating domain, and thereby activates AR transcription factor activity. Agonist binding is required for dimerization and binding to target DNA. The transcription factor activity of the complex formed by ligand-activated AR and DNA is modulated by interactions with coactivator and corepressor proteins (PubMed:25091737). Interaction with RANBP9 is mediated by both the N-terminal domain and the DNA-binding domain. Interaction with EFCAB6/DJBP is mediated by the DNA-binding domain. Sumoylated on Lys-388 (major) and Lys-521. Ubiquitinated. Deubiquitinated by USP26. 'Lys-6' and 'Lys-27'-linked polyubiquitination by RNF6 modulates AR transcriptional activity and specificity. Phosphorylated in prostate cancer cells in response to several growth factors including EGF. Phosphorylation is induced by c-Src kinase (CSK). Tyr-535 is one of the major phosphorylation sites and an increase in phosphorylation and Src kinase activity is associated with prostate cancer progression. Phosphorylation by TNK2 enhances the DNA-binding and transcriptional activity and may be responsible for androgen-independent progression of prostate cancer. Phosphorylation at Ser-83 by CDK9 regulates AR promoter selectivity and cell growth. Phosphorylation by PAK6 leads to AR-mediated transcription inhibition. Palmitoylated by ZDHHC7 and ZDHHC21. Palmitoylation is required for plasma membrane targeting and for rapid intracellular signaling via ERK and AKT kinases and cAMP generation. The poly-Gln region of AR is highly polymorphic and the number of Gln varies in the population (from 17 to 26). A smaller size of the poly-Gln region may be associated with the development of prostate cancer. Long poly-Gln alleles (>23) may be associated with higher testosterone levels and severe clinical outcome in COVID-19 disease (PubMed:33647767). The poly-Gly region of AR is polymorphic and ranges from 24 to 31 Gly. A poly-Gly region shorter or equal to 23 may be associated with the development of androgenetic alopecia. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Caused by trinucleotide CAG repeat expansion. In SMAX1 patients the number of Gln ranges from 38 to 62. Longer expansions result in earlier onset and more severe clinical manifestations of the disease. Defects in AR may play a role in metastatic prostate cancer. The mutated receptor stimulates prostate growth and metastases development despite of androgen ablation. This treatment can reduce primary and metastatic lesions probably by inducing apoptosis of tumor cells when they express the wild-type receptor. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity. The hormone-receptor complex appears to recognize discrete DNA sequences upstream of transcriptional start sites. Transcriptional activity is enhanced by binding to RANBP9. The level of tyrosine phosphorylation may serve as a diagnostic tool to predict patient outcome in response to hormone-ablation therapy. Inhibition of tyrosine phosphorylation may be an effective intervention target for hormone-refractory prostate cancer. Minor isoform up-regulated in prostate cancer cells. Minor isoform identified in prostate cancer cells. Belongs to the nuclear hormone receptor family. NR3 subfamily. Had previously been shown to interact with PELP1. However this paper was retracted as cell-based data was viewed as unreliable. Androgen receptor entry Leiden Open Variation Database (LOVD) +Encapsidates the negative strand viral RNA, protecting it from nucleases. The encapsidated genomic RNA is termed the ribonucleoprotein (RNP) and serves as template for transcription and replication. The RNP needs to be localized in the host nucleus to start an infectious cycle, but is too large to diffuse through the nuclear pore complex. NP comprises at least 2 nuclear localization signals that are responsible for the active RNP import into the nucleus through cellular importin alpha/beta pathway. Later in the infection, nclear export of RNPs are mediated through viral proteins NEP interacting with M1 which binds nucleoproteins. It is possible that nucleoprotein binds directly host exportin-1/XPO1 and plays an active role in RNPs nuclear export. M1 interaction with RNP seems to hide nucleoprotein's nuclear localization signals. Soon after a virion infects a new cell, M1 dissociates from the RNP under acidification of the virion driven by M2 protein. Dissociation of M1 from RNP unmasks nucleoprotein's nuclear localization signals, targeting the RNP to the nucleus. Homomultimerizes to form the nucleocapsid. May bind host exportin-1/XPO1. Binds to viral genomic RNA. Protein-RNA contacts are mediated by a combination of electrostatic interactions between positively charged residues and the phosphate backbone and planar interactions between aromatic side chains and bases. Late in virus-infected cells, may be cleaved from a 56-kDa protein to a 53-kDa protein by a cellular caspase. This cleavage might be a marker for the onset of apoptosis in infected cells or have a specific function in virus host interaction. Belongs to the influenza viruses nucleoprotein family. +3' to 5' exoribonuclease required for proper 3' end maturation of MRP RNA and of the U5L snRNA. Belongs to the REXO1/REXO3 family. +Has lost the two conserved residues (Ser and His) proposed to be part of the active site. Therefore it could be inactive. Belongs to the peptidase S14 family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Catalyzes the excretion of spermidine. Forms a complex with MdtI. Belongs to the drug/metabolite transporter (DMT) superfamily. Small multidrug resistance (SMR) (TC 2.A.7.1) family. MdtJ subfamily. +Belongs to the FAM3 family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Belongs to the SecA family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase gamma chain family. +This protein is involved in control of the biosynthesis of threonine. Belongs to the thr operon leader peptide family. +Core component of nucleosome which plays a central role in DNA double strand break (DSB) repair. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family. Phosphorylated to form H2AS128ph (gamma-H2A) in response to DNA double-strand breaks (DSBs) generated by exogenous genotoxic agents and by stalled replication forks. Phosphorylation is dependent on the DNA damage checkpoint kinases MEC1/ATR and TEL1/ATM, spreads on either side of a detected DSB site and may mark the surrounding chromatin for recruitment of proteins required for DNA damage signaling and repair. Gamma-H2A is removed from the DNA prior to the strand invasion-primer extension step of the repair process and subsequently dephosphorylated. Dephosphorylation is necessary for efficient recovery from the DNA damage checkpoint (By similarity). Acetylated by ESA1 to form H2AK4ac and H2AK7ac. In contrast to vertebrates and insects, its C-terminus is not monoubiquitinated. Belongs to the histone H2A family. To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-9; H2AK7ac = acetylated Lys-13; H2AS128ph = phosphorylated Ser-136. +Major component of the type IV fimbriae that plays an essential role in twitching motility, natural transformation, and protease secretion. The pili are polar flexible filaments of about 5.4 nanometers diameter and 2.5 micrometers average length; they consist of only a single polypeptide chain arranged in a helical configuration of five subunits per turn in the assembled pilus. Belongs to the N-Me-Phe pilin family. +Uptake of L-rhamnose across the cytoplasmic membrane with the concomitant transport of protons into the cell (symport system). H(+)(in) + L-rhamnopyranose(in) = H(+)(out) + L-rhamnopyranose(out) Belongs to the L-rhamnose transporter (TC 2.A.7.6) family. +Oligomerizes in the host endoplasmic reticulum into predominantly trimers. In a second time, gp160 transits in the host Golgi, where glycosylation is completed. The precursor is then proteolytically cleaved in the trans-Golgi and thereby activated by cellular furin or furin-like proteases to produce gp120 and gp41. Attaches the virus to the host lymphoid cell by binding to the primary receptor CD4. This interaction induces a structural rearrangement creating a high affinity binding site for a chemokine coreceptor like CXCR4 and/or CCR5. Acts as a ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on dendritic cells (DCs), and on endothelial cells of liver sinusoids and lymph node sinuses. These interactions allow capture of viral particles at mucosal surfaces by these cells and subsequent transmission to permissive cells. HIV subverts the migration properties of dendritic cells to gain access to CD4+ T-cells in lymph nodes. Virus transmission to permissive T-cells occurs either in trans (without DCs infection, through viral capture and transmission), or in cis (following DCs productive infection, through the usual CD4-gp120 interaction), thereby inducing a robust infection. In trans infection, bound virions remain infectious over days and it is proposed that they are not degraded, but protected in non-lysosomal acidic organelles within the DCs close to the cell membrane thus contributing to the viral infectious potential during DCs' migration from the periphery to the lymphoid tissues. On arrival at lymphoid tissues, intact virions recycle back to DCs' cell surface allowing virus transmission to CD4+ T-cells. Acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During fusion of viral and target intracellular membranes, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Complete fusion occurs in host cell endosomes and is dynamin-dependent, however some lipid transfer might occur at the plasma membrane. The virus undergoes clathrin-dependent internalization long before endosomal fusion, thus minimizing the surface exposure of conserved viral epitopes during fusion and reducing the efficacy of inhibitors targeting these epitopes. Membranes fusion leads to delivery of the nucleocapsid into the cytoplasm. The mature envelope protein (Env) consists of a homotrimer of non-covalently associated gp120-gp41 heterodimers. The resulting complex protrudes from the virus surface as a spike. There seems to be as few as 10 spikes on the average virion. Interacts with host CD4, CCR5 and CXCR4. Gp120 also interacts with the C-type lectins CD209/DC-SIGN and CLEC4M/DC-SIGNR (collectively referred to as DC-SIGN(R)). Gp120 and gp41 interact with GalCer. Gp120 interacts with host ITGA4/ITGB7 complex; on CD4+ T-cells, this interaction results in rapid activation of integrin ITGAL/LFA-1, which facilitates efficient cell-to-cell spreading of HIV-1. Gp120 interacts with cell-associated heparan sulfate; this interaction increases virus infectivity on permissive cells and may be involved in infection of CD4- cells. The mature envelope protein (Env) consists of a homotrimer of non-covalently associated gp120-gp41 heterodimers. The resulting complex protrudes from the virus surface as a spike. There seems to be as few as 10 spikes on the average virion. The surface protein is not anchored to the viral envelope, but associates with the extravirion surface through its binding to TM. It is probably concentrated at the site of budding and incorporated into the virions possibly by contacts between the cytoplasmic tail of Env and the N-terminus of Gag. It is probably concentrated at the site of budding and incorporated into the virions possibly by contacts between the cytoplasmic tail of Env and the N-terminus of Gag. Some of the most genetically diverse regions of the viral genome are present in Env. They are called variable regions 1 through 5 (V1 through V5). Coreceptor usage of gp120 is determined mainly by the primary structure of the third variable region (V3) in the outer domain of gp120. The sequence of V3 determines which coreceptor, CCR5 and/or CXCR4 (corresponding to R5/macrophage, X4/T cell and R5X4/T cell and macrophage tropism), is used to trigger the fusion potential of the Env complex, and hence which cells the virus can infect. Binding to CCR5 involves a region adjacent in addition to V3. The membrane proximal external region (MPER) present in gp41 is a tryptophan-rich region recognized by the antibodies 2F5, Z13, and 4E10. MPER seems to play a role in fusion. The 17 amino acids long immunosuppressive region is present in many retroviral envelope proteins. Synthetic peptides derived from this relatively conserved sequence inhibit immune function in vitro and in vivo. The YXXL motif is involved in determining the exact site of viral release at the surface of infected mononuclear cells and promotes endocytosis. YXXL and di-leucine endocytosis motifs interact directly or indirectly with the clathrin adapter complexes, opperate independently, and their activities are not additive. The CD4-binding region is targeted by the antibody b12. Highly glycosylated by host. The high number of glycan on the protein is reffered to as 'glycan shield' because it contributes to hide protein sequence from adaptive immune system. Palmitoylation of the transmembrane protein and of Env polyprotein (prior to its proteolytic cleavage) is essential for their association with host cell membrane lipid rafts. Palmitoylation is therefore required for envelope trafficking to classical lipid rafts, but not for viral replication. Specific enzymatic cleavages in vivo yield mature proteins. Envelope glycoproteins are synthesized as an inactive precursor that is heavily N-glycosylated and processed likely by host cell furin in the Golgi to yield the mature SU and TM proteins. The cleavage site between SU and TM requires the minimal sequence [KR]-X-[KR]-R. About 2 of the 9 disulfide bonds of gp41 are reduced by P4HB/PDI, following binding to CD4 receptor. Inhibitors targeting HIV-1 viral envelope proteins are used as antiretroviral drugs. Attachment of virions to the cell surface via non-specific interactions and CD4 binding can be blocked by inhibitors that include cyanovirin-N, cyclotriazadisulfonamide analogs, PRO 2000, TNX 355 and PRO 542. In addition, BMS 806 can block CD4-induced conformational changes. Env interactions with the coreceptor molecules can be targeted by CCR5 antagonists including SCH-D, maraviroc (UK 427857) and aplaviroc (GW 873140), and the CXCR4 antagonist AMD 070. Fusion of viral and cellular membranes can be inhibited by peptides such as enfuvirtide and tifuvirtide (T 1249). Resistance to inhibitors associated with mutations in Env are observed. Most of the time, single mutations confer only a modest reduction in drug susceptibility. Combination of several mutations is usually required to develop a high-level drug resistance. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Belongs to the HIV-1 env protein family. HIV drug resistance database +Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate from the periplasm across the membrane. Belongs to the dicarboxylate/amino acid:cation symporter (DAACS) (TC 2.A.23) family. +Catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1). 7-aminomethyl-7-carbaguanine + 2 NADP(+) = 7-cyano-7-deazaguanine + 3 H(+) + 2 NADPH tRNA modification; tRNA-queuosine biosynthesis. Belongs to the GTP cyclohydrolase I family. QueF type 1 subfamily. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Endonuclease involved in 16S rRNA intron I-alpha homing. Recognizes the minimal target 5'-GCAAGGCTGAAACTTAAAGG-3'; generates 4 base 3' protruding ends 5'-AAAC-3' and 5'-GTTT-3'. 1-5 mM manganese gives higher cleavage activity than the same concentration of magnesium. Optimum pH is 7.5. Optimum temperature is 90 degrees Celsius. Active from 70 to 90 degrees Celsius. Probably functions as a monomer. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP). (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate Cofactor biosynthesis; molybdopterin biosynthesis. Homohexamer; trimer of dimers. Belongs to the MoaC family. +With EpmB is involved in the beta-lysylation step of the post-translational modification of translation elongation factor P (EF-P). Catalyzes the ATP-dependent activation of (R)-beta-lysine produced by EpmB, forming a lysyl-adenylate, from which the beta-lysyl moiety is then transferred to the epsilon-amino group of a conserved specific lysine residue in EF-P. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. EpmA subfamily. +Synthesizes alpha-1,4-glucan chains using ADP-glucose. [(1->4)-alpha-D-glucosyl](n) + ADP-alpha-D-glucose = [(1->4)-alpha-D-glucosyl](n+1) + ADP + H(+) Glycan biosynthesis; glycogen biosynthesis. Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily. +Positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. Belongs to the PNO1 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 1 family. +Sodium transporter protein, which plays a central role in plant tolerance to salt. Upon prolongated exposure to high concentrations, Na(+) translocates from the roots to the transpiring leaves where it can increase to toxic level. Involved in Na(+) recirculation from shoots to roots, probably by mediating Na(+) loading into the phloem sap in shoots and unloading in roots, thereby removing large amounts of Na(+) from the shoot. Does not transport K(+) but regulates K(+) nutrient status via its ability to facilitate Na(+) homeostasis. Probably not involved in root uptake of Na(+). Na(+)(in) = Na(+)(out) Highly expressed in roots. Expressed in flowers, leaves and stems. Expressed in the vascular tissues of every organs. In roots, leaves and flower peduncles, it is only expressed in the phloem tissues. Not expressed in root peripheral cells. N-glycosylated. Not essential for functional expression and membrane targeting. In contrast to K(+) channel proteins, it lacks a conserved Gly at position 68, explaining why it does not act as a K(+) transporter. Belongs to the TrkH potassium transport family. HKT (TC 2.A.38.3) subfamily. +Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has activity toward Muc5Ac and EA2 peptide substrates (By similarity). L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H(+) + UDP L-threonyl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H(+) + UDP Protein modification; protein glycosylation. Expressed at higher level than GALNT9. In the developing hindbrain region of 14.5 dpc embryos it accumulates in the rapidly dividing, undifferentiated ventricular zone adjacent to the pons. It also accumulates in the regions immediately rostral and caudal to the dorsal rhombic lips differentiating into the cerebellum. Not expressed in the developing choroid plexus. There are two conserved domains in the glycosyltransferase region: the N-terminal domain (domain A, also called GT1 motif), which is probably involved in manganese coordination and substrate binding and the C-terminal domain (domain B, also called Gal/GalNAc-T motif), which is probably involved in catalytic reaction and UDP-Gal binding. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. Belongs to the glycosyltransferase 2 family. GalNAc-T subfamily. According to experiments made in rat, this enzyme is unable to transfer GalNAc onto serine or threonine residue on the protein receptor, but instead requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties, thereby acting as a glycopeptide transferase. Polypeptide N-acetylgalactosaminyltransferase 10 +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Calcium-dependent protein kinase which acts as a sensor and effector of intracellular Ca(2+) levels probably in part downstream of cGMP-activated PKG kinase. Plays a central role in the host erythrocytes and hepatocytes infection cycles, sexual reproduction and mosquito transmission of the parasite. During the liver stage, involved in sporozoite motility and thus in sporozoite invasion of host hepatocytes, probably together with CDPK1 and CDPK5. Involved in merosome egress from host hepatocytes, probably together with CDPK5. During the asexual blood stage, involved in merozoite invasion of host erythrocytes and motility by stabilizing the inner membrane complex, a structure below the plasma membrane which acts as an anchor for the glidosome, an acto-myosin motor. Required for cell cycle progression in the male gametocyte. During male gametogenesis in the mosquito gut, required to initiate the first round of DNA replication, probably by facilitating the assembly of the pre-replicative MCM complex, to assemble the first mitotic spindle and, at the end of gametogenesis, to initiate axoneme motility, cytokinesis and subsequent exflagellation. For each of these steps, may phosphorylate SOC1, SOC2 and SOC3, respectively. Together with CDPK1, regulates ookinete gliding in the mosquito host midgut. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by calcium. Upon calcium binding to the EF-hand domains, the C-terminus of the junction domain (J domain) undergoes a conformational change which results in the dissociation of the pseudo-substrate inhibitory motif from the catalytic domain. This, in turn, may facilitate the autophosphorylation of the activation loop at Thr-234, which leads to the kinase activation. Intracellular calcium increase is triggered by xanthurenic acid (XA), a small mosquito molecule that induces the differentiation of specialized transmission stages, the gametocytes, into male and female gametes. Activated by a decrease in temperature (20 degrees Celsius) and an increase in pH (7.6) occurring when the parasite is ingested by in the mosquito. May interact with the pre-replication MCM complex prior male gametogenesis activation. The junction domain (J domain) is composed of 2 motifs that maintain the kinase inactive. The N-terminal autoinhibitory motif acts as a pseudosubstrate inhibiting the catalytic domain while the C-terminal motif binds the EF-hand domains. Myristoylated; myristoylation may target it to different subcellular compartments. During male gametogenesis, myristoylation is required to initiate DNA replication but not for mitotic spindle assembly or axoneme activation. Not palmitoylated. May be autophosphorylated on Thr-234 in vitro. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. CDPK subfamily. +Transcriptional coactivator for steroid receptors and nuclear receptors (PubMed:8670870, PubMed:23508108, PubMed:9430642). Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1) (PubMed:8670870, PubMed:23508108, PubMed:9430642). Required with NCOA1 to control energy balance between white and brown adipose tissues (PubMed:8670870, PubMed:23508108, PubMed:9430642). Critical regulator of glucose metabolism regulation, acts as RORA coactivator to specifically modulate G6PC1 expression (PubMed:8670870, PubMed:23508108, PubMed:9430642). Involved in the positive regulation of the transcriptional activity of the glucocorticoid receptor NR3C1 by sumoylation enhancer RWDD3 (PubMed:23508108). Positively regulates the circadian clock by acting as a transcriptional coactivator for the CLOCK-ARNTL/BMAL1 heterodimer (By similarity). Present in a complex containing NCOA3, IKKA, IKKB, IKBKG and CREBBP. Interacts (via C-terminus) with CREBBP. Interacts with ESR1, HIF1A, NCOA1, APEX1, NR3C1, NR3C2, CARM1, RARA, and RXRA. Present in a complex containing CARM1 and EP300/P300. Interacts with CASP8AP2 and TTLL5/STAMP. Interacts with PSMB9 and DDX5. Interacts (via LXXLL 1, 2 and 3 motifs) with RORA and RORC (via AF-2 motif). Interacts with RWDD3. Interacts with CLOCK and ARNTL/BMAL1 (By similarity). Interacts with NR4A3; potentiates the activity of the NR4A3 (By similarity). Interacts with NR1H3 (PubMed:19481530). Contains four Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs. The LXXLL motifs are essential for the association with nuclear receptors and are, at least in part, functionally redundant. The LLXXLXXXL motif is involved in transcriptional coactivation and CREBBP/CBP binding. Contains 2 C-terminal transcription activation domains (AD1 and AD2) that can function independently. Acetylated. Deacetylation at Lys-780 by SIRT6 stimulates its ability to coactivate PPARA. Chromosomal aberrations involving NCOA2 may be a cause of acute myeloid leukemias. Inversion inv(8)(p11;q13) generates the KAT6A-NCOA2 oncogene, which consists of the N-terminal part of KAT6A and the C-terminal part of NCOA2/TIF2. KAT6A-NCOA2 binds to CREBBP and disrupts its function in transcription activation. Belongs to the SRC/p160 nuclear receptor coactivator family. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Probable ATP-dependent RNA helicase involved in a variety of mitochondrial post-transcriptional processes and in translation. It is a key control element in nuclear-mitochondrial interactions. ATP + H2O = ADP + H(+) + phosphate Belongs to the helicase family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +To M.tuberculosis ERP. +Product of a dubious CDS prediction. Found in the 3'-UTR of TLE4. No homolog. Large scale identification of a phosphorylated peptide (PubMed:15302935) would require further confirmation. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Catalyzes the NADPH-dependent reduction of beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, the first reductive step in the elongation cycle of fatty acid biosynthesis. a (3R)-hydroxyacyl-[ACP] + NADP(+) = a 3-oxoacyl-[ACP] + H(+) + NADPH Lipid metabolism; fatty acid biosynthesis. Homotetramer. Belongs to the short-chain dehydrogenases/reductases (SDR) family. Extended N-terminus. +Involved in the utilization of cholesterol as the sole carbon and energy source by degrading the side chain. Primarily catalyzes the sequential oxidation of the terminal methyl of cholest-4-en-3-one into (25S)-26-hydroxycholest-4-en-3-one (alcohol), (25S)-26-oxocholest-4-en-3-one (aldehyde), to finally yield the carboxylic acid (25S)-3-oxocholest-4-en-26-oate. Also able to sequentially oxidize cholesterol itself, not only cholest-4-en-3-one. cholest-4-en-3-one + 5 H(+) + 3 O2 + 6 reduced [2Fe-2S]-[ferredoxin] = (25S)-3-oxocholest-4-en-26-oate + 4 H2O + 6 oxidized [2Fe-2S]-[ferredoxin] Steroid metabolism; cholesterol degradation. By cholesterol. Cells lacking this gene show lower accumulation of 26-hydroxycholest-4-en-3-one and cholest-4-en-3-one-26-oate when compared with the wild-type and display a strong induction of cyp142A2. The levels of 26-hydroxycholest-4-en-3-one and cholest-4-on-3-one-26-oate are drastically reduced in cells lacking both cyp125A3 and cyp142A2. Belongs to the cytochrome P450 family. +Catalyzes the conversion of UDP-4-keto-arabinose (UDP-Ara4O) to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N). The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. 2-oxoglutarate + UDP-4-amino-4-deoxy-beta-L-arabinose = L-glutamate + UDP-beta-L-threo-pentopyranos-4-ulose Nucleotide-sugar biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose from UDP-alpha-D-glucuronate: step 2/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Homodimer. Belongs to the DegT/DnrJ/EryC1 family. ArnB subfamily. +To M.tuberculosis Rv3776. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Sterol-C4-methyl oxidase; part of the third module of ergosterol biosynthesis pathway that includes the late steps of the pathway (By similarity). Erg26 is a catalytic component of the C-4 demethylation complex that catalyzes the conversion of 4,4-dimethylfecosterol into fecosterol via 4-methylfecosterol (By similarity). The third module or late pathway involves the ergosterol synthesis itself through consecutive reactions that mainly occur in the endoplasmic reticulum (ER) membrane. Firstly, the squalene synthase erg9 catalyzes the condensation of 2 farnesyl pyrophosphate moieties to form squalene, which is the precursor of all steroids. Squalene synthase is crucial for balancing the incorporation of farnesyl diphosphate (FPP) into sterol and nonsterol isoprene synthesis. Secondly, squalene is converted into lanosterol by the consecutive action of the squalene epoxidase erg1 and the lanosterol synthase erg7. Then, the delta(24)-sterol C-methyltransferase erg6 methylates lanosterol at C-24 to produce eburicol. Eburicol is the substrate of the sterol 14-alpha demethylase encoded by cyp51A and cyp51B, to yield 4,4,24-trimethyl ergosta-8,14,24(28)-trienol. The C-14 reductase erg24 then reduces the C14=C15 double bond which leads to 4,4-dimethylfecosterol. A sequence of further demethylations at C-4, involving the C-4 demethylation complex containing the C-4 methylsterol oxidases erg25A or erg25B, the sterol-4-alpha-carboxylate 3-dehydrogenase erg26 and the 3-keto-steroid reductase erg27, leads to the production of fecosterol via 4-methylfecosterol. The C-8 sterol isomerase erg2 then catalyzes the reaction which results in unsaturation at C-7 in the B ring of sterols and thus converts fecosterol to episterol. The sterol-C5-desaturase erg3B then catalyzes the introduction of a C-5 double bond in the B ring to produce 5-dehydroepisterol. The 2 other sterol-C5-desaturases, erg3A and erg3C, seem to be less important in ergosterol biosynthesis. The C-22 sterol desaturase erg5 further converts 5-dehydroepisterol into ergosta-5,7,22,24(28)-tetraen-3beta-ol by forming the C-22(23) double bond in the sterol side chain. Finally, ergosta-5,7,22,24(28)-tetraen-3beta-ol is substrate of the C-24(28) sterol reductases erg4A and erg4B to produce ergosterol. Possible alternative sterol biosynthetic pathways might exist from fecosterol to ergosterol, depending on the activities of the erg3 isoforms (PubMed:18191972) (Probable). Steroid metabolism; ergosterol biosynthesis. Heterotetramer of erg25, erg26, erg27 and erg28 (By similarity). Erg28 acts as a scaffold to tether erg27 and other 4,4-demethylation-related enzymes, forming a demethylation enzyme complex, in the endoplasmic reticulum (By similarity). In Aspergillus, the biosynthesis pathway of the sterol precursors leading to the prevalent sterol ergosterol differs from yeast. The ring system of lanosterol in S.cerevisiae is firstly demethylised in three enzymatic steps leading to the intermediate zymosterol and secondly a methyl group is added to zymosterol by the sterol 24-C-methyltransferase to form fecosterol. In Aspergillus, lanosterol is firstly transmethylated by the sterol 24-C-methyltransferase leading to the intermediate eburicol and secondly demethylated in three steps to form fecosterol. Belongs to the 3-beta-HSD family. +Inhibits zinc finger homeodomain (ZHD) transcription factors by interacting with them to prevent both their nuclear localization and their DNA-binding properties. Involved in integrating signals from multiple hormones by regulating the expression of specific genes. Homo- and heterodimers (By similarity). Interacts with ZHD1, ZHD3, ZHD5, ZHD8, ZHD10 and ZHD13. Mostly expressed in stems, flowers and siliques, and, to a lower extent, in inflorescence. +One of the major non-collagenous components of the tectorial membrane (By similarity). The tectorial membrane is an extracellular matrix of the inner ear that covers the neuroepithelium of the cochlea and contacts the stereocilia bundles of specialized sensory hair cells. Sound induces movement of these hair cells relative to the tectorial membrane, deflects the stereocilia and leads to fluctuations in hair-cell membrane potential, transducing sound into electrical signals. May form homomeric filament after self-association or heteromeric filament after association with alpha-tectorin (Probable). Interacts with CEACAM16 (By similarity). Found in the non-collagenous matrix of the tectorial membrane. Zona pellucida domain may enable to form filaments. The presence of a hydrophobic C-terminus preceded by a potential cleavage site strongly suggests that tectorins are synthesized as glycosylphosphatidylinositol-linked, membrane-bound precursors. Tectorins are targeted to the apical surface of the inner ear epithelia by the lipid and proteolytically released into the extracellular compartment. +NADP(+) + shikimate = 3-dehydroshikimate + H(+) + NADPH Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 4/7. Belongs to the shikimate dehydrogenase family. +Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis. Component of the chaperonin-containing T-complex (TRiC), a heterooligomeric complex of about 850 to 900 kDa that forms two stacked rings, 12 to 16 nm in diameter. Belongs to the TCP-1 chaperonin family. +H(+) + NADP(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADPH + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Homodimer. Belongs to the ferredoxin--NADP reductase type 2 family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, HCO(3)(-)/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate. ATP + hydrogencarbonate + L-threonine = diphosphate + H2O + L-threonylcarbamoyladenylate Belongs to the SUA5 family. TsaC subfamily. +Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity. May play a role in cell proliferation. Component of the CSN complex, probably composed of cops1, cops2, cops3, cops4, cops5, cops6, cops7, cops8 and cops9. Belongs to the CSN9 family. +Plays a role in the translocation of terminally misfolded proteins from the endoplasmic reticulum lumen to the cytoplasm and their degradation by the proteasome (By similarity). Plays a role in lipid droplet formation (By similarity). Induces lipid droplet clustering (By similarity). Belongs to the AUP1 family. +Catalyzes the decarboxylation of L-aspartate to produce beta-alanine. H(+) + L-aspartate = beta-alanine + CO2 Cofactor biosynthesis; coenzyme A biosynthesis. Belongs to the group II decarboxylase family. MfnA subfamily. +Acts as a transcriptional regulator. Inhibits myogenesis by sequestrating E proteins, inhibiting trans-activation by MEF2, and inhibiting DNA-binding by MYOD1 through physical interaction. This interaction probably involves the basic domains of both proteins. Also represses expression of pro-inflammatory cytokines such as TNFA and IL1B. Regulates cranial suture patterning and fusion. Activates transcription as a heterodimer with E proteins. Regulates gene expression differentially, depending on dimer composition. Homodimers induce expression of FGFR2 and POSTN while heterodimers repress FGFR2 and POSTN expression and induce THBS1 expression. Heterodimerization is also required for osteoblast differentiation. Represses the activity of the circadian transcriptional activator: NPAS2-ARNTL/BMAL1 heterodimer (By similarity). Efficient DNA binding requires dimerization with another bHLH protein. Homodimer or heterodimer with E proteins such as TCF3. ID1 binds preferentially to TCF3 but does not interact efficiently with TWIST1 so ID1 levels control the amount of TCF3 available to dimerize with TWIST and thus determine the type of dimer formed (By similarity). +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +Belongs to the bacterial ribosomal protein bL32 family. +Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A. 3'-dephospho-CoA + ATP = ADP + CoA + H(+) Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 5/5. Belongs to the CoaE family. +Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids. Binds 2 magnesium ions per subunit. Homodimer. Belongs to the UPP synthase family. +Catalyzes the reversible stereospecific interconversion of fumarate to L-malate. Catalyzes the hydration of fumarate to L-malate in the tricarboxylic acid (TCA) cycle to facilitate a transition step in the production of energy in the form of NADH. (S)-malate = fumarate + H2O Carbohydrate metabolism; tricarboxylic acid cycle; (S)-malate from fumarate: step 1/1. Homotetramer. There are 2 substrate-binding sites: the catalytic A site, and the non-catalytic B site that may play a role in the transfer of substrate or product between the active site and the solvent. Alternatively, the B site may bind allosteric effectors. Belongs to the class-II fumarase/aspartase family. Fumarase subfamily. +Additional factor that functions in concert with eIF-2 and the initiator tRNA in directing the ribosome to the proper start site of translation. Belongs to the SUI1 family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Nucleoside transporter involved in adenosine transport and required for nucleotide metabolism which influences growth and pollen germination. Has high affinity for adenosine when expressed in a heterologous system (yeast). Tonoplast. In young seedlings, expressed in root elongation zone, root cortex, root-hair, at the transition to the shoot and cotyledons. Expressed in hydathodes of fully developed leaves and pollen. By nitrogen deficiency and 5-fluorouracil plus methotrexate. Plants over-expressing ENT1 have decreased leaf content of adenosine and show growth deficiencies. Plants silencing ENT1 have increased leaf content of adenosine and decreased rate of pollen germination. Belongs to the SLC29A/ENT transporter (TC 2.A.57) family. Truncated N-terminus. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. In this organism, the P 'protein' is a heterodimer of two subunits. Belongs to the GcvP family. N-terminal subunit subfamily. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Belongs to the FARP (FMRFamide related peptide) family. +Histones H1 are necessary for the condensation of nucleosome chains into higher-order structures. Belongs to the histone H1/H5 family. +Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS11 family. +Cytoplasmic aldehyde dehydrogenase involved in ethanol oxidation. Involved in pantothenic acid production through the conversion of 3-aminopropanal to beta-alanine, an intermediate in pantothenic acid (vitamin B5) and coenzyme A (CoA) biosynthesis. an aldehyde + H2O + NAD(+) = a carboxylate + 2 H(+) + NADH 3-aminopropanal + H2O + NAD(+) = beta-alanine + 2 H(+) + NADH Expression is under the control of MSN2 and MSN4, and is induced during diauxic shift and osmotic stress. Present with 172 molecules/cell in log phase SD medium. Belongs to the aldehyde dehydrogenase family. +Catalyzes the oxidation of L-aspartate to iminoaspartate, the first step in the de novo biosynthesis of NAD(+). L-aspartate + O2 = H2O2 + iminosuccinate Binds 1 FAD per subunit. Cofactor biosynthesis; NAD(+) biosynthesis; iminoaspartate from L-aspartate (oxidase route): step 1/1. Belongs to the FAD-dependent oxidoreductase 2 family. NadB subfamily. +Catalyzes the conversion of urocanate to 4-imidazolone-5-propionate. 4-imidazolone-5-propanoate = H2O + trans-urocanate Binds 1 NAD(+) per subunit. Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 2/3. Belongs to the urocanase family. +Belongs to the UPF0759 family. +Structural component of the T=16 icosahedral capsid. The capsid is composed of pentamers and hexamers of major capsid protein/MCP, which are linked together by heterotrimers called triplexes. These triplexes are formed by a single molecule of triplex protein 1/TRX1 and two copies of triplex protein 2/TRX2. Additionally, TRX1 is required for efficient transport of TRX2 to the nucleus, which is the site of capsid assembly. Interacts with TRX1 and major capisd protein/MCP. Belongs to the herpesviridae TRX2 protein family. +Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE). Homodimer (in vitro). Heterodimer with other retinoic acid receptor family members. Binds DNA preferentially as a RAR/RXR heterodimer. Interacts with NR1H3 (By similarity). Interacts with AKAP13 (By similarity). Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain. Belongs to the nuclear hormone receptor family. NR2 subfamily. +E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC1 and UBC7 E2 ligases, and transfers it to substrates promoting their degradation. Mediates the degradation of endoplasmic reticulum proteins (ERQC), also called ER-associated degradation (ERAD). Component of the HRD1 ubiquitin ligase complex, which is part of the ERAD-L and ERAD-M pathways responsible for the rapid degradation of soluble lumenal and membrane proteins with misfolded lumenal domains (ERAD-L), or ER-membrane proteins with misfolded transmembrane domains (ERAD-M). In ERAD-L, facilitates retrotranslocation of misfolded proteins from the ER lumen through the ER membrane in conjunction with DER1 (PubMed:32327568). Both proteins have lateral gates facing each other which form a channel through the ER membrane and which distort the membrane region between the lateral gates, making it much thinner than a normal phospholipid bilayer (PubMed:32327568). Substrates insert into the membrane as a hairpin loop with one strand interacting with DER1 and the other with HRD1. ERAD-L substrates are ubiquitinated through HRD1 in conjunction with the E2 ubiquitin-conjugating enzymes UBC1 and UBC7-CUE1. Ubiquitinated substrates are then removed to the cytosol via the action of the CDC48-NPL4-UFD1 ATPase complex and targeted to the proteasome. ERAD-M substrates are processed by the same HRD1-HRD3 core complex, but only a subset of the other components is required for ERAD-M. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Monomer (PubMed:32327568). Has also been shown to form homodimers (PubMed:28682307). However, dimer assembly is likely to be non-physiological (PubMed:32327568). Forms homooligomers in a USA1-dependent manner (PubMed:20005842, PubMed:21074049). However, can function as a monomer in ERAD-L so the role of USA1-dependent oligomerization remains unclear (PubMed:32327568). Component of the HRD1 ubiquitin ligase complex which contains the E3 ligase HRD1, its cofactors HRD3, USA1 and DER1, substrate recruiting factor YOS9 and CDC48-binding protein UBX2 (PubMed:16873066). Within the complex, interacts directly with HRD3 and USA1 and indirectly with DER1 (PubMed:11018054, PubMed:16619026, PubMed:20005842, PubMed:21074049, PubMed:28682307). In ERAD-L, HRD3 and YOS9 jointly bind misfolded glycoproteins in the endoplasmic reticulum (ER) lumen (PubMed:32327568). Movement of ERAD-L substrates through the ER membrane is facilitated by HRD1 and DER1 which have lateral gates facing each other and which distort the membrane region between the lateral gates, making it much thinner than a normal phospholipid bilayer (PubMed:32327568). Substrates insert into the membrane as a hairpin loop with one strand interacting with DER1 and the other with HRD1 (PubMed:32327568). The HRD1 complex interacts with the heterotrimeric CDC48-NPL4-UFD1 ATPase complex which is recruited by UBX2 via its interaction with CDC48 and which moves ubiquitinated substrates to the cytosol for targeting to the proteasome (PubMed:16873066, PubMed:16619026). The HRD1 complex interacts with the ERAD substrates HMG1 and HMG2 (PubMed:11390656). Interacts with the associated E2 ubiquitin conjugating enzymes UBC1 and UBC7 with its membrane anchor CUE1 (PubMed:11146622). Impaired degradation of proteins with misfolded intramembrane or lumenal domains. Present with 2660 molecules/cell in log phase SD medium. Belongs to the HRD1 family. +adenine + H(+) + H2O = hypoxanthine + NH4(+) Belongs to the metallo-dependent hydrolases superfamily. Adenine deaminase family. +Heme-binding protein able to scavenge peroxynitrite and to protect free L-tyrosine against peroxynitrite-mediated nitration, by acting as a peroxynitrite isomerase that converts peroxynitrite to nitrate. Therefore, this protein likely plays a role in peroxynitrite sensing and in the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively). Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo. peroxynitrite = nitrate Binds 1 heme b group per subunit, that coordinates a highly solvent-exposed Fe(III) atom. Nitrogen metabolism. Homodimer. Forms a 10-stranded antiparallel beta-barrel structure able to accommodate a hydrophobic ligand in its interior. In fact, this fold hosts the heme group, which is located in a wide surface cleft. Belongs to the nitrobindin family. +Catalyzes the NADPH-dependent reduction of N-acetyl-5-glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde. N-acetyl-L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + N-acetyl-L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 3/4. Belongs to the NAGSA dehydrogenase family. Type 1 subfamily. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system. The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. Belongs to the TatA/E family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and probably 6 low-molecular weight proteins. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Transcriptional regulator of the switch between 2 heritable states, the white and opaque states. These 2 cell types differ in many characteristics, including cell structure, mating competence, and virulence. Each state is heritable for many generations, and switching between states occurs stochastically, at low frequency. Contributes to formation of the opaque state, but is not necessary for heritability of the opaque state. Plays a role in cell adhesion and pseudohyphal growth. Involved in acquisition of drug resistance and acts as a repressor of beta-glucan synthesis, thus negatively regulating cell wall integrity. Plays a role in adherence, invasion and damage to oral epithelial cells. Interacts with EFG1. Regulated in response to carbon source, temperature, growth phase, and physical environment. Expression is up-regulated by rapamycine, and thus is under the regulation of the TOR pathway. Binds its own promoter and is also under the control of EFG1. +Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Heterohexamer, formed by a dimer of trimers. The hexameric TusBCD complex contains 2 copies each of TusB, TusC and TusD. The TusBCD complex interacts with TusE. Belongs to the DsrF/TusC family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Removes the pyruvyl group from chorismate, with concomitant aromatization of the ring, to provide 4-hydroxybenzoate (4HB) for the ubiquinone pathway. chorismate = 4-hydroxybenzoate + pyruvate Cofactor biosynthesis; ubiquinone biosynthesis. Monomer. Belongs to the UbiC family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Required for chromosome synapsis and regulates crossover frequency during meiosis. Acts as transverse filament protein and constitutes the central element of the synaptonemal complex. Interacts with CRC1. During zygotene in meiocytes, initially localizes onto the chromosomes as punctate foci and quickly extends into linear signals (PubMed:20154151, PubMed:22393242). Associates with chromosomal axes at zygotene (PubMed:27436711). Highly expressed in panicles. Decreased pollen fertility due to abnormal synaptic behaviors and increased crossover formation during prophase I. +Probable GPI-anchored aspartic-type endopeptidase which contributes to virulence. Belongs to the peptidase A1 family. +Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. [protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family. +Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. 2-oxoglutarate + O-phospho-L-serine = 3-phosphooxypyruvate + L-glutamate 2-oxoglutarate + 4-(phosphooxy)-L-threonine = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate Binds 1 pyridoxal phosphate per subunit. Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 2/3. Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 3/5. Homodimer. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. SerC subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Component of the ubiquinol-cytochrome c oxidoreductase, a multisubunit transmembrane complex that is part of the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. The cytochrome b-c1 complex catalyzes electron transfer from ubiquinol to cytochrome c, linking this redox reaction to translocation of protons across the mitochondrial inner membrane, with protons being carried across the membrane as hydrogens on the quinol. In the process called Q cycle, 2 protons are consumed from the matrix, 4 protons are released into the intermembrane space and 2 electrons are passed to cytochrome c. The Rieske protein is a catalytic core subunit containing a [2Fe-2S] iron-sulfur cluster. It cycles between 2 conformational states during catalysis to transfer electrons from the quinol bound in the Q(0) site in cytochrome b to cytochrome c1 (By similarity). Incorporation of UQCRFS1 is the penultimate step in complex III assembly (By similarity). Component of the ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII). UQCRFS1 undergoes proteolytic processing once it is incorporated in the complex III dimer. One of the fragments, called subunit 9, corresponds to its mitochondrial targeting sequence (MTS) (By similarity). The proteolytic processing is necessary for the correct insertion of UQCRFS1 in the complex III dimer, but the persistence of UQCRFS1-derived fragments may prevent newly imported UQCRFS1 to be processed and assembled into complex III and is detrimental for the complex III structure and function (By similarity). a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)-[cytochrome c](out) + 2 H(+)(out) Binds 1 [2Fe-2S] cluster per subunit. Fe-S cluster delivery to the Rieske protein is mediated by components of the iron sulfur (Fe-S) cluster assembly machinery that reside in the mitochondrial matrix (including HSC20 and LYRM7) (By similarity). Component of the ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), a multisubunit enzyme composed of 11 subunits. The complex is composed of 3 respiratory subunits cytochrome b, cytochrome c1 and Rieske protein UQCRFS1, 2 core protein subunits UQCRC1/QCR1 and UQCRC2/QCR2, and 6 low-molecular weight protein subunits UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and subunit 9, the cleavage product of Rieske protein UQCRFS1. The complex exists as an obligatory dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and cytochrome c oxidase (complex IV, CIV), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Incorporation of the Rieske protein UQCRFS1 is the penultimate step in complex III assembly. Interacts with TTC19, which is involved in the clearance of UQCRFS1 fragments (By similarity). Component of the ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII). Subunit 9 corresponds to the mitochondrial targeting sequence (MTS) of Rieske protein UQCRFS1. It is retained after processing and incorporated inside complex III, where it remains bound to the complex and localizes between the 2 core subunits UQCRC1/QCR1 and UQCRC2/QCR2. Proteolytic processing is necessary for the correct insertion of UQCRFS1 in the complex III dimer. Several fragments are generated during UQCRFS1 insertion, most probably due to the endogenous matrix-processing peptidase (MPP) activity of the 2 core protein subunits UQCRC1/QCR1 and UQCRC2/QCR2, which are homologous to the 2 mitochondrial-processing peptidase (MPP) subunits beta-MPP and alpha-MPP respectively. The action of the protease is also necessary for the clearance of the UQCRFS1 fragments. The Rieske protein is a high potential 2Fe-2S protein. Belongs to the Rieske iron-sulfur protein family. Several peptides are generated during UQCRFS1 insertion. According to some authors, the identification of the transit peptide as the subunit 9, does not necessary imply that it must be considered as a structural subunit of the complex III dimer as additional fragments from UQCRFS1 are also present. +Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. Binds to the N-terminal domain of the chaperone ClpA. Belongs to the ClpS family. +Belongs to the UPF0349 family. +Promotes dimerization of NF-kappa-B subunits and regulates NF-kappa-B transcription factor activity. Promotes growth of cardiomyocytes, but not cardiomyocyte proliferation. Promotes cardiac muscle hypertrophy. Plays a role in the regulation of the growth of actin filaments. Inhibits the activity of the F-actin-capping protein complex formed by the CAPZA1 and CAPZB heterodimer (By similarity). Interacts with RELA. Interacts with the heterodimer formed by CAPZA1 and CAPZB (By similarity). Belongs to the myotrophin family. +Specifically cleaves olefinic bonds in cyclic enones. Involved in the biosynthesis of jasmonic acid (JA) and perhaps in biosynthesis or metabolism of other oxylipin signaling moleclules. It is required for the spatial and temporal regulation of JA levels during dehiscence of anthers, promoting the stomium degeneration program (By similarity). In vitro, reduces 9S,13S-12-oxophytodienoic acid (9S,13S-OPDA) and 9R,13R-OPDA to 9S,13S-OPC-8:0 and 9R,13R-OPC-8:0, respectively. NADP(+) + OPC-8 = (10Z,15Z)-12-oxophytodienoate + H(+) + NADPH Lipid metabolism; oxylipin biosynthesis. Expressed in roots and to a lower extent in leaves and flowers. By wounding, locally and systemically. Belongs to the NADH:flavin oxidoreductase/NADH oxidase family. +Required for respiratory activity and maintenance and expression of the mitochondrial genome. Belongs to the RRG9 family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 1 family. +Catalyzes the epimerization of (2R)- and (2S)-methylacyl-coenzyme A (CoA) thioesters (PubMed:15632186, PubMed:19854148, PubMed:26348625). Accepts as substrates a wide range of alpha-methylacyl-CoAs, including (2R)-2-methylmyristoyl-CoA and (2S)-2-methylmyristoyl-CoA, (2R)-pristanoyl-CoA and (2S)-pristanoyl-CoA, and the cholesterol esters (25R)-3-oxo-cholest-4-en-26-oyl-CoA and (25S)-3-oxo-cholest-4-en-26-oyl-CoA (PubMed:15632186, PubMed:26348625). Can also catalyze the interconversion of the non-physiologic substrates (2R)-ibuprofenoyl-CoA and (2S)-ibuprofenoyl-CoA, which are potential competitive inhibitors of the enzyme (PubMed:19854148). a (2S)-2-methylacyl-CoA = a (2R)-2-methylacyl-CoA (2S)-2-methyltetradecanoyl-CoA = (2R)-2-methyltetradecanoyl-CoA (2R)-pristanoyl-CoA = (2S)-pristanoyl-CoA (25S)-3-oxocholest-4-en-26-oyl-CoA = (25R)-3-oxocholest-4-en-26-oyl-CoA (2S)-ibuprofenoyl-CoA = (2R)-ibuprofenoyl-CoA Inactivated by N,N-dialkylcarbamoyl-CoA substrate-product analogs. kcat is 3.7 sec(-1) with (25R)-3-oxo-cholest-4-en-26-oyl-CoA as substrate (PubMed:26348625). kcat is 450 sec(-1) with (2S)-ibuprofenoyl-CoA as substrate (PubMed:19854148). kcat is 291 sec(-1) with (2R)-ibuprofenoyl-CoA as substrate (PubMed:19854148). Homodimer. Development of gem-disubstituted substrate-product analogs as inhibitors of racemases and epimerases is elaborated using alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis as a model enzyme. These non-physiologic substrates could be used as a therapeutic agent to inhibit human AMACR, which is overexpressed in prostate cancer. Interconversion is achieved via a planar enolate intermediate. Belongs to the CoA-transferase III family. +A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis. Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes. Belongs to the type II topoisomerase GyrA/ParC subunit family. +Belongs to the UPF0357 family. +Together with zig-5, required postembryonically to maintain the position of ASI and ASH head neuron cell bodies and ventral nerve cord axons of PVQ, PVP and HSN neurons by preventing their displacement that could occur during body growth and movement. May act by reducing L1CAM-like protein sax-7 (long isoform) adhesion. Expressed in PVT neurons and pharyngeal muscles. Expression begins at the late L1 larval stage. No visible phenotype. In a zig-5 mutant background, 74 percent of animals have cell bodies of ASI and ASH head neurons displaced either on the top of or anterior to the nerve ring. In addition, double mutants show defects in the positioning of the ventral nerve cord (VNC) axons characterized by axons of embryonically generated PVQ, PVP and HSN neurons from the left and right VNC drifting into the opposite cord (axon flip-over). Both defects begin at the L3 larval stage and become more pronounced at the L4 larval and adult stages. Cell body and axon positioning is normal in embryos and in L1 larvae. In a zig-1, zig-2, zig-3 or zig-4 mutant background, cell body positioning of ASI and ASH head neurons is normal. In unc-13 or unc-54 mutant background, where locomotion is impaired, cell body positioning of ASI and ASH neurons is normal. In a sax-7 (nj53) mutant background, cell body and axon positioning is normal. Simultaneous RNAi-mediated knockdown of zig-5 and zig-8 at the embryonic, larval or adult stage causes a displacement of ASI and ASH head neurons in 6 to 9 percent of animals. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. Although the small subunit is not catalytic it is essential for maximal activity. Heterohexadecamer of 8 large and 8 small subunits. In this alga, in contrast to plants, the small subunit is encoded in the chloroplast. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO small chain family. +Highly active in the 15-alpha-hydroxylation of testosterone. Also active in the 15-alpha-hydroxylation of progesterone and androstenedione. Little or no activity on corticosterone, pregnenolone, dehydroepiandrosterone, estradiol or estriol. an organic molecule + O2 + reduced [NADPH--hemoprotein reductase] = an alcohol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Kidney and lung. Expressed in liver, with a strong circadian rhythmicity. Circadian expression is regulated by DBP. There are only 11 differences between the sequence of testosterone 15-alpha-hydroxylase and that of coumarin 7-hydroxylase. By site-directed mutagenesis it has been shown that modification of position 209 is sufficient to convert the specificity of the two forms of the enzyme. Belongs to the cytochrome P450 family. +Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is transferred onto alpha-ketoisovalerate to form ketopantoate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = (6S)-5,6,7,8-tetrahydrofolate + 2-dehydropantoate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantoate from 3-methyl-2-oxobutanoate: step 1/2. Homodecamer; pentamer of dimers. Belongs to the PanB family. +With CysD forms the ATP sulfurylase (ATPS) that catalyzes the adenylation of sulfate producing adenosine 5'-phosphosulfate (APS) and diphosphate, the first enzymatic step in sulfur assimilation pathway. APS synthesis involves the formation of a high-energy phosphoric-sulfuric acid anhydride bond driven by GTP hydrolysis by CysN coupled to ATP hydrolysis by CysD. ATP + H(+) + sulfate = adenosine 5'-phosphosulfate + diphosphate Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 1/3. Heterodimer composed of CysD, the smaller subunit, and CysN. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. CysN/NodQ subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Plays a role in keeping cristae membranes connected to the inner boundary membrane. Also promotes protein import via the mitochondrial intermembrane space assembly (MIA) pathway (By similarity). Component of the mitochondrial contact site and cristae organizing system (MICOS) complex. Belongs to the MICOS complex subunit Mic60 family. +Probable carboxypeptidase. Expressed in seedlings and roots. Belongs to the peptidase S10 family. +Nuclear transcriptional activator of viral gene expression, that is essential for viral transcription from the LTR promoter and replication. Acts as a sequence-specific molecular adapter, directing components of the cellular transcription machinery to the viral RNA to promote processive transcription elongation by the RNA polymerase II (RNA pol II) complex, thereby increasing the level of full-length transcripts. In the absence of Tat, the RNA Pol II generates short or non-processive transcripts that terminate at approximately 60 bp from the initiation site. Tat associates with the CCNT1/cyclin-T1 component of the P-TEFb complex (CDK9 and CCNT1), which promotes RNA chain elongation. This binding increases Tat's affinity for a hairpin structure at the 5'-end of all nascent viral mRNAs referred to as the transactivation responsive RNA element (TAR RNA) and allows Tat/P-TEFb complex to bind cooperatively to TAR RNA. The CDK9 component of P-TEFb and other Tat-activated kinases hyperphosphorylate the C-terminus of RNA Pol II that becomes stabilized and much more processive. Other factors such as HTATSF1/Tat-SF1, SUPT5H/SPT5, and HTATIP2 are also important for Tat's function. Besides its effect on RNA Pol II processivity, Tat induces chromatin remodeling of proviral genes by recruiting the histone acetyltransferases (HATs) CREBBP, EP300 and PCAF to the chromatin. This also contributes to the increase in proviral transcription rate, especially when the provirus integrates in transcriptionally silent region of the host genome. To ensure maximal activation of the LTR, Tat mediates nuclear translocation of NF-kappa-B. In this purpose, it activates EIF2AK2/PKR which, in turns, may phosphorylate and target to degradation the inhibitor IkappaB-alpha which normally retains NF-kappa-B in the cytoplasm of unstimulated cells. Through its interaction with TBP, Tat may be involved in transcription initiation as well. Interacts with the cellular capping enzyme RNGTT to mediate co-transcriptional capping of viral mRNAs. Tat protein exerts as well a positive feedback on the translation of its cognate mRNA. Tat can reactivate a latently infected cell by penetrating in it and transactivating its LTR promoter. In the cytoplasm, Tat is thought to act as a translational activator of HIV-1 mRNAs (By similarity). Extracellular circulating Tat can be endocytosed by surrounding uninfected cells via the binding to several surface receptors such as CD26, CXCR4, heparan sulfate proteoglycans (HSPG) or LDLR. Neurons are rarely infected, but they internalize Tat via their LDLR. Endosomal low pH allows Tat to cross the endosome membrane to enter the cytosol and eventually further translocate into the nucleus, thereby inducing severe cell dysfunctions ranging from cell activation to cell death. Through its interaction with nuclear HATs, Tat is potentially able to control the acetylation-dependent cellular gene expression. Tat seems to inhibit the HAT activity of KAT5/Tip60 and TAF1, and consequently modify the expression of specific cellular genes. Modulates the expression of many cellular genes involved in cell survival, proliferation or in coding for cytokines (such as IL10) or cytokine receptors. May be involved in the derepression of host interleukin IL2 expression. Mediates the activation of cyclin-dependent kinases and dysregulation of microtubule network. Tat plays a role in T-cell and neurons apoptosis. Tat induced neurotoxicity and apoptosis probably contribute to neuroAIDS. Host extracellular matrix metalloproteinase MMP1 cleaves Tat and decreases Tat's mediated neurotoxicity. Circulating Tat also acts as a chemokine-like and/or growth factor-like molecule that binds to specific receptors on the surface of the cells, affecting many cellular pathways. In the vascular system, Tat binds to ITGAV/ITGB3 and ITGA5/ITGB1 integrins dimers at the surface of endothelial cells and competes with bFGF for heparin-binding sites, leading to an excess of soluble bFGF. Binds to KDR/VEGFR-2. All these Tat-mediated effects enhance angiogenesis in Kaposi's sarcoma lesions (By similarity). Interacts with host CCNT1. Associates with the P-TEFb complex composed at least of Tat, P-TEFb (CDK9 and CCNT1), TAR RNA, RNA Pol II. Recruits the HATs CREBBP, TAF1/TFIID, EP300, PCAF and GCN5L2. Interacts with host KAT5/Tip60; this interaction targets the latter to degradation. Interacts with the host deacetylase SIRT1. Interacts with host capping enzyme RNGTT; this interaction stimulates RNGTT. Binds to host KDR, and to the host integrins ITGAV/ITGB3 and ITGA5/ITGB1. Interacts with host KPNB1/importin beta-1 without previous binding to KPNA1/importin alpha-1. Interacts with EIF2AK2. Interacts with host nucleosome assembly protein NAP1L1; this interaction may be required for the transport of Tat within the nucleus, since the two proteins interact at the nuclear rim. Interacts with host C1QBP/SF2P32; this interaction involves lysine-acetylated Tat. Interacts with the host chemokine receptors CCR2, CCR3 and CXCR4. Interacts with host DPP4/CD26; this interaction may trigger an anti-proliferative effect. Interacts with host LDLR. Interacts with the host extracellular matrix metalloproteinase MMP1. Interacts with host PRMT6; this interaction mediates Tat's methylation. Interacts with, and is ubiquitinated by MDM2/Hdm2. Interacts with host PSMC3 and HTATIP2. Interacts with STAB1; this interaction may overcome SATB1-mediated repression of IL2 and IL2RA (interleukin) in T cells by binding to the same domain than HDAC1. Interacts (when acetylated) with human CDK13, thereby increasing HIV-1 mRNA splicing and promoting the production of the doubly spliced HIV-1 protein Nef (By similarity). Probably localizes to both nuclear and nucleolar compartments. Nuclear localization is mediated through the interaction of the nuclear localization signal with importin KPNB1. Secretion occurs through a Golgi-independent pathway. Tat is released from infected cells to the extracellular space where it remains associated to the cell membrane, or is secreted into the cerebrospinal fluid and sera. Extracellular Tat can be endocytosed by surrounding uninfected cells via binding to several receptors depending on the cell type (By similarity). The transactivation domain mediates the interaction with CCNT1, GCN5L2, and MDM2. The Arg-rich RNA-binding region binds the TAR RNA. This region also mediates the nuclear localization through direct binding to KPNB1 and is involved in Tat's transfer across cell membranes (protein transduction). The same region is required for the interaction with EP300, PCAF, EIF2AK2 and KDR (By similarity). The Cys-rich region may bind 2 zinc ions (Potential). This region is involved in binding to KAT5 (By similarity). The cell attachment site mediates the interaction with ITGAV/ITGB3 and ITGA5/ITGB1 integrins, leading to vascular cell migration and invasion. This interaction also provides endothelial cells with the adhesion signal they require to grow in response to mitogens (By similarity). Acetylation by EP300, CREBBP, GCN5L2/GCN5 and PCAF regulates the transactivation activity of Tat. EP300-mediated acetylation of Lys-50 promotes dissociation of Tat from the TAR RNA through the competitive binding to PCAF's bromodomain. In addition, the non-acetylated Tat's N-terminus can also interact with PCAF. PCAF-mediated acetylation of Lys-28 enhances Tat's binding to CCNT1. Lys-50 is deacetylated by SIRT1 (By similarity). Phosphorylated by EIF2AK2 on serine and threonine residues adjacent to the basic region important for TAR RNA binding and function. Phosphorylation of Tat by EIF2AK2 is dependent on the prior activation of EIF2AK2 by dsRNA (By similarity). Asymmetrical arginine methylation by host PRMT6 seems to diminish the transactivation capacity of Tat and affects the interaction with host CCNT1. Polyubiquitination by MDM2 does not target Tat to degradation, but activates its transactivation function and fosters interaction with CCNT1 and TAR RNA. The Z-84 isolate was taken from a 54 year-old Zairean male. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Expressed in the late stage of the infection cycle, when unspliced viral RNAs are exported to the cytoplasm by the viral Rev protein. Belongs to the lentiviruses Tat family. +Acts as an inhibitor of histone acetyltransferase activity; prevents acetylation of all core histones by the EP300/p300 histone acetyltransferase at p53/TP53-regulated target promoters in a histone deacetylases (HDAC)-independent manner. Acts as a transcription corepressor of p53/TP53- and TP63-mediated transactivation of the p21/CDKN1A promoter. Involved in the regulation of p53/TP53-dependent apoptosis. Associates together with TP63 isoform TA*-gamma to the p21/CDKN1A promoter. Interacts with p53/TP53. Interacts (via the N- and C-terminus domains) with AURKB (via the middle kinase domain). Interacts with TP63 isoform TA*-gamma (via activation domain). Interacts with histone H3 (via N-terminus and non-acetylated form preferentially). Associates with core histones and nucleosomes. Translocates from the nucleoli to the nucleoplasm in presence of several stressors like ultraviolet irradiation and actinomycin-D. Predominantly detected in the nucleoli in non-mitotic cells. Predominantly detected in nucleoplasma in cells undergoing mitosis. Up-regulated by IL4 and CD40L in B-cells. Belongs to the NOC2 family. +Plays an essential role in budded virus production and occlusion body formation. Envelope structural protein associated with both budded viruses (BV) and occlusion-derived viruses (ODV). +beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Binds 2 magnesium ions per subunit. Carbohydrate biosynthesis; gluconeogenesis. Homotetramer. Belongs to the FBPase class 1 family. +Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NAD(+) (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADPH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NADP(+) Belongs to the MnmG family. TrmFO subfamily. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Cell division protein that is part of the divisome complex and is recruited early to the Z-ring. Probably stimulates Z-ring formation, perhaps through the cross-linking of FtsZ protofilaments. Its function overlaps with FtsA. Homodimer. Interacts with FtsZ. Localizes to the division site, in a FtsZ-dependent manner. Belongs to the SepF family. +Part of the gene cluster that mediates the biosynthesis of oxaleimides, cytotoxic compounds containing an unusual disubstituted succinimide moiety (PubMed:28365998). The first step of the pathway is provided by the HR-PKS poxF that serves in a new mode of collaborative biosynthesis with the PKS-NRPS poxE, by providing the olefin containing amino acid substrate via the synthesis of an ACP-bound dec-4-enoate (PubMed:28365998). The cytochrome P450 monooxygenase poxM-catalyzed oxidation at the alpha-position creates the enzyme-bound 2-hydroxydec-4-enoyl-ACP thioester, which may be prone to spontaneous hydrolysis to yield 2-hydroxydec-4-enoic acid due to increased electrophilicity of the carbonyl (PubMed:28365998). 2-hydroxydec-4-enoic acid can then be further oxidized by poxM to yield the alpha-ketoacid 2-oxodec-4-enoicacid, which is reductively aminated by the aminotransferase poxL to yield (S,E)-2-aminodec-4-enoic acid (PubMed:28365998). The Hybrid PKS-NRPS synthetase poxE then performs condensation between the octaketide product of its PKS modules and the amino group of (S,E)-2-aminodec-4-enoic acid which is activated and incorporated by the adenylation domain (PubMed:28365998). The resulting aminoacyl product can be cyclized by the Diels-Alderase PoxQ and reductively released by the reductive (R) domain of poxE to yield an aldehyde intermediate (PubMed:28365998) (Probable). The released aldehyde is then substrate for a Knoevenagel condensation by the hydrolyase poxO followed by an oxidation at the 5-position of the pyrrolidone ring (PubMed:28365998). The presence of the olefin from the amino acid building block allows for migration of the substituted allyl group to occur (PubMed:28365998). This allylic transposition reaction takes place in a conjugate addition, semipinacol-like fashion to yield a succinimide intermediate (PubMed:28365998). Iterative two-electron oxidations of the C7 methyl of the succinimide intermediate to the carboxylic acid can be catalyzed by one of two remaining cytochrome P450 monooxygenasess poxC or poxD to yield oxaleimide A (PubMed:28365998). Subsequent oxidation yields the maleimide scaffold oxaleimide I (PubMed:28365998). Both oxaleimide A and oxaleimide I can undergo oxidative modifications in the decalin ring to yield the series of products oxaleimides B to H (PubMed:28365998). Secondary metabolite biosynthesis. Expression is positively regulated by the oxaleimides biosynthesis cluster-specific transcription factor poxB. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +ATP-binding (A) component of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates including 5-formyltetrahydrofolate and thiamine. Expression of the complex plus FolT or ThiT in Lactococcus lactis subsp. cremoris (strain NZ9000) allows 5-formyltetrahydrofolate or thiamine uptake respectively; 5-formyltetrahydrofolate or thiamine are not taken up in the absence of FolT/ThiT or the EcfA1A2T complex. Deenergized L.lactis subsp. cremoris (treated with 2-deoxyglucose) do not take up substrate. Forms a stable energy-coupling factor (ECF) transporter complex probably composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). This complex interacts with a number of substrate-specific components, including FolT and ThiT for 5-formyltetrahydrofolate and thiamine respectively. Belongs to the ABC transporter superfamily. Energy-coupling factor EcfA family. +Functions in replication-dependent translation of histone mRNAs which differ from other eukaryotic mRNAs in that they do not end with a poly-A tail but a stem-loop. May participate in circularizing those mRNAs specifically enhancing their translation (By similarity). Interacts with eif4g1, eif4g2 and slbp; probably tethered by SLBP to the 3'-end of mRNAs ending with the histone stem-loop, it also interacts with eif4g1 which is bound to their 5'-end. Belongs to the MIF4GD family. +Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). Belongs to the conotoxin O3 superfamily. +2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + ADP + H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole from N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide: step 2/2. Belongs to the AIR synthase family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation (By similarity). Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). The b'-subunit is a diverged and duplicated form of b found in plants and photosynthetic bacteria (By similarity). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains (By similarity). Belongs to the ATPase B chain family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Zinc phosphodiesterase, which has both exoribonuclease and endoribonuclease activities. Binds 2 Zn(2+) ions. Homodimer. Belongs to the RNase Z family. RNase BN subfamily. Extended N-terminus. Extended N-terminus. +Seems to be required for maximal rate of protein biosynthesis. Enhances ribosome dissociation into subunits and stabilizes the binding of the initiator Met-tRNA(I) to 40 S ribosomal subunits (By similarity). Belongs to the eIF-1A family. Extended N-terminus. +Antitoxin component of a potential type II toxin-antitoxin (TA) system. Acts as an antitoxin against host toxins RnlA and LsoA, preventing them from degrading T4 bacteriophage-derived mRNA and thus permitting successful virus infection. Stabilizes middle (8-10 minutes) and late (18 to 28 minutes) T4 gene transcripts. Can form a complex with non-cognate host toxins LsoA and RnlA. Phage grows very poorly in wild-type E.coli K12 or in cells expressing plasmid-derived toxin-antitoxin system LsoA-LsoB; if the host has a deletion in rnlA-rnlB no effect is seen. Absence of full-length transcripts of late (18 to 28 minutes) T4 genes, and thus loss of synthesis of late proteins. Partially suppressed by overexpression of host IscR. Enterobacteria phage T4 probably has no corresponding toxin gene. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Monothiol glutaredoxin involved in mitochondrial iron-sulfur (Fe/S) cluster transfer (By similarity). Receives iron-sulfur clusters from scaffold protein ISCU and mediates their transfer to apoproteins, to the 4Fe/FS cluster biosynthesis machinery, or export from mitochondrion (By similarity). Homodimer. Belongs to the glutaredoxin family. Monothiol subfamily. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +Component of the microsomal membrane bound fatty acid elongation system, which produces the 26-carbon very long-chain fatty acids (VLCFA) from palmitate. Catalyzes the reduction of the 3-ketoacyl-CoA intermediate that is formed in each cycle of fatty acid elongation. VLCFAs serve as precursors for ceramide and sphingolipids. a very-long-chain (3R)-3-hydroxyacyl-CoA + NADP(+) = a very-long-chain 3-oxoacyl-CoA + H(+) + NADPH 3-oxooctadecanoyl-CoA + H(+) + NADPH = (3R)-hydroxyoctadecanoyl-CoA + NADP(+) 3-oxoeicosanoyl-CoA + H(+) + NADPH = (3R)-hydroxyeicosanoyl-CoA + NADP(+) 3-oxodocosanoyl-CoA + H(+) + NADPH = (3R)-hydroxydocosanoyl-CoA + NADP(+) 3-oxotetracosanoyl-CoA + H(+) + NADPH = (3R)-hydroxytetracosanoyl-CoA + NADP(+) 3-oxohexacosanoyl-CoA + H(+) + NADPH = (3R)-hydroxyhexacosanoyl-CoA + NADP(+) Lipid metabolism; fatty acid biosynthesis. Interacts with the fatty acid elongation system components ELO3 and TSC13. Present with 41900 molecules/cell in log phase SD medium. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +alpha-D-xylose = alpha-D-xylulofuranose Binds 2 magnesium ions per subunit. Homotetramer. Belongs to the xylose isomerase family. +Required for the formation of axial filaments and for anchoring the origin regions at the cell poles in sporulating cells, thus ensuring proper chromosome segregation in the prespore. Binds in a dispersed manner throughout the chromosome but preferentially to sites clustered in the origin portion of the chromosome, causing condensation of the chromosome and its remodeling into an elongated, anchored structure. Localizes to cell poles and nucleoid. Belongs to the RacA family. +N-methyltransferase that catalyzes the formation of anserine (beta-alanyl-N(Pi)-methyl-L-histidine) from carnosine. Anserine, a methylated derivative of carnosine (beta-alanyl-L-histidine), is an abundant constituent of vertebrate skeletal muscles. Also methylates other L-histidine-containing di- and tripeptides such as Gly-Gly-His, Gly-His and homocarnosine (GABA-His). carnosine + S-adenosyl-L-methionine = anserine + H(+) + S-adenosyl-L-homocysteine kcat is 0.15 min(-1) for carnosine. kcat is 4.69 min(-1) for S-adenosyl-L-methionine. Optimum pH is 7.0-7.5. Optimum temperature is 50 degrees Celsius. Homodimer. Each monomer accommodates one molecule of carnosine in its active pocket, precisely anchoring the histidine imidazole ring such that only N1 is exposed and deprotonated for methylation. Expressed at higher level in skeletal muscle compared to other tissues. The Gly-Xaa-Gly-Xaa-Gly (GXGXG) motif binds the adenosyl part of S-adenosyl-L-methionine. The carnosine-binding region forms hydrophobic and hydrogen bonds with carnosine, defining a flipping orientation of the imidazole ring so that N1 is present next to S-adenosyl-L-methionine for methylation. Belongs to the carnosine N-methyltransferase family. +Involved in resistance to gentamicin, tobramycin, and kanamycin. Tobramycin and kanamycin resistance is due to the ACC activity, specified by N-terminal region. The C-terminal region is a kinase that phosphorylates several 4,6-disubstituted aminoglycosides. a gentamycin + GTP = a gentamycin 2''-phosphate + GDP + H(+) In the C-terminal section; belongs to the aminoglycoside phosphotransferase family. +Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units. Binds 2 calcium ions per subunit. Calcium is inhibitory at high concentrations. Belongs to the glycosyl hydrolase 13 family. +Polyol dehydrogenase that catalyzes the reversible NAD(+)-dependent oxidation of various sugar alcohols. Is mostly active with xylitol, D-sorbitol (D-glucitol) and L-iditol as substrates, leading to the C2-oxidized products D-xylulose, D-fructose and L-sorbose, respectively (PubMed:9143345). Is a key enzyme in the polyol pathway that interconverts glucose and fructose via sorbitol, which constitutes an important alternate route for glucose metabolism. May play a role in sperm motility by using sorbitol as an alternative energy source for sperm motility (By similarity). Cannot use NADP(+) as the electron acceptor. Has no activity on ethanol, methanol, glycerol, galactitol and fructose 6-phosphate (PubMed:9143345). NAD(+) + xylitol = D-xylulose + H(+) + NADH H(+) + keto-D-fructose + NADH = D-sorbitol + NAD(+) L-iditol + NAD(+) = H(+) + keto-L-sorbose + NADH Binds 1 zinc ion per subunit. Inhibited in vitro by metal chelators such as EDTA and 1,10-phenanthroline. kcat is 29 sec(-1) for D-sorbitol oxidation (at pH 8.0). kcat is 26 sec(-1) for xylitol oxidation (at pH 8.0). kcat is 21 sec(-1) for L-iditol oxidation (at pH 8.0). kcat is 22 sec(-1) for ribitol oxidation (at pH 8.0). kcat is 24 sec(-1) for D-mannitol oxidation (at pH 8.0). kcat is 12 sec(-1) for L-threitol oxidation (at pH 8.0). kcat is 162 sec(-1) for D-fructose reduction (at pH 7.4). kcat is 153 sec(-1) for L-sorbose reduction (at pH 7.4). kcat is 198 sec(-1) for D-ribulose reduction (at pH 7.4). Optimum pH is about 9 for D-sorbitol oxidation, and 7.4 for D-fructose reduction. Homotetramer. Associated with mitochondria of the midpiece and near the plasma membrane in the principal piece of the flagellum. Also found in the epididymosome, secreted by the epididymal epithelium and that transfers proteins from the epididymal fluid to the sperm surface. Expressed in lens. Belongs to the zinc-containing alcohol dehydrogenase family. +Endoribonuclease that initiates mRNA decay. Belongs to the RNase Y family. +Catalyzes the ATP-dependent phosphorylation of N-acetyl-L-glutamate. ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamyl 5-phosphate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 2/4. Belongs to the acetylglutamate kinase family. ArgB subfamily. +Plays an essential role in spindle orientation and organizing cellular and embryonic polarity by controlling the localization and activity of PAR (partitioning-defective) proteins. Required for maintaining the asymmetric cortical localization of the anterior complex proteins par-3 and par-6, the posterior cortical protein par-2, and pkc-3 (PubMed:11412996, PubMed:11412997). Involved in hypodermal cell fusion, together with pak-1 and ced-10, leading to embryonic body elongation, which involves dramatic cytoskeletal reorganization (PubMed:8824291). During gonad morphogenesis, plays a role in distal tip cell (DTC)-mediated guidance of gonad elongation, probably by activating max-2 (PubMed:19797046, PubMed:19023419). May play a role in controlling canal length and in maintaining Golgi and ER stability during excretory canal elongation, probably downstream of ccm-3, which may regulate its activity and expression levels (PubMed:25743393). May play a role in yolk protein clatherin-mediated endocytosis by oocytes during oogenesis (PubMed:19798448). Involved in toca-1 and toca-2-mediated protein trafficking controlling the recycling of endocytic cargo protein mig-14 to the Golgi apparatus (PubMed:25775511). Plays a role in male tail tip morphogenesis (PubMed:21408209). Together with kpc-1 and chin-1, plays a role in guiding axons from neurons, including AIY interneurons, into the nerve ring (PubMed:28846083). The GTP-bound, but not the GDP-bound, form binds to the p21-activated kinase (pak-1) (PubMed:8824291). Interaction with par-6 required for activation of the par-3/par-6/pkc-3 complex (PubMed:11412997). Interacts with toca-1 and toca-2 (PubMed:25775511). May interact with unc-89 (via DH and PH domains); the interaction does not stimulate GTPase activity in vitro (PubMed:18801371). Co-localizes with ced-10/rac-1 and pak-1 at hypodermal cell boundaries during embryo elongation (PubMed:8824291). Localizes in punctate cytoplasmic structures along the length of excretory canals (PubMed:25743393). Co-localizes with rme-1 and toca-1 on recycling endosomes (PubMed:25775511). Diffusely localizes in the cytoplasm of tail tip cells, but then localizes to the apical surfaces of the tail tip cells before male tail tip retraction during the L4 larval stage (PubMed:21408209). During male tail tip retraction localizes to the cytoplasm (PubMed:21408209). Expressed in the intestine and seam cells. Highest levels at the embryonic stage, decreasing progressively during development, except for an increase at the L3 stage (PubMed:8514766). Expressed in hypodermal cells during elongation throughout the second phase of embryogenesis (PubMed:8824291). RNAi-mediated knockdown disrupts tail tip morphogenesis resulting in retention of the pointed larval tail tip in adult males (also known as the Lep phenotype) (PubMed:21408209). RNAi-mediated knockdown in distal tip cells (DTC) causes additional turns during their migration (PubMed:19023419). RNAi-mediated knockdown in addition, causes a truncation of excretory canals associated with the formation of cysts and a reduced distribution of Golgi and ER components along the excretory canal length (PubMed:25743393). RNAi-mediated knockdown results in defective endocytosis by oocytes characterized by an accumulation of aggregated yolk protein in the pseudocoelomatic space, and accumulation of endocytic cargo protein mig-14 in late endosomes and expansion of recycling endosomes that express toca-1 and toca-2 (PubMed:19798448, PubMed:25775511). RNAi-mediated knockdown enhances the axon guidance defects in glia and sublateral neurons of the kpc-1 gk mutant, in which non-commissural interneurons AIY fail to extend dorsally and enter the nerve ring (PubMed:28846083). Belongs to the small GTPase superfamily. Rho family. CDC42 subfamily. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +Chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Has a low intrinsic ATPase activity which is markedly stimulated by HscB. Belongs to the heat shock protein 70 family. +Belongs to the UPF0301 (AlgH) family. +GTPase-activating protein (GAP) for the ADP ribosylation factor 1 (ARF1). Involved in membrane trafficking and /or vesicle transport. Promotes hydrolysis of the ARF1-bound GTP and thus, is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles, a prerequisite for vesicle's fusion with target compartment. Probably regulates ARF1-mediated transport via its interaction with the KDELR proteins and TMED2. Overexpression induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, as when ARF1 is deactivated. Its activity is stimulated by phosphoinosides and inhibited by phosphatidylcholine (By similarity). Interacts with ARF1. Interacts with the COPI coat proteins, KDELR1 and TMED2. The interaction with TMED2 inhibits the GAP activity (By similarity). Associates with the Golgi complex. The region downstream of Arf-GAP domain is essential to GAP activity in vivo. This region may be required for its targeting to Golgi membranes (By similarity). Truncated N-terminus. Truncated N-terminus. Intron retention. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Belongs to the mimivirus L31/R44 family. +Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins. Interacts with the Sec translocase complex via SecD. Specifically interacts with transmembrane segments of nascent integral membrane proteins during membrane integration. Belongs to the OXA1/ALB3/YidC family. Type 1 subfamily. +Involved in the uptake of dipeptides and tripeptides. May influence host-pathogen interactions. Involved in motility and agglutination, and has a role in stimulation of dendritic cells. Deletion mutant has a reduced ability to utilize a number of di- and tri-peptides as nitrogen sources, displays reduced motility and reduced agglutination compared to wild type. Belongs to the peptide transporter carbon starvation (CstA) (TC 2.A.114) family. +Hydrolyzes the non-reducing end N-acetyl-D-hexosamine and/or sulfated N-acetyl-D-hexosamine of glycoconjugates, such as the oligosaccharide moieties from proteins and neutral glycolipids, or from certain mucopolysaccharides. The isozyme B does not hydrolyze each of these substrates, however hydrolyzes efficiently neutral oligosaccharide. Only the isozyme A is responsible for the degradation of GM2 gangliosides in the presence of GM2A. During fertilization is responsible, at least in part, for the zona block to polyspermy. Present in the cortical granules of non-activated oocytes, is exocytosed during the cortical reaction in response to oocyte activation and inactivates the sperm galactosyltransferase-binding site, accounting for the block in sperm binding to the zona pellucida (PubMed:8253842). Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. H2O + N-acetyl-beta-D-galactosaminyl-(1->4)-beta-D-3-sulfogalactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide = a beta-D-3-sulfogalactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + N-acetyl-beta-D-galactosamine ganglioside GM2 (d18:1(4E)) + H2O = ganglioside GM3 (d18:1(4E)) + N-acetyl-beta-D-galactosamine ganglioside GM2 + H2O = ganglioside GM3 + N-acetyl-beta-D-galactosamine beta-D-GalNAc-(1->4)-alpha-L-IdoA-(1->3)-beta-D-GalNAc-4-sulfate-(1->4)-alpha-L-IdoA-(1->3)-D-GalNAc-4-sulfate + H2O = alpha-L-IdoA-(1->3)-beta-D-GalNAc-4-sulfate-(1->4)-alpha-L-IdoA-(1->3)-D-GalNAc-4-sulfate + N-acetyl-D-galactosamine H2O + N-acetyl-beta-D-6-sulfogalactosaminyl-(1->4)-alpha-L-iduronyl-(1->3)-N-acetyl-D-6-sulfogalactosamine = alpha-L-iduronyl-(1->3)-N-acetyl-D-6-sulfogalactosamine + N-acetyl-D-6-sulfogalactosamine Addition of GM2A stimulates the hydrolysis of sulfated glycosphingolipid SM2 and the ganglioside GM2. There are 3 forms of beta-hexosaminidase: hexosaminidase A is an heterodimer composed of one subunit alpha and one subunit beta (chain A and B); hexosaminidase B is an homodimer of two beta subunits (two chains A and B); hexosaminidase S is a homodimer of two alpha subunits (By similarity). The composition of the dimer (isozyme A versus isozyme S) has a significant effect on the substrate specificity of the alpha subunit active site (By similarity). In oocytes, the enzyme is released from cortical granules after fertilization. Belongs to the glycosyl hydrolase 20 family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate. ATP + shikimate = 3-phosphoshikimate + ADP + H(+) Binds 1 Mg(2+) ion per subunit. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 5/7. Monomer. Belongs to the shikimate kinase family. +Acts as a receptor for urokinase plasminogen activator. Plays a role in localizing and promoting plasmin formation. Mediates the proteolysis-independent signal transduction activation effects of U-PA. Monomer (Probable). Interacts (via the UPAR/Ly6 domains) with SRPX2. Interacts with MRC2 (By similarity). Interacts with SORL1 (via N-terminal ectodomain); this interaction decreases PLAUR internalization (By similarity). The ternary complex composed of PLAUR-PLAU-SERPINE1 also interacts with SORL1 (By similarity). Expressed in angiogenic endothelial cells (at protein level). GPI-anchored form. +SbcCD cleaves DNA hairpin structures. These structures can inhibit DNA replication and are intermediates in certain DNA recombination reactions. The complex acts as a 3'->5' double strand exonuclease that can open hairpins. It also has a 5' single-strand endonuclease activity (By similarity). Heterodimer of SbcC and SbcD. Belongs to the SMC family. SbcC subfamily. +Dimethyl sulfoxide (DMSO) reductase catalyzes the reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS) during anaerobic respiration; it can also use trimethylamine N-oxide (TMAO) as terminal electron acceptor. Required for anaerobic respiration on DMSO and TMAO; subunit A is proposed to be catalytically active. a menaquinone + dimethyl sulfide + H2O = a menaquinol + dimethyl sulfoxide Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit. Binds 1 [4Fe-4S] cluster. Probable multiprotein complex that likely consists of DmsA, DmsB and DmsC. By anaerobic conditions. Its expression is under the control of DmsR. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Cells lacking this gene fail to grow under anaerobic conditions using either DMSO or TMAO as terminal electron acceptors. Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. +Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit is responsible for energy coupling to the transport system and for the release of the potassium ions to the cytoplasm. ATP + H2O + K(+)(out) = ADP + H(+) + K(+)(in) + phosphate The system is composed of three essential subunits: KdpA, KdpB and KdpC. Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IA subfamily. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homodimer. Belongs to the ThiC family. +Belongs to the universal ribosomal protein uS2 family. +Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. ATP + CoA + succinate = ADP + phosphate + succinyl-CoA Binds 1 Mg(2+) ion per subunit. Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. Heterotetramer of two alpha and two beta subunits. Belongs to the succinate/malate CoA ligase beta subunit family. +Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly. Belongs to the UreE family. +Belongs to the bacterial ribosomal protein bL34 family. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +Belongs to the major facilitator superfamily. TCR/Tet family. +Together with PML, this tumor suppressor is a major constituent of the PML bodies, a subnuclear organelle involved in a large number of physiological processes including cell growth, differentiation and apoptosis. Functions as a transcriptional coactivator of ETS1 and ETS2. Under certain conditions, it may also act as a corepressor of ETS1 preventing its binding to DNA. Through the regulation of ETS1 it may play a role in angiogenesis, controlling endothelial cell motility and invasion. Through interaction with the MRN complex it may be involved in the regulation of telomeres lengthening. May also regulate TP53-mediated transcription and through CASP8AP2, regulate FAS-mediated apoptosis. May also play a role in infection by viruses through mechanisms that may involve chromatin and/or transcriptional regulation (By similarity). Homodimer. Interacts with members of the HP1 family of nonhistone chromosomal protein, such as CBX5 and CBX3 via the PxVxL motif. Interacts with ETS1; the interaction is direct and modulates ETS1 transcriptional activity. Interacts with the MRN complex which is composed of two heterodimers RAD50/MRE11 associated with a single NBN; recruits the complex to PML-related bodies. Interacts with HIPK2; positively regulates TP53-dependent transcription. Interacts with CASP8AP2; may negatively regulate CASP8AP2 export from the nucleus to the cytoplasm (By similarity). Accumulates in the cytoplasm upon FAS activation. Sumoylated. Sumoylated with SUMO1. Sumoylation depends on a functional nuclear localization signal but is not necessary for nuclear import or nuclear body targeting. Sumoylation may stabilize the interaction with CBX5 (By similarity). Phosphorylated. +Histone chaperone that facilitates histone deposition and histone exchange and removal during nucleosome assembly and disassembly. Interacts with histone H3 (including both histone H3.1 and H3.3) and histone H4. Belongs to the ASF1 family. +Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA) (PubMed:12110301, PubMed:15556614). Also catalyzes the irreversible transamination of several amino acids including cysteine, tyrosine, glutamine, methionine, histidine and phenylalanine (PubMed:15556614). Can use various keto-acids as the amino group acceptor (PubMed:15556614, PubMed:12110301). L-kynurenine + pyruvate = H2O + kynurenate + L-alanine 2-oxoglutarate + L-kynurenine = H2O + kynurenate + L-glutamate glyoxylate + L-kynurenine = glycine + H2O + kynurenate 2-oxobutanoate + L-kynurenine = (2S)-2-aminobutanoate + H2O + kynurenate 2-oxobutanoate + L-cysteine = (2S)-2-aminobutanoate + 2-oxo-3-sulfanylpropanoate 2-oxobutanoate + L-tyrosine = (2S)-2-aminobutanoate + 3-(4-hydroxyphenyl)pyruvate 2-oxobutanoate + L-glutamine = (2S)-2-aminobutanoate + 2-oxoglutaramate 2-oxobutanoate + L-methionine = (2S)-2-aminobutanoate + 4-methylsulfanyl-2-oxobutanoate 2-oxobutanoate + L-histidine = (2S)-2-aminobutanoate + 3-(imidazol-5-yl)pyruvate 2-oxobutanoate + L-phenylalanine = (2S)-2-aminobutanoate + 3-phenylpyruvate indole-3-pyruvate + L-kynurenine = H2O + kynurenate + L-tryptophan 2-oxohexanoate + L-kynurenine = H2O + kynurenate + L-2-aminohexanoate 4-methyl-2-oxopentanoate + L-kynurenine = H2O + kynurenate + L-leucine 2-oxopentanoate + L-kynurenine = H2O + kynurenate + L-2-aminopentanoate L-kynurenine + oxaloacetate = H2O + kynurenate + L-aspartate 3-phenylpyruvate + L-kynurenine = H2O + kynurenate + L-phenylalanine 3-(4-hydroxyphenyl)pyruvate + L-kynurenine = H2O + kynurenate + L-tyrosine Competitive inhibition of L-kynurenine transamination by glutamine, methionine and histidine but not by tyrosine and phenylalanine (PubMed:15556614). Cysteine concentration between 0.31-2.5 mM increases L-kynurenine transamination while concentration above 2.5 mM inhibits L-kynurenine transamination (PubMed:15556614). Keto-acids as amino acceptors modulate the transamination activity toward L-kynurenine (PubMed:15556614). kcat is 206 min(-1) for cysteine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 139 min(-1) for tyrosine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 561 min(-1) for glutamine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 163 min(-1) for methionine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 168 min(-1) for histidine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 283 min(-1) for cysteine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 172 min(-1) for kynurenine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 230 min(-1) for asparagine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 283 min(-1) for tryptophan (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 758 min(-1) for leucine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 345 min(-1) for serine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 1540 min(-1) for alanine (at 45 degrees Celsius, at pH 8.5 and with ketobutyrate as cosubstrate) (PubMed:15556614). kcat is 317 min(-1) for amino-butyrate (at 45 degrees Celsius, at pH 8.5 and with pyruvate as cosubstrate) (PubMed:15556614). Optimum pH is 8.5 and 10 (with pyruvate as cosubstrate). Optimum temperature is 60 degrees Celsius (at pH 8.5 and with pyruvate as cosubstrate). Amino-acid degradation; L-kynurenine degradation; kynurenate from L-kynurenine: step 1/2. Homodimer. Expressed in developing ovaries (PubMed:12110301). Expressed at high levels in the head (PubMed:12110301). Expressed in larvae, pupae and adults (PubMed:12110301). Expressed at low levels in larvae, then expression increases at the beginning of pupal development to reach high expression levels in adults (PubMed:12110301). Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. X-ray structure in 1YIZ has been refined and redeposited in 5VEH. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +Transcriptional activator that regulates the expression of genes involved in symbiosis. Among other targets it acts on the nolWBTUV operon. Belongs to the LysR transcriptional regulatory family. +Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system. The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. Belongs to the TatA/E family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Belongs to the UPF0434 family. +Belongs to the UPF0344 family. +Belongs to the bacterial ribosomal protein bL36 family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Constitutively expressed. Belongs to the IF-1 family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Catalyzes the hydroxylation of the N(6)-(4-aminobutyl)-L-lysine intermediate to form hypusine, an essential post-translational modification only found in mature eIF-5A factor. [eIF5A protein]-deoxyhypusine + AH2 + O2 = [eIF5A protein]-hypusine + A + H2O Binds 2 Fe(2+) ions per subunit. Optimum pH is 7.5. Active from pH 6 to 10. Protein modification; eIF5A hypusination. Present with 39900 molecules/cell in log phase SD medium. Belongs to the deoxyhypusine hydroxylase family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). Belongs to the conotoxin O3 superfamily. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 2 subfamily. +Multifunctional actin-bundling protein. Plays a major role in regulating the organization, dimension, dynamics and signaling capacities of the actin filament-rich microvilli in the mechanosensory and chemosensory cells (PubMed:14657236, PubMed:15190118). Required for the assembly and stabilization of the stereociliary parallel actin bundles. Plays a crucial role in the formation and maintenance of inner ear hair cell stereocilia (PubMed:21455486). Involved in the elongation of actin in stereocilia (PubMed:19287378, PubMed:22264607). In extrastriolar hair cells, required for targeting MYO3B to stereocilia tips, and for regulation of stereocilia diameter and staircase formation (PubMed:26926603). Monomer (Probable). Binds F-actin in a Ca(2+)-resistant fashion (PubMed:10588661). Interacts (via N-terminus) with BAIAP2 (via SH3-domain) (PubMed:12598619). Interacts with PFN2 (PubMed:15190118). Interacts with MYO3A (via C-terminus) (PubMed:26926603). Interacts with MYO3B (via C-terminus) (PubMed:26926603, PubMed:26785147). Isoform 8 localizes to parallel actin bundles of ectoplasmic specializations between neighboring Sertoli cells and at sites where Sertoli cells contact the heads of elongate spermatids. Expressed at high concentration in the microvillar parallel actin bundle (PAB) of hair cells stereocilia in the cochlea and vestibular system. Detected also at high levels of a number of other sensory cell types, including taste receptor cells, solitary chemoreceptor cells, vomeronasal sensory neurons and Merkel cells. Isoforms 2, 3, 4 and 5 are expressed in Purkinje cells dendritic spines. Expressed in utricle hair bundles (at protein level) (PubMed:26926603). The WH2-domain binds actin monomer and mediates actin bundle assembly. Jerker mice have a frameshift mutation that affect the espin C-terminus. This mutation cause deafness, vestibular dysfunction and hair cell degeneration. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +May contribute to protect cells against stress due to ethanol and related compounds. an aldehyde + H2O + NAD(+) = a carboxylate + 2 H(+) + NADH Activated by SigB in response to stress due to ethanol. No effect on vanillin degradation. Belongs to the aldehyde dehydrogenase family. +Part of an ATP-driven transport system for manganese. Belongs to the ABC-3 integral membrane protein family. +Selectively expressed in uterine mast cells. Belongs to the peptidase S1 family. Granzyme subfamily. +Has a post-transcriptional repressor function in flagellum biogenesis. Associates with the 5'-UTR of fljK mRNA and promotes its degradation. Belongs to the FlbT family. +ATP + L-asparagine + tRNA(Asn) = AMP + diphosphate + H(+) + L-asparaginyl-tRNA(Asn) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +Encapsidates the RNA. Belongs to the tospovirus nucleocapsid protein family. +May be involved in a rapid plant ppGpp (guanosine 3'-diphosphate 5'-diphosphate)-mediated response to pathogens and other stresses. ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate Interacts with RPP5. Belongs to the RelA/SpoT family. +Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate. AH2 + GTP + S-adenosyl-L-methionine = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + A + H(+) + L-methionine Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate. Cofactor biosynthesis; molybdopterin biosynthesis. Belongs to the radical SAM superfamily. MoaA family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 2 subfamily. +Probable transcription factor, which may be involved in embryonic patterning (PubMed:14711878). May be required for basal embryo development after fertilization (PubMed:14711878). Acts partially redundantly with STIP in promoting embryonic cell division and proliferation (PubMed:17706632). Promotes cotyledon boundary formation by maintaining the symmetry in CUC genes expression domains (PubMed:22827849). Expressed only in the egg cell (PubMed:21316593). Not detected in the pollen tube (PubMed:21316593). Expressed in the zygote, the basal cell, and later the suspensor (PubMed:21802295). Expressed in all suspensor cells, except the hypophysis, and in the embryo surrounding region (ESR) endosperm cells (PubMed:22427333). Strongly expressed in the suspensor cells, with a weak expression also detected throughout the developing embryo (PubMed:22827849). Detected in the egg cell and the central cell of the embryo sac (PubMed:14711878). After fertilization, it is expressed in the zygote (PubMed:14711878). After the first division of the zygote, it is detected exclusively in the basal daughter cell, while WOX2 is expressed in the apical daughter cell (PubMed:14711878). Through the 16-cell stage, it is expressed in all descendants of the basal daughter, the developing suspensor and the hypophyseal cell (PubMed:14711878). After the hypophysis had divided, expression stops in descendants, but remains present in the extra embryonic suspensor (PubMed:14711878). Moreover it is found in the cellularized endosperm of the micropylar region during the globular and heart stages of embryogenesis (PubMed:14711878). Not expressed later in embryogenesis or in postembryonic stages (PubMed:14711878). Activated in the zygote after fertilization (PubMed:21316593). Up-regulated in the zygote after fertilization by the transcription factor WRKY2 (PubMed:21316593). Up-regulated by CLE8 (PubMed:22427333). No visible phenotype, due to the redundancy with WOX9 (PubMed:17706632). Wox8 and wox9 double mutants are embryo lethal, with embryos disrupted as early as the first cell division in the embryo proper (PubMed:17706632). Belongs to the WUS homeobox family. +Could be involved in insertion of integral membrane proteins into the membrane. Belongs to the UPF0161 family. +Anchors the catalytic components of the fumarate reductase complex to the cell membrane, binds quinones. Part of an enzyme complex containing four subunits: a flavoprotein (FrdA), an iron-sulfur protein (FrdB), and two hydrophobic anchor proteins (FrdC and FrdD). Belongs to the FrdC family. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Picornain 3C-like protease is a thiol protease that probably cleaves the B and M polyproteins. Viral genome-linked protein (VPg) plays a role in RNA replication. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Specific enzymatic cleavages by picornain 3C-like protease in vivo yield mature proteins. Picornain 3C-like protease is autocatalytically processed (By similarity). Viral genome-linked protein (VPg) is uridylylated by the polymerase and is covalently linked to the 5'-end of genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase (By similarity). Belongs to the comoviridae genome polyprotein B family. +Secreted metalloproteinase that allows assimilation of proteinaceous substrates. Binds 1 zinc ion per subunit. Expression is controlled by the prtT transcription factor. Belongs to the peptidase M36 family. +Key component of the 4EHP-GYF2 complex, a multiprotein complex that acts as a repressor of translation initiation. Component of the 4EHP-GYF2 complex (By similarity). Belongs to the GIGYF family. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +Trichothecene 8-O-acetyltransferase; part of 2-gene cluster involved in trichothecene C-8 modification that mediates the biosynthesis of T2-toxin (PubMed:14532047, PubMed:14690377). The biosynthesis of trichothecenes begins with the cyclization of farnesyl diphosphate to trichodiene and is catalyzed by the trichodiene synthase TRI5 (PubMed:3800398). Trichodiene undergoes a series of oxygenations catalyzed by the cytochrome P450 monooxygenase TRI4 (PubMed:7651333). TRI4 controls the addition of four oxygens at C-2, C-3, C-11, and the C-12, C-13-epoxide to form the intermediate isotrichotriol (PubMed:16917519). Isotrichotriol then undergoes a non-enzymatic isomerization and cyclization to form isotrichodermol (PubMed:2317042). During this process, the oxygen at the C-2 position becomes the pyran ring oxygen and the hydroxyl group at C-11 is lost (PubMed:2317042). More complex type A trichothecenes are built by modifying isotrichodermol through a series of paired hydroxylation and acetylation or acylation steps (PubMed:11352533). Isotrichodermol is converted to isotrichodermin by the acetyltransferase TRI101 (PubMed:10583973). TRI101 encodes a C-3 transacetylase that acts as a self-protection or resistance factor during biosynthesis and that the presence of a free C-3 hydroxyl group is a key component of Fusarium trichothecene phytotoxicity (PubMed:10583973). A second hydroxyl group is added to C-15 by the trichothecene C-15 hydroxylase TRI11, producing 15-decalonectrin, which is then acetylated by TRI3, producing calonectrin (PubMed:9435078, PubMed:8593041). A third hydroxyl group is added at C-4 by the cytochrome P450 monooxygenase TRI13, converting calonectrin to 3,15-diacetoxyspirpenol, which is subsequently acetylated bythe acetyltransferase TRI7 (PubMed:12135578, PubMed:11352533). A fourth hydroxyl group is added to C-8 by the cytochrome P450 monooxygenase TRI1, followed by the addition of an isovaleryl moiety by TRI16 (PubMed:12620849, PubMed:14532047). Finally, the acetyl group is removed from the C-3 position by the trichothecene C-3 esterase TRI8 to produce T-2 toxin (PubMed:12039755). Sesquiterpene biosynthesis; trichothecene biosynthesis. Expression is positively regulated by the TRI6 and TRI10 core trichothecenes biosynthesis gene cluster transcription factor (PubMed:12620849). Impairs the production of the three C-8 esterified compounds T-2 toxin, 8-propionyl-neosolaniol (P-NEO) and 8-isobutyryl-neosolaniol (B-NEO), and accumulates the C-8-hydroxylated compound neosolaniol (NEO) along with secondary levels of 4,15-diacetoxyscirpenol (DAS) (PubMed:14532047). Trichothecenes are sesquiterpenoid toxins that act by inhibiting protein biosynthesis. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +Involved in DNA repair and RecF pathway recombination. Belongs to the RecO family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. +Cell division inhibitor that blocks the formation of polar Z ring septums. Rapidly oscillates between the poles of the cell to destabilize FtsZ filaments that have formed before they mature into polar Z rings. Prevents FtsZ polymerization. Interacts with MinD and FtsZ. Belongs to the MinC family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Belongs to the DMRL synthase family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Catalyzes the pyrimidine ring opening between N-3 and C-4 by an unusual flavin hydroperoxide-catalyzed mechanism, adding oxygen atoms in the process to yield ureidoacrylate peracid, that immediately reacts with FMN forming ureidoacrylate and FMN-N(5)-oxide. The FMN-N(5)-oxide reacts spontaneously with NADH to produce FMN. Requires the flavin reductase RutF to regenerate FMN in vivo. FMNH2 + NADH + O2 + uracil = (Z)-3-ureidoacrylate + FMN + H(+) + H2O + NAD(+) FMNH2 + NADH + O2 + thymine = (Z)-2-methylureidoacrylate + FMN + H(+) + H2O + NAD(+) Up-regulated by the nitrogen regulatory protein C (NtrC also called GlnG) and repressed by RutR. Belongs to the NtaA/SnaA/DszA monooxygenase family. RutA subfamily. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Belongs to the UPF0482 family. +Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. 2 D-sedoheptulose 7-phosphate = D-glycero-alpha-D-manno-heptose 7-phosphate + D-glycero-beta-D-manno-heptose 7-phosphate Binds 1 zinc ion per subunit. Carbohydrate biosynthesis; D-glycero-D-manno-heptose 7-phosphate biosynthesis; D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate from sedoheptulose 7-phosphate: step 1/1. Homotetramer. The reaction produces a racemic mixture of D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate. Belongs to the SIS family. GmhA subfamily. +Component of the microprocessor complex that acts as a RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, DGCR8 function as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11 bp away form the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. The heme-bound DGCR8 dimer binds pri-miRNAs as a cooperative trimer (of dimers) and is active in triggering pri-miRNA cleavage, whereas the heme-free DGCR8 monomer binds pri-miRNAs as a dimer and is much less active. Both double-stranded and single-stranded regions of a pri-miRNA are required for its binding. Specifically recognizes and binds N6-methyladenosine (m6A)-containing pri-miRNAs, a modification required for pri-miRNAs processing (By similarity). Involved in the silencing of embryonic stem cell self-renewal (By similarity). Binds 1 heme group per homodimer. Monomer; in absence of heme. Homodimer; the association with heme promotes its dimerization. Component of the microprocessor complex, or pri-miRNA processing protein complex, which is composed of DROSHA and DGCR8. The microprocessor complex is a heterotrimer; each of the two DROSHA RNase III domains binds one DGCR8 (via C-terminal region). Interacts with ILF3, NCL and DROSHA. Interacts with CPSF3 and ISY1; this interaction is in an RNA dependent manner (By similarity). Interacts with PUS10; interaction promotes pri-miRNAs processing. Colocalizes with nucleolin and DROSHA in the nucleolus. Mostly detected in the nucleolus as electron-dense granular patches around the fibrillar center (FC) and granular component (GC). Also detected in the nucleoplasm as small foci adjacent to splicing speckles near the chromatin structure. Localized with DROSHA in GW bodies (GWBs), also known as P-bodies. +Belongs to the bacterial ribosomal protein bL33 family. +Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. [sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Monomer. Belongs to the methylthiotransferase family. MiaB subfamily. +Catalyzes the formation of methylglyoxal from dihydroxyacetone phosphate. dihydroxyacetone phosphate = methylglyoxal + phosphate Belongs to the methylglyoxal synthase family. +Regulates ADAM17 protease, a sheddase of the epidermal growth factor (EGF) receptor ligands and TNF, thereby plays a role in sleep, cell survival, proliferation, migration and inflammation. Does not exhibit any protease activity on its own. Interacts with EGF (PubMed:21439629). Interacts (via cytoplasmic N-terminus) with FRMD8/iTAP; this interaction leads to mutual protein stabilization (PubMed:29897336). Interacts with ADAM17/TACE (By similarity). Belongs to the peptidase S54 family. +CNTF is a survival factor for various neuronal cell types. Seems to prevent the degeneration of motor axons after axotomy. Homodimer. Nervous system. Belongs to the CNTF family. Ciliary neurotrophic factor entry +Can mediate activation of c-Jun and NF-kappa-B. May promote caspase-independent cell death (By similarity). Isoform 2 and isoform 3 may act as decoy receptors. Associates with TRAF1, TRAF2, TRAF3 and TRAF5. Interacts with LINGO1. Highly expressed in adult brain, and in embryos from day 11-17, but not earlier. Detected in embryonic brain and epithelium, and at lower levels in adult heart, lung and liver. In neonatal mice, mainly in hair follicles and neuron-like cells in the cerebellum, but not in the skin epidermis. Isoform 3 was found in embryonic day 17.5 skin but not in brain and liver. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate + H(+) Light regulated via thioredoxin by reversible oxidation/reduction of sulfhydryl/disulfide groups. Carbohydrate biosynthesis; Calvin cycle. Belongs to the phosphoribulokinase family. +The MdtABC tripartite complex confers resistance against novobiocin and deoxycholate. Part of a tripartite efflux system composed of MdtA, MdtB and MdtC. MdtB forms a heteromultimer with MdtC. The mdtABC operon is transcriptionally activated by BaeR. Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family. MdtB subfamily. +Belongs to the major facilitator superfamily. +Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. glutathione + RX = a halide anion + an S-substituted glutathione + H(+) Homodimer. The N-terminus is blocked. On the basis of immunological and kinetics data, GST 5.7 is distinct from alpha, mu and pI classes of GTS. However it has been postulated that this protein may be part of a distinct subgroup within this alpha class. The variations were found from AA sequencing and imply there are multiple forms of this protein. These variations are likely to be sex-linked and tissue specific. Belongs to the GST superfamily. Alpha family. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine. L-leucyl-tRNA(Leu) + N-terminal L-lysyl-[protein] = H(+) + N-terminal L-leucyl-L-lysyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-arginyl-[protein] = H(+) + N-terminal L-leucyl-L-arginyl-[protein] + tRNA(Leu) an N-terminal L-alpha-aminoacyl-[protein] + L-phenylalanyl-tRNA(Phe) = an N-terminal L-phenylalanyl-L-alpha-aminoacyl-[protein] + tRNA(Phe) Belongs to the L/F-transferase family. +Belongs to the bacterial ribosomal protein bL34 family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Plays a crucial role in the structural integrity of mitotic centrosomes and in the maintenance of spindle bipolarity by promoting PLK1 activity at the spindle poles in early mitosis. May function as a scaffold promoting the interaction between AURKA and PLK1, thereby enhancing AURKA-mediated PLK1 phosphorylation. When phosphorylated by CDK1, interacts with PLK1; this interaction occurs in mitotic cells, but not in interphase cells, and leads to further FRY phosphorylation by PLK1. Distributed diffusely throughout the cytoplasm in interphase. Localizes to the separating centrosomes in prophase, to the spindle poles and spindle microtubules in prometaphase to metaphase, to spindle microtubules in anaphase and to the distal sections of the midbody in cytokinesis. Colocalizes with PLK1 to separating centrosomes and spindle poles from prophase to metaphase in mitosis, but not in other stages of the cell cycle (By similarity). Phosphorylated by AURKA, CDK1 and PLK1. May be due to an intron retention. Belongs to the furry protein family. Truncated N-terminus. +Probable lipolytic acyl hydrolase (LAH), an activity which is thought to be involved in the response of tubers to pathogens. Tuber. Accumulates progressively during tuber formation from stolon. The nitrogen atoms of the two glycine residues in the GGXR motif define the oxyanion hole, and stabilize the oxyanion that forms during the nucleophilic attack by the catalytic serine during substrate cleavage. Patatin have a dual role as a somatic storage protein and as an enzyme involved in host resistance. Belongs to the patatin family. +(6S)-5,6,7,8-tetrahydrofolate + ATP + formate = (6S)-10-formyltetrahydrofolate + ADP + phosphate One-carbon metabolism; tetrahydrofolate interconversion. Belongs to the formate--tetrahydrofolate ligase family. +NDH-1 shuttles electrons from an unknown electron donor, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH-1 can be composed of about 15 different subunits; different subcomplexes with different compositions have been identified which probably have different functions. Belongs to the complex I NdhO subunit family. +Prevents the establishment of the cellular antiviral state by inhibiting TRIM25-mediated DDX58 ubiquitination, which normally triggers the antiviral transduction signal that leads to the activation of type I IFN genes by transcription factors IRF3 and IRF7. Prevents human EIF2AK2/PKR activation, either by binding double-strand RNA, or by interacting directly with EIF2AK2/PKR. This function may be important at the very beginning of the infection, when NS1 is mainly present in the cytoplasm. Also binds poly(A) and U6 snRNA. Inhibits post-transcriptional processing of cellular pre-mRNA, by binding and inhibiting two cellular proteins that are required for the 3'-end processing of cellular pre-mRNAs: the 30 kDa cleavage and polyadenylation specificity factor/CPSF4 and the poly(A)-binding protein 2/PABPN1. In turn, unprocessed 3' end pre-mRNAs accumulate in the host nucleus and are no longer exported to the cytoplasm. Cellular protein synthesis is thereby shut off very early after virus infection. Viral protein synthesis is not affected by the inhibition of the cellular 3' end processing machinery because the poly(A) tails of viral mRNAs are produced by the viral polymerase through a stuttering mechanism. Homodimer. Interacts with host TRIM25 (via coiled coil); this interaction specifically inhibits TRIM25 multimerization and TRIM25-mediated DDX58 CARD ubiquitination. Interacts with human EIF2AK2/PKR, CPSF4, IVNS1ABP and PABPN1. In uninfected, transfected cells, NS1 is localized in the nucleus. Only in virus infected cells, the nuclear export signal is unveiled, presumably by a viral protein, and a fraction of NS1 is exported in the cytoplasm. The dsRNA-binding region is required for suppression of RNA silencing. Upon interferon induction, ISGylated via host HERC5; this results in the impairment of NS1 interaction with RNA targets due to its inability to form homodimers and to interact with host EIF2AK2/PKR. Belongs to the influenza A viruses NS1 family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 2/4. Belongs to the GPI family. +Elementary body. Belongs to the PMP outer membrane protein family. +[thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(R)-S-oxide-[protein] Binds 1 zinc ion per subunit. The zinc ion is important for the structural integrity of the protein. Belongs to the MsrB Met sulfoxide reductase family. +Disulfide cross-linked either to itself or to CotZ. Outer coat. To B.subtilis CotZ. +Blocks contraction of smooth muscle elicited by high potassium-induced depolarization (PubMed:12047379). May target voltage-gated calcium channels (Cav) on smooth muscle. Forms a stable, non-covalent complex with SSP-2. Expressed by the venom gland. Belongs to the CRISP family. +Belongs to the DNA2/NAM7 helicase family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Belongs to the cytochrome P450 family. The gene for this protein is duplicated in strains AX3 and AX4. These strains contain a duplication of a segment of 750 kb of chromosome 2 compared to the corresponding sequence in strain AX2. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. Interacts with UvrB in an incision complex. Belongs to the UvrC family. +Chaperone that interacts with the histone acetyltransferase HAT1 and mediates its translocation from the nucleus to the cytoplasm during germination and starvation conditions. Within the cytoplasm, HAT1 regulates autophagy via acetylation of the autophagy-related proteins ATG3 and ATG9. ATP + H2O = ADP + H(+) + phosphate Interacts with HAT1 in starvation conditions. Impairs the translocation of HAT1 from the nucleus to the cytoplasm upon starvation. Belongs to the heat shock protein 70 family. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily. +Expressed by the parotoid glands. +Envelope glycoprotein that forms spikes at the surface of virion envelope. Essential for the initial attachment to heparan sulfate moieties of the host cell surface proteoglycans. Involved in fusion of viral and cellular membranes leading to virus entry into the host cell. Following initial binding to its host receptors, membrane fusion is mediated by the fusion machinery composed at least of gB and the heterodimer gH/gL. May be involved in the fusion between the virion envelope and the outer nuclear membrane during virion egress. Homotrimer; disulfide-linked. Binds to heparan sulfate proteoglycans. Interacts with gH/gL heterodimer (By similarity). Interacts with gE. During virion morphogenesis, this protein probably accumulates in the endosomes and trans-Golgi where secondary envelopment occurs. It is probably transported to the cell surface from where it is endocytosed and directed to the trans-Golgi network (TGN). A proteolytic cleavage by host furin generates two subunits that remain linked by disulfide bonds. Belongs to the herpesviridae glycoprotein B family. +May play an important role in promoting lung pathology in both primary viral infection and secondary bacterial infection. Is not encoded in all strains, and seems to be dispensable for replication. Belongs to the influenza viruses PB1-F2 family. +Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Heterohexamer, formed by a dimer of trimers. The hexameric TusBCD complex contains 2 copies each of TusB, TusC and TusD. The TusBCD complex interacts with TusE. Belongs to the DsrH/TusB family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways. AMP + ATP = 2 ADP Monomer. Predominantly mitochondrial. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. AK2 subfamily. +Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins. Belongs to the glycosyl hydrolase 22 family. +Functions as 15-oxo-prostaglandin 13-reductase and acts on 15-keto-PGE1, 15-keto-PGE2, 15-keto-PGE1-alpha and 15-keto-PGE2-alpha with highest activity towards 15-keto-PGE2. Overexpression represses transcriptional activity of PPARG and inhibits adipocyte differentiation. 13,14-dihydro-15-oxo-prostaglandin E2 + NAD(+) = 15-oxoprostaglandin E2 + H(+) + NADH 13,14-dihydro-15-oxo-prostaglandin E2 + NADP(+) = 15-oxoprostaglandin E2 + H(+) + NADPH 13,14-dihydro-15-oxo-PGF2alpha + NADP(+) = 15-oxoprostaglandin F2alpha + H(+) + NADPH 13,14-dihydro-15-oxo-prostaglandin E1 + NADP(+) = 15-oxoprostaglandin E1 + H(+) + NADPH 13,14-dihydro-15-oxo-prostaglandin F1alpha + NADP(+) = 15-oxoprostaglandin F1alpha + H(+) + NADPH Monomer. Belongs to the NADP-dependent oxidoreductase L4BD family. +Plays a central role in ribosomal RNA processing. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Pseudouridine ('psi') residues may serve to stabilize the conformation of rRNAs (By similarity). a uridine in RNA = a pseudouridine in RNA Component of the small nucleolar ribonucleoprotein particles containing H/ACA-type snoRNAs (H/ACA snoRNPs). Belongs to the pseudouridine synthase TruB family. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). H2O + O2 + pyridoxamine 5'-phosphate = H2O2 + NH4(+) + pyridoxal 5'-phosphate O2 + pyridoxine 5'-phosphate = H2O2 + pyridoxal 5'-phosphate Binds 1 FMN per subunit. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1. Homodimer. Belongs to the pyridoxamine 5'-phosphate oxidase family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Present with 158000 molecules/cell in log phase SD medium. Belongs to the class-I aminoacyl-tRNA synthetase family. +With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS12 family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +May play a role in the modulation of host immune response. Belongs to the influenza viruses PA-X family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccA family. +Binds to oleoyl-L-alpha-lysophosphatidic acid (LPA). Intracellular cAMP is involved in the receptor activation. Important for the maintenance of hair growth and texture (By similarity). Belongs to the G-protein coupled receptor 1 family. +Transcriptional regulator essential for Nod-factor-induced gene expression (PubMed:15961669). Acts downstream of calcium spiking (PubMed:15961669). May be a target of DMI3, a calcium/calmodulin-dependent protein kinase (CCaMK) (PubMed:15961669). Is essential for Nod factor-elicited expression of ERN1 (PubMed:23077241). Transcription factor involved in the control of strigolactone biosynthesis in roots through the activation of the beta-carotene isomerase D27, which participates in a pathway leading to biosynthesis of strigolactones (PubMed:22039214, PubMed:26503135). Expressed in epidermal and cortical root cells. Not induced after treatment with Sinorhizobium meliloti. Belongs to the GRAS family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Belongs to the RRP7 family. Could be the product of a pseudogene. +Involved in the foliar biosynthesis of vindoline, a precursor of vinblastine and vincristine (PubMed:24108213). Hydroxylates specifically tabersonine, 2,3-dihydrotabersonine and 2,3-dihydro-3-hydroxytabersonine, but has no activity with naringenin, tryptamine, secologanin, strictosidine, ajmalicine, vindoline and catharanthine (PubMed:24108213). (-)-tabersonine + O2 + reduced [NADPH--hemoprotein reductase] = 16-hydroxytabersonine + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Expressed at low levels in roots, fruits, stems, flower buds and flowers, but highly expressed in young leaves. Detected in adaxial and abaxial epidermis cells. Not regulated by methyl jasmonate treatment. Tabersonine 16-hydroxylation is orchestrated in an organ-dependent manner by two genes including CYP71D351, which encodes the T16H2 isoform acting in the foliar vindoline biosynthesis, and CYP71D12, which encodes the T16H1 isoform acting in the flower vindoline biosynthesis. Belongs to the cytochrome P450 family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Essential cell division protein. Localizes to the division septum where it forms a ring structure. Belongs to the FtsL family. +ABC1 family protein; part of the gene cluster that mediates the biosynthesis of the lipopeptide antibiotics leucinostatins that show extensive biological activities, including antimalarial, antiviral, antibacterial, antifungal, and antitumor activities, as well as phytotoxic (PubMed:27416025). The function of lcsO within the leucinostatins biosynthesis has not been identified yet (Probable). Expression is positively regulated by the leucinostatins biosynthesis cluster-specific transcription regulator lcsF. Belongs to the protein kinase superfamily. ADCK protein kinase family. +Converts GTP to 7,8-dihydroneopterin triphosphate. GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Belongs to the GTP cyclohydrolase IV family. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate, the first intermediate in the biosynthesis of coenzyme methanopterin. GTP + H2O = 7,8-dihydroneopterin 2',3'-cyclic phosphate + diphosphate + formate + H(+) Binds 1 Fe(2+) ion per subunit. Cofactor biosynthesis; 5,6,7,8-tetrahydromethanopterin biosynthesis. Homodimer. Belongs to the GTP cyclohydrolase IV family. +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Belongs to the urease beta subunit family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 4L family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site. Although the small subunit is not catalytic it is essential for maximal activity. Heterohexadecamer of 8 large and 8 small subunits. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO small chain family. +Murein-degrading enzyme. May play a role in recycling of muropeptides during cell elongation and/or cell division. Exolytic cleavage of the (1->4)-beta-glycosidic linkage between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues in peptidoglycan, from either the reducing or the non-reducing ends of the peptidoglycan chains, with concomitant formation of a 1,6-anhydrobond in the MurNAc residue. Belongs to the transglycosylase Slt family. +Orphan G-protein coupled receptor. Belongs to the G-protein coupled receptor 1 family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Component of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis and may function in phospholipid exchange. MDM10 is involved in the late assembly steps of the general translocase of the mitochondrial outer membrane (TOM complex). Functions in the TOM40-specific route of the assembly of outer membrane beta-barrel proteins, including the association of TOM40 with the receptor TOM22 and small TOM proteins. Can associate with the SAM(core) complex as well as the MDM12-MMM1 complex, both involved in late steps of the major beta-barrel assembly pathway, that is responsible for biogenesis of all outer membrane beta-barrel proteins. May act as a switch that shuttles between both complexes and channels precursor proteins into the TOM40-specific pathway. Plays a role in mitochondrial morphology and in the inheritance of mitochondria. Component of the ER-mitochondria encounter structure (ERMES) or MDM complex, composed of MMM1, MDM10, MDM12 and MDM34. Associates with the mitochondrial outer membrane sorting assembly machinery SAM(core) complex. The ERMES/MDM complex localizes to a few discrete foci (around 10 per single cell), that represent mitochondria-endoplasmic reticulum junctions. These foci are often found next to mtDNA nucleoids. Lacks alpha-helical transmembrane segments, suggesting that it resides in the membrane via beta-sheet conformations similar to those predicted for other outer membrane proteins and porin. Belongs to the MDM10 family. +The subtype gamma methyltransferase (M) subunit of a type I restriction enzyme. The M and S subunits together form a methyltransferase (MTase) that methylates two adenine residues of the sequence 5'-GAGN(6)GTRC-3'. In the presence of the R subunit the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance MTase modifying the DNA so that both strands become methylated. After locating a non-methylated recognition site, the enzyme complex serves as a molecular motor that translocates DNA in an ATP-dependent manner until a collision occurs that triggers cleavage. a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an N(6)-methyl-2'-deoxyadenosine in DNA + H(+) + S-adenosyl-L-homocysteine The type I restriction/modification system is composed of three polypeptides R, M and S; the restriction enzyme has stoichiometry R(2)M(2)S(1) while the methyltransferase is M(2)S(1). Type I restriction and modification enzymes are complex, multifunctional systems which require ATP, S-adenosyl methionine and Mg(2+) as cofactors and, in addition to their endonucleolytic and methylase activities, are potent DNA-dependent ATPases. Belongs to the N(4)/N(6)-methyltransferase family. +With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits (By similarity). Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS12 family. +Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). 5,6-dimethylbenzimidazole + nicotinate beta-D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate Nucleoside biosynthesis; alpha-ribazole biosynthesis; alpha-ribazole from 5,6-dimethylbenzimidazole: step 1/2. Belongs to the CobT family. +Transcription factor that binds specifically to the DRE (dual repressor element) and represses HTR1A gene transcription in neuronal cells. Widely distributed in brain and peripheral tissues. Belongs to the CC2D1 family. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the radical SAM superfamily. Lipoyl synthase family. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +Belongs to the bacterial ribosomal protein bL27 family. +Purine salvage pathway enzyme that catalyzes the transfer of the ribosyl-5-phosphate group from 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to the N9 position of the 6-oxopurines guanine and xanthine to form the corresponding ribonucleotides GMP (guanosine 5'-monophosphate) and XMP (xanthosine 5'-monophosphate), with the release of PPi. To a lesser extent, also acts on hypoxanthine. diphosphate + GMP = 5-phospho-alpha-D-ribose 1-diphosphate + guanine diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine diphosphate + IMP = 5-phospho-alpha-D-ribose 1-diphosphate + hypoxanthine Purine metabolism; GMP biosynthesis via salvage pathway; GMP from guanine: step 1/1. Purine metabolism; XMP biosynthesis via salvage pathway; XMP from xanthine: step 1/1. Homotetramer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. XGPT subfamily. +Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate. 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = H(+) + 2 H2O + phosphate + pyridoxine 5'-phosphate Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. Homooctamer; tetramer of dimers. Belongs to the PNP synthase family. +Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Belongs to the thiamine-phosphate synthase family. +Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. (2E,6E,10E)-geranylgeranyl diphosphate + sn-glycerol 1-phosphate = diphosphate + sn-3-O-(geranylgeranyl)glycerol 1-phosphate Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the GGGP/HepGP synthase family. Group II subfamily. +Post-transcriptional repressor of mRNAs containing a conserved stem loop motif, called constitutive decay element (CDE), which is often located in the 3'-UTR, as in HMGXB3, ICOS, IER3, NFKBID, NFKBIZ, PPP1R10, TNF and in many more mRNAs. Binds to CDE and promotes mRNA deadenylation and degradation. This process does not involve miRNAs (PubMed:23663784). In follicular helper T (Tfh) cells, represses of ICOS and TNFRSF4 expression, thus preventing spontaneous Tfh cell differentiation, germinal center B-cell differentiation in the absence of immunization and autoimmunity. In resting or LPS-stimulated macrophages, controls inflammation by suppressing TNF expression. Also recognizes CDE in its own mRNA and in that of paralogous RC3H1, possibly leading to feedback loop regulation (PubMed:23583643, PubMed:23583642). Inhibits cooperatively with ZC3H12A the differentiation of helper T cells Th17 in lungs. They repress target mRNA encoding the Th17 cell-promoting factors IL6, ICOS, REL, IRF4, NFKBID and NFKBIZ. The cooperation requires RNA-binding by RC3H1 and the nuclease activity of ZC3H12A (PubMed:25282160). miRNA-binding protein that regulates microRNA homeostasis. Enhances DICER-mediated processing of pre-MIR146a but reduces mature MIR146a levels through an increase of 3' end uridylation. Both inhibits ICOS mRNA expression and they may act together to exert the suppression (PubMed:25697406). Acts as a ubiquitin E3 ligase. Pairs with E2 enzymes UBE2B, UBE2D2, UBE2E2, UBE2E3, UBE2G2, UBE2K and UBE2Q2 and produces polyubiquitin chains. Shows the strongest activity when paired with UBE2N:UBE2V1 or UBE2N:UBE2V2 E2 complexes and generate both short and long polyubiquitin chains. Involved in the ubiquitination of MAP3K5 (By similarity). Able to interact with double-stranded RNA (dsRNA). S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Binding to dsRNA, but not CDE RNA, crosstalks with the E3 ubiquitin ligase activity and may inhibit ubiquitination. Protein modification; protein ubiquitination. Interacts with EDC4 (PubMed:23583643). Interacts with CCR4-NOT deadenylase complex (PubMed:23663784). Interacts with MAP3K5; the interaction is probably stimulus-dependent (By similarity). During stress, such as that induced by arsenite, localizes to cytosolic stress granules. Localization to stress granules, but not to P-bodies, depends upon the RING-type zinc finger. Highest levels in lymph node and thymus and slightly lesser amounts in brain, lung, and spleen (at protein level). Very weak expression in heart, muscle, and kidney (at protein level). Expressed in CD4(+) helper T-cells (at protein level). The RING-type zinc finger is required for proper localization to stress granules, but not to P-bodies. The ROQ region is required for CDE RNA-binding. Has 2 separate RNA-binding sites, one for CDE RNA and the other for dsRNA (PubMed:23663784). It may also be involved in localization to stress granules (By similarity). HEPN (higher eukaryotes and prokaryotes nucleotide-binding) are observed in both N- and C-terminal sides of ROQ domain with 3D structure even if they are poredcted on the basis of sequence. Proteolytically cleaved by MALT1 in activated CD4(+) T cells; cleavage at Arg-509 is critical for promoting RC3H1 degradation in response to T-cell receptor (TCR) stimulation, and hence is necessary for prolonging the stability of a set of mRNAs controlling Th17 cell differentiation. Mutant animals are born at Mendelian ratio, but very few reach adulthood, a large proportion die within the first days after birth. Lethality can be rescued by changing the genetic background from C57BL/6 to outbred NMRI, on which mutant animals appear healthy and fertile, although smaller. Immune cell homeostasis is normal (PubMed:23583643). However, Mice lacking both Rc3h1 and Rc3h2 genes in CD4(+) T-cells develop lymphadenopathy and splenomegaly with increased spleen weight and cellularity, already at young age. They show a prominent lung pathology with a progressive reduction in the alveolar space concomitant with inflammation. They show an average survival of 130 days. CD4(+) T-cells of these mutants show a pronounced bias toward Th17 differentiation (PubMed:23583643, PubMed:25282160). +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a 'molecular matchmaker', a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex. Belongs to the DNA mismatch repair MutL/HexB family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +Catalyzes the deamination of dCTP to dUTP. dCTP + H(+) + H2O = dUTP + NH4(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 1/2. Homotrimer. Belongs to the dCTP deaminase family. +Catalyzes the ATP-dependent phosphorylation of L-homoserine to L-homoserine phosphate. ATP + L-homoserine = ADP + H(+) + O-phospho-L-homoserine Amino-acid biosynthesis; L-threonine biosynthesis; L-threonine from L-aspartate: step 4/5. Belongs to the GHMP kinase family. Homoserine kinase subfamily. +Catalyzes the synthesis of Und-PP-GlcNAc-ManNAcA-Fuc4NAc (Lipid III), the third lipid-linked intermediate involved in ECA synthesis. beta-D-ManNAcA-(1->4)-alpha-D-GlcNAc-di-trans,octa-cis-undecaprenyl diphosphate + dTDP-4-acetamido-4,6-dideoxy-alpha-D-galactose = alpha-D-FucNAc4-(1->4)-beta-D-ManNAcA-(1->4)-D-GlcNAc-undecaprenyl diphosphate + dTDP + H(+) Bacterial outer membrane biogenesis; enterobacterial common antigen biosynthesis. Belongs to the glycosyltransferase 56 family. +Hydrolyzes indole-3-acetamide (IAM) into indole-3-acetic acid (IAA). Plant hormone metabolism; auxin biosynthesis. Belongs to the amidase family. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. +Function in general translation initiation by promoting the binding of the formylmethionine-tRNA to ribosomes. Seems to function along with eIF-2. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +Belongs to the UPF0758 family. YicR subfamily. +DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit is less well bound than the others. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Part of the 13-subunit RNA polymerase complex. Forms a stalk with Rpo7 that extends from the main structure. Belongs to the eukaryotic RPB4 RNA polymerase subunit family. +Involved in specifying the paraxial, but not dorsal, mesoderm. May regulate the expression of T-box transcription factors required for mesoderm formation and differentiation (By similarity). Coexpression of ntl and spt is required for expression. Expression is first detected in the marginal zone of the blastoderm. Expression becomes more apparent at the germ-ring stage. In the early gastrula, expressed only in hypoblast cells of the germ ring. At mid-gastrula stage, expressed in ventrolateral mesoderm and is subsequently restricted to the segmental plate at late gastrula stage. At the segmentation period, expressed in the presomitic mesoderm including the tailbud. Expression is also detected in the adaxial cells in the vicinity of the presomitic mesoderm. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +Catalyzes the phosphorylation of adenosine 5'-phosphosulfate to 3'-phosphoadenylyl sulfate, which is the activated sulfate form for sulfation reactions. Essential for plant reproduction and viability. adenosine 5'-phosphosulfate + ATP = 3'-phosphoadenylyl sulfate + ADP + H(+) Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 2/3. Homodimer; disulfide-linked. Expressed in root vasculature, root tips, leaf epidermal and guard cells, pollen grains and radicle of immature seeds. No visible phenotype under normal growth conditions. Belongs to the APS kinase family. Truncated N-terminus. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of the DREAM complex (By similarity). Binds directly to histone H4, probably via helix 1 of the histone fold, a region that is not accessible when histone H4 is in chromatin (PubMed:10454532). Probably forms a large corepressor complex that contains ncor1, sin3a, hdac1-A and/or hdac1-B, hdac2, rbbp4-A and/or rbbp4-B and possibly rbbp7 (PubMed:11254656). Belongs to the WD repeat RBAP46/RBAP48/MSI1 family. +Snake venom phospholipase A2 (PLA2) homolog that lacks enzymatic activity (PubMed:7660366). Is myotoxic and displays edema-inducing activities (PubMed:7660366). Induces neuromuscular blockage (PubMed:26192963). A model of myotoxic mechanism has been proposed: an apo Lys49-PLA2 is activated by the entrance of a hydrophobic molecule (e.g. fatty acid) at the hydrophobic channel of the protein leading to a reorientation of a monomer (By similarity). This reorientation causes a transition between 'inactive' to 'active' states, causing alignment of C-terminal and membrane-docking sites (MDoS) side-by-side and putting the membrane-disruption sites (MDiS) in the same plane, exposed to solvent and in a symmetric position for both monomers (By similarity). The MDoS region stabilizes the toxin on membrane by the interaction of charged residues with phospholipid head groups (By similarity). Subsequently, the MDiS region destabilizes the membrane with penetration of hydrophobic residues (By similarity). This insertion causes a disorganization of the membrane, allowing an uncontrolled influx of ions (i.e. calcium and sodium), and eventually triggering irreversible intracellular alterations and cell death (By similarity). Rosmarinic acid inhibits the myotoxic activity (PubMed:22205953). Bromophenacyl bromide (BPB) inhibits the myotoxic activity through a covalent binding (PubMed:19616648). Caffeic acid and aristolochic acid, two plant compounds used in folk medicine used to treat envenomation, inhibit the myotoxic activity (PubMed:26192963). Homodimer; non-covalently linked. Expressed by the venom gland. LD(50) is 8 mg/kg by intraperitoneal injection into mice. Belongs to the phospholipase A2 family. Group II subfamily. K49 sub-subfamily. Does not bind calcium as one of the calcium-binding sites is lost (Asp->Lys in position 48, which corresponds to 'Lys-49' in the current nomenclature). +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreA releases sequences of 2 to 3 nucleotides. Belongs to the GreA/GreB family. +Belongs to the asfivirus MGF 110 family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Involved in the biosynthesis of the dTDP-L-rhamnose which is an important component of lipopolysaccharide (LPS). Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well. dTDP-beta-L-rhamnose + NADP(+) = dTDP-4-dehydro-beta-L-rhamnose + H(+) + NADPH Binds 1 Mg(2+) ion per monomer. Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis. Homodimer. Belongs to the dTDP-4-dehydrorhamnose reductase family. +Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell. Belongs to the MinE family. +a quinone + H(+) + NADH = a quinol + NAD(+) a quinone + H(+) + NADPH = a quinol + NADP(+) Binds 1 FMN per monomer. Belongs to the WrbA family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Catalyzes the hydration of fosfomycin. Homodimer. Belongs to the fosfomycin resistance protein family. +Specifically methylates the cytosine at position 1962 (m5C1962) of 23S rRNA. cytidine(1962) in 23S rRNA + S-adenosyl-L-methionine = 5-methylcytidine(1962) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RlmI family. +Catalyzes an oxidative deamination of predominantly hydrophobic and aromatic L-amino acids, thus producing hydrogen peroxide that may contribute to the toxicity of the venom (PubMed:17320169). Shows very high activity on L-Met, and L-Leu, high activity on L-Ile, L-Phe and L-Tyr and moderate activity on L-His, L-Val and L-Ala (PubMed:17320169, PubMed:30534149). Exhibits diverse biological activities, such as edema, apoptosis of tumor cell lines, antibacterial activities against both Gram-positive and Gram-negative bacteria, as well as induction of platelet aggregation. Effects of snake L-amino oxidases on platelets are controversial, since they either induce aggregation or inhibit agonist-induced aggregation. These different effects are probably due to different experimental conditions. Unlike other snake venom L-amino acid oxidases, does not induce hemorrhage. It may also induce hemolysis. Has parasiticidal activities against and leishmania, as a result of enzyme-catalyzed hydrogen peroxide production (PubMed:11162565, PubMed:17292326). an L-alpha-amino acid + H2O + O2 = a 2-oxocarboxylate + H2O2 + NH4(+) H2O + L-leucine + O2 = 4-methyl-2-oxopentanoate + H2O2 + NH4(+) H2O + L-phenylalanine + O2 = 3-phenylpyruvate + H2O2 + NH4(+) H2O + L-tryptophan + O2 = H2O2 + indole-3-pyruvate + NH4(+) H2O + L-methionine + O2 = 4-methylsulfanyl-2-oxobutanoate + H2O2 + NH4(+) H2O + L-isoleucine + O2 = (S)-3-methyl-2-oxopentanoate + H2O2 + NH4(+) H2O + L-histidine + O2 = 3-(imidazol-5-yl)pyruvate + H2O2 + NH4(+) H2O + L-tyrosine + O2 = 3-(4-hydroxyphenyl)pyruvate + H2O2 + NH4(+) H2O + L-alanine + O2 = H2O2 + NH4(+) + pyruvate H2O + L-valine + O2 = 3-methyl-2-oxobutanoate + H2O2 + NH4(+) Its enzymatic activities is reduced when it is exposed to Ca(2+), Zn(2+), Al(3+), Cu(2+) or Ni(2+) salts. Optimum pH is 5.5-9.5. Optimum temperature depends on the study: 5-38 degrees Celsius (PubMed:17320169) and 60 degrees Celsius (PubMed:30534149). Homodimer; non-covalently linked. Expressed by the venom gland. N-glycosylated (Probable). The enzymatic activity is not affected by deglycosylation (PubMed:17320169). Shows low or absent catalytic activity on L-Arg, L-Glu, L-Asp, L-Lys, L-Asn, L-Ser, L-Thr, L-Pro, L-Gln, L-Gly, and L-Cys (PubMed:17320169, PubMed:30534149). catalytic activity on L-Val and L-Ala is moderate or low, depending on the study (PubMed:17320169, PubMed:30534149). Belongs to the flavin monoamine oxidase family. FIG1 subfamily. +Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Involved in pre-mRNA splicing. Associated with the spliceosome. Belongs to the CWC15 family. +Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. A number of isoforms are produced. According to EST sequences. Belongs to the glycosyl hydrolase 35 family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Hemoglobin epsilon chain is a beta-type chain found in early embryos. Red blood cells. Belongs to the globin family. +Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. Extensively phosphorylated on serine residues in the RS domain. Belongs to the splicing factor SR family. +Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins. Interacts with the Sec translocase complex via SecD. Specifically interacts with transmembrane segments of nascent integral membrane proteins during membrane integration. Belongs to the OXA1/ALB3/YidC family. Type 1 subfamily. +Belongs to the BUD31 (G10) family. +May function as a regulator of both motility- and head-associated functions such as capacitation and the acrosome reaction. Interacts with ROPN1 AND ROPN1L. Interacts with QRICH2 (By similarity). Ribs of the fibrous sheath in the principal piece of the sperm tail. Dorsal margin of the acrosomal segment. RII-binding site, predicted to form an amphipathic helix, could participate in protein-protein interactions with a complementary surface on the R-subunit dimer. Phosphorylated on tyrosine. Belongs to the AKAP110 family. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. WNK subfamily. Was named WNK/'with no lysine(K)' because key residues for catalysis, including the lysine involved in ATP binding, are either not conserved or differ compared to the residues described in other kinase family proteins. +Promotes CCP110 ubiquitination and proteasome-dependent degradation. By counteracting accumulation of CP110, maintains normal centriolar homeostasis and preventing formation of ectopic microtubular organizing centers. Interacts with CCP110; this interaction propmotes CCP110 ubiquitination and degradation via the proteasome pathway. Via its interaction with CCP110, may indirectly interact with CEP97. Interacts with the E3 ubiquitin-protein ligase HERC2 and UBE3A. May interact with MAPK6 and hence mediate MAPK6 interaction with UBE3A. Interaction with UBE3A may be indirect and mediated by HERC2. Localizes to procentriole and daughter centriole in growing and quiescent cells (PubMed:22441691). May loose association with centrosomes during mitosis (PubMed:22261722). Widely expressed at high levels (including brain). The third NHR domain (NHR 3) is required for localization to both mother and daughter centrioles. NHR 1 restricts targeting to daughter centriole (PubMed:22441691). NHR 3 and 4 are required for CCP110/CEP97-binding, but not for HERC2-binding. NHR 5 and 6 are important for HERC2-binding and centrosomal localization (PubMed:22261722). Ubiquitinated; undergoes HERC2-dependent 'Lys-48' ubiquitination. This ubiquitination leads to proteasomal degradation. Extended N-terminus. +Cytochrome P450 monooxygenase; part of the gene cluster that mediates the biosynthesis of the indole diterpenes nodulisporic acids (NA). Nodulisporic acid A (NAA) and its chemically modified derivatives are of particular significance because of their highly potent insecticidal activity against blood-feeding arthropods and lack of observable adverse effects on mammals, in particular the tremogenicity associated with the paspaline-derived IDTs is not observed (PubMed:29283570). The geranylgeranyl diphosphate (GGPP) synthase ggs1, localized outside of the cluster, is proposed to catalyze the first step in nodulisporic acid biosynthesis via conversion of farnesyl pyrophosphate and isopentyl pyrophosphate into geranylgeranyl pyrophosphate (GGPP) (PubMed:29283570). Condensation of indole-3-glycerol phosphate with GGPP by the prenyl transferase nodC then forms 3-geranylgeranylindole (3-GGI) (PubMed:29283570). Epoxidation by the FAD-dependent monooxygenase nodM leads to a single-epoxidized-GGI that is substrate of the terpene cyclase nodB for cyclization to yield emindole SB (PubMed:29283570). The terminal methyl carbon, C28, of emindole SB is then oxidized by the cytochrome P450 monooxygenase nodW to produce nodulisporic acid F (NAF), the pentacyclic core of NAA (PubMed:29283570). NAF is converted to nodulisporic acid E (NAE) via prenylation. This step is probably performed by one of the indole diterpene prenyltransferases nodD1 or nodD2 (Probable). Several oxidation steps performed by the FAD-linked oxidoreductase nodO and one of the cytochrome P450 monooxygenase nodR, nodX or nodZ further convert NAE to nodulisporic acid D (NAD) (Probable). NAD is substrate of cytochrome P450 monooxygenase nodJ to produce the precursor of nodulisporic acid C (NAC), converted to NAC by one of the indole diterpene prenyltransferases nodD1 or nodD2 (Probable). The FAD-dependent monooxygenase nodY2 then oxidizes NAC to nodulisporic acid B (NAB) (Probable). Finally NAB is converted to NAA by one of the cytochrome P450 monooxygenases nodR, nodX or nodZ (Probable). Secondary metabolite biosynthesis. Belongs to the cytochrome P450 family. +To B.subtilis protein YnzH. +Terpene synthase (TPS) involved in the biosynthesis of sesquiterpene natural products included in conifer oleoresin secretions and volatile emissions; these compounds contribute to biotic and abiotic stress defense against herbivores and pathogens (PubMed:21385377). Catalyzes the conversion of (2E,6E)-farnesyl diphosphate (FPP) to alpha-longipinene (PubMed:21385377). (2E,6E)-farnesyl diphosphate = alpha-longipinene + diphosphate Binds 3 Mg(2+) or Mn(2+) ions per subunit. Sesquiterpene biosynthesis. Terpene metabolism; oleoresin biosynthesis. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg(2+). Belongs to the terpene synthase family. Tpsd subfamily. +Catalyzes the dephosphorylation of diacylglycerol diphosphate (DGPP) to phosphatidate (PA) and the subsequent dephosphorylation of PA to diacylglycerol (DAG). Also has undecaprenyl pyrophosphate phosphatase activity, required for the biosynthesis of the lipid carrier undecaprenyl phosphate. Can also use lysophosphatidic acid (LPA) and phosphatidylglycerophosphate as substrates. The pattern of activities varies according to subcellular location, PGP phosphatase activity is higher in the cytoplasmic membrane, whereas PA and LPA phosphatase activities are higher in the outer membrane. Activity is independent of a divalent cation ion and insensitive to inhibition by N-ethylmaleimide (By similarity). 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycero-3'-phosphate) + H2O = 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + phosphate a 1,2-diacyl-sn-glycerol 3-diphosphate + H2O = a 1,2-diacyl-sn-glycero-3-phosphate + H(+) + phosphate a 1,2-diacyl-sn-glycero-3-phosphate + H2O = a 1,2-diacyl-sn-glycerol + phosphate di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Phospholipid metabolism; phosphatidylglycerol biosynthesis; phosphatidylglycerol from CDP-diacylglycerol: step 2/2. Belongs to the PA-phosphatase related phosphoesterase family. +H(+) + 2 pyruvate = (2S)-2-acetolactate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 1/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 1/4. Belongs to the TPP enzyme family. +Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Belongs to the nitroreductase family. HadB/RutE subfamily. +Granulins have possible cytokine-like activity. They may play a role in inflammation, wound repair, and tissue remodeling. Ubiquitous. Granulins are disulfide bridged. Belongs to the granulin family. +Transport of potassium into the cell. Belongs to the HAK/KUP transporter (TC 2.A.72) family. +Belongs to the CTO1 family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Involved in the regulation of apoptosis versus cell survival, and in the maintenance of viability but not of proliferation. Mediates its effects by interactions with a number of other regulators of apoptosis. Isoform 1 inhibits apoptosis. Isoform 2 promotes apoptosis. Interacts with HIF3A (via C-terminus domain) (By similarity). Interacts with BAD, BOK, BIK and BMF (By similarity). Interacts with PMAIP1 (PubMed:17389404). Interacts with BBC3 (By similarity). Isoform 1 interacts with BAX, BAK1 and TPT1 (PubMed:10837489, PubMed:12149273, PubMed:15077116). Heterodimer of isoform 1 and isoform 2. Homodimers of isoform 1 or isoform 2 are not detected. Isoform 2 does not interact with pro-apoptotic BCL2-related proteins (PubMed:10837489). Interacts with RTL10/BOP (PubMed:23055042). Interacts with BCL2L11; may sequester BCL2L11 to prevent its pro-apoptotic activity (PubMed:10837489, PubMed:27013495, PubMed:17389404, PubMed:20562877). Interacts with GIMAP5 and HSPA8/HSC70; the interaction between HSPA8 and MCL1 is impaired in the absence of GIMAP5 (By similarity). Cytoplasmic, associated with mitochondria. Expression increases early during phorbol ester-induced differentiation along the monocyte/macrophage pathway in myeloid leukemia cell line ML-1. Rapidly up-regulated by CSF2 in ML-1 cells. Up-regulated by heat shock-induced differentiation. Expression increases early during retinoic acid-induced differentiation. Cleaved by CASP3 during apoptosis. In intact cells cleavage occurs preferentially after Asp-127, yielding a pro-apoptotic 28 kDa C-terminal fragment. Rapidly degraded in the absence of phosphorylation on Thr-163 in the PEST region. Phosphorylated on Ser-159, by GSK3, in response to IL3/interleukin-3 withdrawal. Phosphorylation at Ser-159 induces ubiquitination and proteasomal degradation, abrogating the anti-apoptotic activity. Treatment with taxol or okadaic acid induces phosphorylation on additional sites. Ubiquitinated. Ubiquitination is induced by phosphorylation at Ser-159. Belongs to the Bcl-2 family. +Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA. Belongs to the ribosome-inactivating protein family. Type 1 RIP subfamily. +Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is responsible for the expression of sporulation specific genes. Belongs to the sigma-70 factor family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has four main subunits: a(1), b(1), b'(1) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta, b and b' chains. In plastids the F-type ATPase is also known as CF(1)CF(0). Belongs to the ATPase C chain family. +May play an important role in formation and fusion of Golgi-derived vesicles during acrosome biogenesis. Interacts (via N-terminus) with TES (via LIM domain 2). Heterodimer with TES; the heterodimer interacts with ENAH to form a heterotrimer. Interacts with ACTL9. Detected at the Golgi apparatus during acrosome biogenesis. Detected at the subacrosomal layer in round spermatids. Detected in sperm head and tail. Belongs to the actin family. +Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Binds 2 divalent ions per subunit. Binds 1 potassium ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Homotetramer; dimer of dimers. Belongs to the AdoMet synthase family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Homodimer. Belongs to the GrpE family. +Required for morphogenesis under gluconeogenic growth conditions. Belongs to the gluconeogenesis factor family. +Defense against chitin-containing fungal pathogens. Has in vitro antifungal activity against F.oxysporum inhibiting its growth and the branching of its hyphae. Has endochitinase activity, but no exochitinase or lysozyme activities. Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins. Expressed in the pulp of the fruit (at protein level) (PubMed:9679856, PubMed:14610495, PubMed:23019098). Expressed in mesocarp (at protein level) (PubMed:9774427). Causes an allergic reaction in human (PubMed:9774427, PubMed:9679856, PubMed:10231327, PubMed:14610495, PubMed:10482846, PubMed:10887324, PubMed:16433216, PubMed:18205857, PubMed:21284746). Involved (at least via the N-terminal chitin-binding hevein-like domain) in cross-reactions with natural rubber latex (latex-fruit allergy syndrome) (PubMed:9774427, PubMed:9679856, PubMed:10231327, PubMed:14610495, PubMed:10482846, PubMed:10887324, PubMed:16433216). Binds to IgE of patients allergic to avocado, chestnut and/or banana (PubMed:9679856, PubMed:10482846, PubMed:16433216, PubMed:21284746). Binds to IgE in 75% of the 20 patients tested allergic to latex (PubMed:9774427). Binds to IgE in 80% of the 15 patients tested allergic to avocado and latex (PubMed:10231327). Binds to IgE in 53% of the 92 and 38% of the 26 kiwifruit-allergic patients tested by ELISA and IgE immunodetection assays, respectively. Only 12% of the 25 kiwifruit-allergic patients tested are found positive by skin prick test (PubMed:18205857). Binds to IgE in 29% of the 51 pediatric patients tested allergic to banana (PubMed:21284746). IgE-binding is not abolished by digestion with artificial gastric juice or simulated gastric fluid (PubMed:10231327, PubMed:14610495). In vitro IgE-binding and in vivo allergenicity (skin prick test) is abolished by heating (PubMed:10887324). Induces degranulation of human basohphils and histamine release (PubMed:16433216). Belongs to the glycosyl hydrolase 19 family. Chitinase class I subfamily. +Probably functions as a manganese efflux pump. Belongs to the MntP (TC 9.B.29) family. +Involved in both DNA replication and cell cycle control. Unprocessed SDE2 interacts with PCNA via its PIP-box. The interaction with PCNA prevents monoubiquitination of the latter thereby inhibiting translesion DNA synthesis. The binding of SDE2 to PCNA also leads to processing of SDE2 by an unidentified deubiquitinating enzyme, cleaving off the N-terminal ubiquitin-like domain. The resulting mature SDE2 is degraded by the DCX(DTL) complex in a cell cycle- and DNA damage dependent manner. Binding of SDE2 to PCNA is necessary to counteract damage due to ultraviolet light induced replication stress. The complete degradation of SDE2 is necessary to allow S-phase progression. The PIP-box (PCNA interacting peptide) motif mediates both the interaction with PCNA and cleavage of the SDE2 precursor by a deubiquitinating enzyme. The SAP domain is necessary for specific binding to DNA. The propeptide displays a ubiquitin-like fold. The protein is cleaved at Gly-71 by a deubiquitinating enzyme to form the active SDE2. Belongs to the SDE2 family. Extended N-terminus. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the cyclophilin-type PPIase family. PPIL4 subfamily. +Inhibits RpoS proteolysis by regulating RssB activity, thereby increasing the stability of the sigma stress factor RpoS especially during phosphate starvation, but also in stationary phase and during nitrogen starvation. Its effect on RpoS stability is due to its interaction with RssB, which probably blocks the interaction of RssB with RpoS, and the consequent delivery of the RssB-RpoS complex to the ClpXP protein degradation pathway. Interacts with RssB. Belongs to the IraP family. +Binds 2 calcium ions per subunit. Widely expressed at low levels with highest levels in small intestine, testis and brain. Very low expression in endothelial cells, monocytes, neutrophils and lymphocytes. Isoform 1 is not expressed in small intestine. Not induced by bacterial lipopolysaccharideS (LPS) or IL1/interleukin-1 in endothelium, monocytes or neutrophils. Not induced by PHA in lymphocytes. Not expressed in small intestine. +Pyrophosphatase that hydrolyzes non-canonical purine nucleotides such as inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) or xanthosine 5'-triphosphate (XTP) to their respective monophosphate derivatives. The enzyme does not distinguish between the deoxy- and ribose forms. Probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions. a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-phosphate + diphosphate + H(+) a 2'-deoxyribonucleoside 5'-triphosphate + H2O = a 2'-deoxyribonucleoside 5'-phosphate + diphosphate + H(+) H2O + ITP = diphosphate + H(+) + IMP dITP + H2O = dIMP + diphosphate + H(+) H2O + XTP = diphosphate + H(+) + XMP Binds 1 divalent metal cation per subunit; can use either Mg(2+) or Mn(2+). Homodimer. Belongs to the HAM1 NTPase family. +Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 magnesium ions per subunit. Monomer. Belongs to the DNA polymerase type-Y family. +This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions. A + H2 = AH2 Binds 1 [3Fe-4S] cluster. Binds 2 [4Fe-4S] clusters. Heterodimer of a large and a small subunit. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the [NiFe]/[NiFeSe] hydrogenase small subunit family. +Catalyzes the ATP-dependent phosphorylation of N-acetyl-L-glutamate. ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamyl 5-phosphate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 2/4. Belongs to the acetylglutamate kinase family. ArgB subfamily. +Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis: the synthesis of acetylglutamate from glutamate and acetyl-CoA, and of ornithine by transacetylation between acetylornithine and glutamate. L-glutamate + N(2)-acetyl-L-ornithine = L-ornithine + N-acetyl-L-glutamate acetyl-CoA + L-glutamate = CoA + H(+) + N-acetyl-L-glutamate Amino-acid biosynthesis; L-arginine biosynthesis; L-ornithine and N-acetyl-L-glutamate from L-glutamate and N(2)-acetyl-L-ornithine (cyclic): step 1/1. Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 1/4. Heterodimer of an alpha and a beta chain. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the ArgJ family. +Belongs to the UPF0758 family. +Component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Plays a role in keeping cristae membranes connected to the inner boundary membrane. Also promotes protein import via the mitochondrial intermembrane space assembly (MIA) pathway (By similarity). Component of the mitochondrial contact site and cristae organizing system (MICOS) complex. Belongs to the MICOS complex subunit Mic60 family. +Part of the ABC transporter complex ZnuABC involved in zinc import. Responsible for energy coupling to the transport system. ATP(in) + H2O(in) + Zn(2+)(out) = ADP(in) + H(+)(in) + phosphate(in) + Zn(2+)(in) The complex is composed of two ATP-binding proteins (ZnuC), two transmembrane proteins (ZnuB) and a solute-binding protein (ZnuA). Belongs to the ABC transporter superfamily. Zinc importer (TC 3.A.1.15.5) family. +Belongs to the bacterial ribosomal protein bL34 family. +Involved in cell division and chromosome segregation. Belongs to the WhiA family. +ATP = 3',5'-cyclic AMP + diphosphate Belongs to the adenylyl cyclase class-1 family. +Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes. Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Homodimer and homohexamer; in equilibrium. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrR subfamily. +Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 2A subfamily. +Belongs to the IS21/IS1162 putative ATP-binding protein family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 13 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 1 family. +Belongs to the UPF0251 family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. Minor subunit located with subunit a in the membrane. The K chain binds the dimeric form by interacting with the G and E chains (By similarity). F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. Belongs to the ATP19 family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by acpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group (By similarity). Belongs to the acyl carrier protein (ACP) family. +Involved in the biosynthesis of gangliosides GM2, GD2, GT2 and GA2 from GM3, GD3, GT3 and GA3, respectively. ganglioside GM3 (d18:1(4E)) + UDP-N-acetyl-alpha-D-galactosamine = ganglioside GM2 (d18:1(4E)) + H(+) + UDP ganglioside GD3 (d18:1(4E)) + UDP-N-acetyl-alpha-D-galactosamine = ganglioside GD2 (d18:1(4E)) + H(+) + UDP ganglioside GM3 + UDP-N-acetyl-alpha-D-galactosamine = ganglioside GM2 + H(+) + UDP ganglioside GD3 + UDP-N-acetyl-alpha-D-galactosamine = ganglioside GD2 + H(+) + UDP ganglioside GD1a + UDP-N-acetyl-alpha-D-galactosamine = ganglioside GalNAc-GD1a + H(+) + UDP ganglioside GT3 (d18:1(4E)) + UDP-N-acetyl-alpha-D-galactosamine = ganglioside GT2 (d18:1(4E)) + H(+) + UDP a beta-D-Gal-(1->4)-beta-D-Glc-(1<->1)-Cer(d18:1(4E)) + UDP-N-acetyl-alpha-D-galactosamine = ganglioside GA2 (d18:1(4E)) + H(+) + UDP alpha-N-glycoloylneuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + UDP-N-acetyl-alpha-D-galactosamine = H(+) + N-acetyl-beta-D-galactosaminyl-(1->4)-[alpha-N-glycoloylneuraminosyl-(2->3)]-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + UDP Sphingolipid metabolism. Homodimer; disulfide-linked. Strongly expressed in brain, testis, spleen, and to a lesser extent in liver. Belongs to the glycosyltransferase 2 family. +Mannosyltransferase involved in glycosylphosphatidylinositol-anchor biosynthesis. Transfers the third mannose to Man2-GlcN-acyl-PI during GPI precursor assembly (By similarity). Glycolipid biosynthesis; glycosylphosphatidylinositol-anchor biosynthesis. Belongs to the glycosyltransferase 22 family. PIGB subfamily. +Belongs to the bacterial ribosomal protein bL32 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+) Binds 1 dipyrromethane group covalently. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. Monomer. The porphobilinogen subunits are added to the dipyrromethane group. Belongs to the HMBS family. +Belongs to the UPF0359 family. +The actions of the proteins TfxB, TfxD and TfxF are implicated in the processing of the inactive trifolitoxin (TfxA) precursor into the active peptide. +Required for 60S ribosomal subunit biogenesis. Belongs to the NOP5/NOP56 family. +(4S)-4-hydroxy-2-oxoglutarate = glyoxylate + pyruvate (4R)-4-hydroxy-2-oxoglutarate = glyoxylate + pyruvate 2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-phosphate + pyruvate Carbohydrate acid metabolism; 2-dehydro-3-deoxy-D-gluconate degradation; D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate: step 2/2. Carbohydrate metabolism; glyoxylate and dicarboxylate metabolism. Homotrimer. Induced by galacturonate and negatively regulated by the KdgR repressor. Is subject to catabolite repression by glucose involving the ccpA gene. Belongs to the KHG/KDPG aldolase family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Plays a role of stimulator of transcription factors and nuclear receptors activities. Activates transcriptional activity of estrogen receptor alpha, nuclear respiratory factor 1 (NRF1) and glucocorticoid receptor in the presence of glucocorticoids. May play a role in constitutive non-adrenergic-mediated mitochondrial biogenesis as suggested by increased basal oxygen consumption and mitochondrial number when overexpressed. May be part of the pathways regulating the elevation of gluconeogenesis, beta-oxidation of fatty acids and ketogenesis during fasting. Stimulates SREBP-mediated lipogenic gene expression in the liver. Induces energy expenditure and antagonizes obesity when overexpressed. Induces also the expression of mitochondrial genes involved in oxidative metabolism. Induces the expression of PERM1 in the skeletal muscle in an ESRRA-dependent manner. Interacts with estrogen receptor alpha/ESR1. Interacts with Sterol regulatory binding transcription factor 1/SREBF1, PPAR-alpha/PPARA, thyroid hormone receptor beta/THRB and host cell factor/HCFC1. Interacts with Estrogen-related receptor gamma/ESRRG and alpha/ESRRA. Interacts with PRDM16 (By similarity). Ubiquitous with higher expression in heart, brown adipose tissue. Induced by combination of forskolin and dexamethasone in primary hepatocytes. Contains 3 Leu-Xaa-Xaa-Leu-Leu (LXXLL) motif, which are usually required for the association with nuclear receptors. +dGTPase preferentially hydrolyzes dGTP over the other canonical NTPs. dGTP + H2O = 2'-deoxyguanosine + H(+) + triphosphate Belongs to the dGTPase family. Type 1 subfamily. As this bacterium is not an Enterobacteriaceae, this protein may not have a true dGTPase activity. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +Belongs to the UPF0391 family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. RnhC subfamily. +Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate. (R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA + diphosphate Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 4/5. Homohexamer. Belongs to the bacterial CoaD family. +Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion. alpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + NH4(+) Allosterically activated by N-acetylglucosamine 6-phosphate (GlcNAc6P). Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 5/5. Homohexamer; trimer of disulfide-linked dimers. Belongs to the glucosamine/galactosamine-6-phosphate isomerase family. NagB subfamily. +Component of the synapsis initiation complex (SIC) necessary for the synaptonemal complex assembly. Stabilizes the ZIP2 component to the chromosomes. The SIC complex loads onto chromosomes and nucleates ZIP1 polymerization, a molecular zipper that acts to bring homologous chromosomes in close apposition, which is required for meiotic crossover. May also be involved in double strand break repair. Component of the synapsis initiation complex composed of at least ZIP2, ZIP3, MSH4 and MSH5. Interacts also with ZIP1, MRE11, RAD51 and RAD53. Synapsed meiotic chromosomes. Expressed during meiosis. +Belongs to the bacterial ribosomal protein bS21 family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +This b-type cytochrome is tightly associated with the reaction center of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. With its partner (PsbE) binds heme. PSII binds additional chlorophylls, carotenoids and specific lipids. Heterodimer of an alpha subunit and a beta subunit. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbE/PsbF family. +Key enzyme in folate metabolism. Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis. (6S)-5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + H(+) + NADPH kcat is 35.9 sec(-1) for dihydrofolate. kcat is 130 sec(-1) for NADPH. Cofactor biosynthesis; tetrahydrofolate biosynthesis; 5,6,7,8-tetrahydrofolate from 7,8-dihydrofolate: step 1/1. Monomer. Belongs to the dihydrofolate reductase family. +Detected in larval hemolymph (at protein level). Expressed in fat body from the fifth larval instar through to the pupal stage (Ref.4, PubMed:26078299). Highest expression levels are found at the wandering stage which marks the transition from larva to pupa (Ref.4). Expression then declines during later pupal stages (Ref.4). This lipoprotein belongs to the group of structurally related '30 kDa proteins' that comprise major protein components of the fifth (and last) instar larvae and of pupae. Belongs to the 30 kDa lipoprotein family. +Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III. 4 H(+) + uroporphyrinogen III = 4 CO2 + coproporphyrinogen III Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 4/4. Homodimer. Belongs to the uroporphyrinogen decarboxylase family. +Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors. Interacts with RXR and RARA (By similarity). Interacts with importin alpha. Upon ligand binding, a conformation change exposes a nuclear localization motif and the protein is transported into the nucleus. By retinoic acid. Forms a beta-barrel structure that accommodates hydrophobic ligands in its interior. Sumoylated in response to retinoic acid binding, sumoylation is critical for dissociation from ER and subsequent nuclear translocation. Belongs to the calycin superfamily. Fatty-acid binding protein (FABP) family. +Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12. [sulfur carrier]-SH + AH2 + L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 2 S-adenosyl-L-methionine = 3-methylsulfanyl-L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Belongs to the methylthiotransferase family. RimO subfamily. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Involved in the biosynthesis of prenylated phenolics natural products which contribute to the bitter taste of beer and display broad biological activities (Probable). Involved in anthocyanin biosynthesis (By similarity). Polyketide binding proteins (PBP) which reduces the catalytic activities of CHS_H1 and PT1L and prevents demethylxanthohumol (DMX) production, by binding to DMX and naringenin chalcone (NC) to stabilize the chalconoids ring-opened structure (PubMed:29760092). a chalcone = a flavanone. Secondary metabolite biosynthesis; flavonoid biosynthesis. Mostly expressed in glandular trichomes (lupulin glands), and, to a lower extent, in cones, cones bracts, leaves, stems and roots. Belongs to the chalcone isomerase family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Catalyzes the formation of the signaling molecule cAMP in response to G-protein signaling (PubMed:1618857, PubMed:8428899, PubMed:10427002, PubMed:11087399, PubMed:15591060, PubMed:16766715, PubMed:19243146). Mediates signaling downstream of ADRB1. Regulates the increase of free cytosolic Ca(2+) in response to increased blood glucose levels and contributes to the regulation of Ca(2+)-dependent insulin secretion (By similarity). Lacks catalytic activity by itself, but can associate with isoform 1 to form active adenylyl cyclase. ATP = 3',5'-cyclic AMP + diphosphate Binds 2 magnesium ions per subunit (PubMed:16766715, PubMed:19243146). Is also active with manganese (in vitro) (PubMed:11087399, PubMed:16766715). Activated by forskolin (PubMed:1618857, PubMed:8428899). Activated by GNAS. Activity is further increased by interaction with the G-protein beta and gamma subunit complex formed by GNB1 and GNG2 (By similarity). Is not activated by calmodulin. Inhibited by adenosine and ATP analogs. Inhibited by calcium ions, already at micromolar concentrations (PubMed:1618857). Phosphorylation by RAF1 results in its activation (By similarity). Interacts with GNAS (PubMed:9417641, PubMed:10427002, PubMed:11087399, PubMed:15591060, PubMed:16766715, PubMed:19243146). Interacts with GNB1 and GNG2 (By similarity). Part of a complex containing AKAP5, ADCY6, PDE4C and PKD2 (By similarity). Interacts with RAF1 (By similarity). Isoform 1 is detected in heart, and at lower levels in brain (PubMed:1618857). Isoform 2 is detected in heart (PubMed:8428899). The protein contains two modules with six transmembrane helices each; both are required for catalytic activity. Isolated N-terminal or C-terminal guanylate cyclase domains have no catalytic activity, but when they are brought together, enzyme activity is restored. The active site is at the interface of the two domains. Both contribute substrate-binding residues, but the catalytic metal ions are bound exclusively via the N-terminal guanylate cyclase domain. Belongs to the adenylyl cyclase class-4/guanylyl cyclase family. +Member of a two-component regulatory system ChvG/ChvI. Activates ChvI by phosphorylation (Potential). ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Could reduce the 13-carbonyl of daunorubicin to produce (13S)-13-dihydrodaunorubicin. Could also be able to reduce the 13-carbonyl of doxorubicin (By similarity). Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Involved in aging, oxidative stress response, and in the regulation of mitochondrial biogenesis. Inactivation of UTH1 increases life span, leads to higher resistance to heat stress and to hydrogen peroxide, and increases sensitivity to the superoxide radical-generating drug paraquat and to copper. Also required for the selective autophagic degradation of mitochondria (mitophagy) in response to nitrogen starvation. May play a role in cell wall morphogenesis and septation. Involved in the remodeling of the cell wall during the various phases of yeast culture development and under various environmental conditions and plays a role in septation. Involved in cell sensitivity to boric acid (By similarity). Non-covalently bound to the cell wall. Belongs to the SUN family. Extended N-terminus. +Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain. Dimer of alpha and beta chains. A typical microtubule is a hollow water-filled tube with an outer diameter of 25 nm and an inner diameter of 15 nM. Alpha-beta heterodimers associate head-to-tail to form protofilaments running lengthwise along the microtubule wall with the beta-tubulin subunit facing the microtubule plus end conferring a structural polarity. Microtubules usually have 13 protofilaments but different protofilament numbers can be found in some organisms and specialized cells. The highly acidic C-terminal region may bind cations such as calcium. The MREI motif is common among all beta-tubulin isoforms and may be critical for tubulin autoregulation. Some glutamate residues at the C-terminus are polyglycylated, resulting in polyglycine chains on the gamma-carboxyl group. Glycylation is mainly limited to tubulin incorporated into axonemes (cilia and flagella) whereas glutamylation is prevalent in neuronal cells, centrioles, axonemes, and the mitotic spindle. Both modifications can coexist on the same protein on adjacent residues, and lowering polyglycylation levels increases polyglutamylation, and reciprocally. Cilia and flagella glycylation is required for their stability and maintenance. Flagella glycylation controls sperm motility. Some glutamate residues at the C-terminus are polyglutamylated, resulting in polyglutamate chains on the gamma-carboxyl group (By similarity). Polyglutamylation plays a key role in microtubule severing by spastin (SPAST). SPAST preferentially recognizes and acts on microtubules decorated with short polyglutamate tails: severing activity by SPAST increases as the number of glutamates per tubulin rises from one to eight, but decreases beyond this glutamylation threshold (By similarity). Glutamylation is also involved in cilia motility (By similarity). Phosphorylated on Ser-172 by CDK1 during the cell cycle, from metaphase to telophase, but not in interphase. This phosphorylation inhibits tubulin incorporation into microtubules. Belongs to the tubulin family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Belongs to the DMRL synthase family. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. Ubiquitously expressed. The PHD-type zinc finger mediates the binding to H3K4me3. Belongs to the Alfin family. Lacks the Tyr (here Asp-204), a conserved feature of the aromatic cage required for the interaction with histone H3K4me3/2. +Responsible for methylating the 5'-cap structure of mRNAs. a 5'-end (5'-triphosphoguanosine)-(ribonucleoside) in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. mRNA cap 0 methyltransferase family. +Belongs to the dGTPase family. Type 2 subfamily. +Acts as a component of the essential kinetochore-associated NDC80 complex, which is required for chromosome segregation and spindle checkpoint activity. Component of the NDC80 complex, which consists of NDC80, NUF2, SPC24 and SPC25. Associated with kinetochores. Belongs to the NUF2 family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The L component serves as a unique electron donor to the NB-component of the complex, and binds Mg-ATP. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per dimer. Porphyrin-containing compound metabolism; chlorophyll biosynthesis (light-independent). Homodimer. Protochlorophyllide reductase is composed of three subunits; ChlL, ChlN and ChlB. Belongs to the NifH/BchL/ChlL family. +Transmembrane (T) component of an energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). May be able to interact with more than 1 S component at a time (By similarity). Belongs to the energy-coupling factor EcfT family. +Regulatory subunit of the DNA primase complex and component of the DNA polymerase alpha complex (also known as the alpha DNA polymerase-primase complex) which play an essential role in the initiation of DNA synthesis (By similarity). During the S phase of the cell cycle, the DNA polymerase alpha complex (composed of a catalytic subunit POLA1, an accessory subunit POLA2 and two primase subunits, the catalytic subunit PRIM1 and the regulatory subunit PRIM2) is recruited to DNA at the replicative forks via direct interactions with MCM10 and WDHD1 (By similarity). The primase subunit of the polymerase alpha complex initiates DNA synthesis by oligomerising short RNA primers on both leading and lagging strands (By similarity). These primers are initially extended by the polymerase alpha catalytic subunit and subsequently transferred to polymerase delta and polymerase epsilon for processive synthesis on the lagging and leading strand, respectively. In the primase complex, both subunits are necessary for the initial di-nucleotide formation, but the extension of the primer depends only on the catalytic subunit (By similarity). Binds RNA:DNA duplex and coordinates the catalytic activities of PRIM1 and POLA2 during primase-to-polymerase switch. Binds 1 [4Fe-4S] cluster. Heterodimer of a catalytic subunit PRIM1 and a regulatory subunit PRIM2, also known as the DNA primase complex. Interacts via (C-terminus) with PRIM1. Component of the alpha DNA polymerase complex (also known as the alpha DNA polymerase-primase complex) consisting of four subunits: the catalytic subunit POLA1, the regulatory subunit POLA2, and the primase complex subunits PRIM1 and PRIM2 respectively (By similarity). Within the complex, POLA1 directly interacts with PRIM2 (By similarity). The RNA:DNA duplex-binding domain interacts with the template phosphates at positions -2, -1, 1, and 2 positioning its bases -1, 1, and 2 for duplex formation. Interacts only with the beta- and gamma-phosphates of triphosphate moiety of initiating NTP of the primer. The side chain of His-303 mimics a RNA base that would be paired with the template nucleotide at position -1 via a hydrogen bond, thereby facilitating the stacking of the initiating NTP. In the initiating primosome a 'mini RNA:DNA' duplex is formed comprising three template nucleotides at positions -1, 1, and 2 on one strand and His-303, initiating NTP, and incoming NTP on the other strand. The interdomain linker provides flexibility in movement relative to primosome platform composed of PRIM1, the N-terminus of PRIM2, the C-terminus of POLA1 and POLA2. Together with POLA1 interdomain linker, allows for large-scale conformational changes of primosome and coordinated autoregulation of catalytic centers of PRIM1 and POLA1. It is proposed to move the C-terminus of PRIM2 close to PRIM1 during initiation, then move it away with the 5'-end of the nascent primer during elongation. The steric hindrance between the N- and C-terminus of PRIM2 as the RNA primer is elongated limits its length to 9 nucleotides. Ultimately a large rotation of the C-terminus of PRIM2 transfers the primer to POLA1 active site for DNA synthesis. Belongs to the eukaryotic-type primase large subunit family. +Proteolytically removes the C-terminal three residues of farnesylated proteins. Acts on lamin A/C. The peptide bond hydrolyzed can be designated -C-|-A-A-X in which C is an S-isoprenylated cysteine residue, A is usually aliphatic and X is the C-terminal residue of the substrate protein, and may be any of several amino acids. Binds 1 zinc ion per subunit. The metalloprotease domain is constituted by the two C-terminal nuclear regions. Belongs to the peptidase M48A family. +Expressed by the venom duct. Causes an allergic reaction in human. Belongs to the peptidase S1 family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Belongs to the bacterial ribosomal protein bS16 family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Belongs to the imidazoleglycerol-phosphate dehydratase family. +Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity. adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue. Belongs to the radical SAM superfamily. RlmN family. +Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short-lived. The second step is the nonenzymatic hydrolysis of the enamine/imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA (By similarity). L-threonine = 2-oxobutanoate + NH4(+) Amino-acid biosynthesis; L-isoleucine biosynthesis; 2-oxobutanoate from L-threonine: step 1/1. Homotetramer. Belongs to the serine/threonine dehydratase family. +High specificity for fatty acids. Forms a beta-barrel structure that accommodates the hydrophobic ligand in its interior. Belongs to the calycin superfamily. Fatty-acid binding protein (FABP) family. Could be the product of a pseudogene. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Component of the chloroplastic Clp protease core complex. Belongs to the peptidase S14 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Catalyzes the conversion of O-acetyl-L-homoserine (OAH) into homocysteine in the methionine biosynthesis pathway. Has weak activity with O-acetyl-L-serine, O-phospho-L-serine, L-serine, O-succinyl-L-homoserine and L-homoserine. Shows low CTT beta-lyase activity and very low CTT gamma-synthase activity. hydrogen sulfide + O-acetyl-L-homoserine = acetate + L-homocysteine Inhibited by the carbonyl reagents hydroxylamine and phenylhydrazine. Also inhibited by methionine and propargylglycine. Optimum pH is 7.8. Shows high pH stability over a wide range of pH (pH 4-12). Optimum temperature is 70 degrees Celsius. Very stable at high temperature. 90% of the activity is retained after treatment at 90 degrees Celsius for 60 min. Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-homocysteine from O-acetyl-L-homoserine: step 1/1. Homotetramer. Belongs to the trans-sulfuration enzymes family. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +mRNA decapping enzyme that specifically removes the nicotinamide adenine dinucleotide (NAD) cap from a subset of mRNAs by hydrolyzing the diphosphate linkage to produce nicotinamide mononucleotide (NMN) and 5' monophosphate mRNA. The NAD-cap is present at the 5'-end of some mRNAs and stabilizes RNA against 5'-processing. Has preference for mRNAs with a 5'-end purine. Catalyzes the hydrolysis of a broad range of dinucleotide pyrophosphates. a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H(+) H2O + NAD(+) = AMP + beta-nicotinamide D-ribonucleotide + 2 H(+) H2O + NADH = AMP + 2 H(+) + reduced beta-nicotinamide D-ribonucleotide Divalent metal cations. Mg(2+) or Mn(2+). Binds 1 zinc ion per subunit. Homodimer. Belongs to the Nudix hydrolase family. NudC subfamily. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Belongs to the V-ATPase D subunit family. +Efflux pump that contributes to intrinsic antibiotic resistance. The pump uses the electrochemical gradient as a source of energy. Belongs to the major facilitator superfamily. Drug:H(+) antiporter-3 (DHA3) (TC 2.A.1.21) family. +Belongs to the ABC transporter superfamily. ABCF family. EF3 subfamily. Lacks transmembrane domains and is probably not involved in transport. +Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. Binds 3 Zn(2+) ions. Belongs to the AP endonuclease 2 family. +Has lytic, hemolytic and antibacterial activities. Expressed by the skin glands. Belongs to the grammistin family. Group 2 subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Snake venom phospholipase A2 (PLA2) that lacks enzymatic activity (PubMed:28633930). Does not show antibacterial activity (PubMed:29928892). Is myotoxic and displays edema-inducing activities (By similarity). A model of myotoxic mechanism has been proposed: an apo Lys49-PLA2 is activated by the entrance of a hydrophobic molecule (e.g. fatty acid) at the hydrophobic channel of the protein leading to a reorientation of a monomer (By similarity). This reorientation causes a transition between 'inactive' to 'active' states, causing alignment of C-terminal and membrane-docking sites (MDoS) side-by-side and putting the membrane-disruption sites (MDiS) in the same plane, exposed to solvent and in a symmetric position for both monomers (By similarity). The MDoS region stabilizes the toxin on membrane by the interaction of charged residues with phospholipid head groups (By similarity). Subsequently, the MDiS region destabilizes the membrane with penetration of hydrophobic residues (By similarity). This insertion causes a disorganization of the membrane, allowing an uncontrolled influx of ions (i.e. calcium and sodium), and eventually triggering irreversible intracellular alterations and cell death (By similarity). Monomer. Expressed by the venom gland. Belongs to the phospholipase A2 family. Group II subfamily. K49 sub-subfamily. Does not bind calcium as one of the calcium-binding ligands is lost (Asp->Lys in position 64, which corresponds to 'Lys-49' in the current nomenclature). +E3 ubiquitin-protein ligase component of the LUBAC complex which conjugates linear ('Met-1'-linked) polyubiquitin chains to substrates and plays a key role in NF-kappa-B activation and regulation of inflammation (PubMed:28701375). LUBAC conjugates linear polyubiquitin to IKBKG and RIPK1 and is involved in activation of the canonical NF-kappa-B and the JNK signaling pathways (By similarity). Linear ubiquitination mediated by the LUBAC complex interferes with TNF-induced cell death and thereby prevents inflammation (PubMed:28701375). LUBAC is recruited to the TNF-R1 signaling complex (TNF-RSC) following polyubiquitination of TNF-RSC components by BIRC2 and/or BIRC3 and to conjugate linear polyubiquitin to IKBKG and possibly other components contributing to the stability of the complex (By similarity). The LUBAC complex is also involved in innate immunity by conjugating linear polyubiquitin chains at the surface of bacteria invading the cytosol to form the ubiquitin coat surrounding bacteria (By similarity). LUBAC is not able to initiate formation of the bacterial ubiquitin coat, and can only promote formation of linear polyubiquitins on pre-existing ubiquitin (By similarity). Recruited to the surface of bacteria by RNF213, which initiates the bacterial ubiquitin coat (By similarity). The bacterial ubiquitin coat acts as an 'eat-me' signal for xenophagy and promotes NF-kappa-B activation (By similarity). Together with OTULIN, the LUBAC complex regulates the canonical Wnt signaling during angiogenesis (By similarity). RNF31 is required for linear ubiquitination of BCL10, thereby promoting TCR-induced NF-kappa-B activation (By similarity). Binds polyubiquitin of different linkage types (By similarity). [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N(6)-ubiquitinyl-L-lysine. Protein modification; protein ubiquitination. Component of the LUBAC complex (linear ubiquitin chain assembly complex) which consists of SHARPIN, RBCK1 and RNF31 (By similarity). LUBAC has a MW of approximately 600 kDa suggesting a heteromultimeric assembly of its subunits (By similarity). Associates with the TNF-R1 signaling complex (TNF-RSC) in a stimulation-dependent manner (By similarity). Interacts (via the PUB domain) with OTULIN (via the PIM motif); the interaction is direct (PubMed:23708998). Interacts (via the PUB domain) with VCP (via the PIM motif) (By similarity). Interacts (via the PUB domain) with SPATA2 (via the PIM motif); interaction is direct and bridges RNF31 and CYLD (By similarity). Interacts with CYLD; the interaction is indirect and is mediated via SPATA2 (By similarity). Interacts with MUSK (PubMed:14678832). Interacts with CARD11, promoting linear ubiquitination of BCL10 (By similarity). Widely expressed (at protein level). Not expressed in heart. The PUB domain mediates interaction with the PIM motifs of VCP and RNF31, with a strong preference for RNF31. The RanBP2-type zinc fingers mediate the specific interaction with ubiquitin. The UBA domain mediates association with RBCK1/HOIL1 via interaction with its UBL domain. RING 1 and IBR zinc-fingers catalyze the first step transfer of ubiquitin from the E2 onto RING 2, to transiently form a HECT-like covalent thioester intermediate. The linear ubiquitin chain determining domain (LDD) mediates the final transfer of ubiquitin from RING 2 onto the N-terminus of a target ubiquitin. Autoubiquitinated (PubMed:29950720). Interaction with OTULIN is required to suppress formation of 'Met-1'-linked polyubiquitin chains and prevent subsequent inactivation of the LUBAC complex (PubMed:29950720). Cleaved by caspase during apoptosis. Belongs to the RBR family. +Functions as an interleukin receptor which binds interleukin-12 with low affinity and is involved in IL12 transduction. Associated with IL12RB2 it forms a functional, high affinity receptor for IL12. Associates also with IL23R to form the interleukin-23 receptor which functions in IL23 signal transduction probably through activation of the Jak-Stat signaling cascade. Dimer or oligomer; disulfide-linked. Interacts with IL12RB2 to form the high affinity IL12 receptor. Heterodimer with IL23R; in presence of IL23. The heterodimer forms the IL23 receptor. The WSXWS motif appears to be necessary for proper protein folding and thereby efficient intracellular transport and cell-surface receptor binding. The box 1 motif is required for JAK interaction and/or activation. The disease is caused by variants affecting the gene represented in this entry. Belongs to the type I cytokine receptor family. Type 2 subfamily. IL12RB1 mutation db +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. +Hydrolyzes intracellular trehalose to glucose (Probable). The disaccharide trehalose serves as a storage carbohydrate that is mobilized during conidial germination (PubMed:10320571). Regulates the level of trehalose as a protectant for cell integrity during heat stress (PubMed:10320571). alpha,alpha-trehalose + H2O = alpha-D-glucose + beta-D-glucose Activated by calcium. Carbohydrate degradation. Expressed during spore germination and growth. Induced during recovery from thermal stress. Abolishes trehalose degradation during conidial germination and delays germ tube formation (PubMed:10320571). Resistance to thermal stress (PubMed:10320571). Belongs to the glycosyl hydrolase 37 family. +Catalyzes the hydrolysis of ferric enterobactin (Fe-Ent). Is responsible for the release of iron from ferric enterobactin. Fe(III)-enterobactin + H(+) + 3 H2O = Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine] + 2 N-(2,3-dihydroxybenzoyl)-L-serine Fe(III)-enterobactin + H2O = Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]3 + H(+) Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]3 + H(+) + H2O = Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]2 + N-(2,3-dihydroxybenzoyl)-L-serine Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]2 + H(+) + H2O = Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine] + N-(2,3-dihydroxybenzoyl)-L-serine Disruption of the gene abrogates enterochelin-supported growth on iron-chelated media. Belongs to the Fes family. +Component of the coenzyme Q biosynthetic pathway. May play a role in organizing a multi-subunit COQ enzyme complex required for coenzyme Q biosynthesis. Required for steady-state levels of other COQ polypeptides. Cofactor biosynthesis; ubiquinone biosynthesis. Component of a multi-subunit COQ enzyme complex, composed of at least COQ3, COQ4, COQ5, COQ6, COQ7 and COQ9. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the COQ4 family. +Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. (2S,6S)-2,6-diaminoheptanedioate = meso-2,6-diaminoheptanedioate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. Homodimer. Belongs to the diaminopimelate epimerase family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Belongs to the BPG-independent phosphoglycerate mutase family. A-PGAM subfamily. +Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). diphosphate + N-(5-phospho-beta-D-ribosyl)anthranilate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate Binds 2 magnesium ions per monomer. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 2/5. Homodimer. Belongs to the anthranilate phosphoribosyltransferase family. +Catalyzes the transfer of one adenosine molecule from an ATP to an mRNA poly(A) tail bearing a 3'-OH terminal group in an ATP hydrolysis-dependent manner. May be involved in maintaining the translation efficiency of at least some genes through preventing degradation of their mRNAs. Prefers RNA molecules that are adenosine-rich close to 3'-end. In addition, may inhibit cell proliferation and cell cycle progression through ubiquitination of beta-catenin/CTNNB1. ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide Belongs to the TENT family. It is uncertain whether Met-1 or Met-2 is the initiator. Truncated N-terminus. +May play a role in vesicle trafficking. H2O + NAD(+) = ADP-D-ribose + H(+) + nicotinamide A number of isoforms are produced. According to EST sequences. The TIR domain mediates NAD(+) hydrolase (NADase) activity. Self-association of TIR domains is required for NADase activity. Belongs to the VAMP-associated protein (VAP) (TC 9.B.17) family. +Amphipathic peptide which probably adopts an alpha-helical structure. When injected in subesophageal ganglia of cockroach P.americana, a natural host for larvae of A.compressa, dampens the escape response for about 1 hour which may contribute to early stages of hypokinesia. Has no antimicrobial activity against E.coli DH5alpha or B.thuringiensis. Is not cytotoxic in vitro. Monomer. Expressed in venom sac and, to a lesser extent, in venom gland. Not expressed in brain. +Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid (By similarity). H2O + NAD(+) + xanthine = H(+) + NADH + urate H2O + hypoxanthine + NAD(+) = H(+) + NADH + xanthine Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit. Binds 2 [2Fe-2S] clusters per subunit. By 2-thiouric acid. Repressed by ammonium. Belongs to the xanthine dehydrogenase family. +Seems to regulate the surface properties of the bacterium in the presence of plant cells or plant cell extracts. (1,4-alpha-D-galacturonosyl)n+m + H2O = (1,4-alpha-D-galacturonosyl)n + (1,4-alpha-D-galacturonosyl)m. By certain acidic polysaccharides found in carrot root extract. Belongs to the glycosyl hydrolase 28 family. +Belongs to the bacterial ribosomal protein bL32 family. +Belongs to the glycosyl hydrolase 92 family. +Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis. (R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) A monovalent cation. Ammonium or potassium. Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Homodimer. Belongs to the type III pantothenate kinase family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Metamorphosin A may be part of an internal signaling system involved in control of metamorphosis. Belongs to the LWamide neuropeptide family. +Decapping scavenger enzyme that catalyzes the cleavage of a residual cap structure following the degradation of mRNAs of the 3'->5' exosome-mediated mRNA decay pathway. Hydrolyzes cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG) and tri-methyl guanosine nucleoside triphosphate (m3(2,2,7)GpppG) with up to 2 nucleotide substrates (small capped oligoribonucleotides) and specifically releases 5'-phosphorylated RNA fragments and 7-methylguanosine monophosphate (m7GMP). Does not hydrolyze unmethylated cap analog (GpppG) and shows no decapping activity on intact m7GpppG-capped mRNA molecules. Does not hydrolyze 7-methylguanosine diphosphate (m7GDP) and tri-methylguanosine diphosphate (m3(2,2,7)GDP) to m(7)GMP and m3(2,2,7)GMP, respectively (PubMed:15383679, PubMed:22985415). May also play a role in the 5'->3 mRNA decay pathway; m7GDP, the downstream product released by the 5'->3' mRNA mediated decapping activity, may be also converted by dcs-1 to m7GMP. Binds to m7GpppG and strongly to m7GDP. a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O = a 5'-end diphospho-ribonucleoside in mRNA + 2 H(+) + N(7)-methyl-GMP a 5'-end (N(2),N(2),N(7)-trimethyl 5'-triphosphoguanosine)-(ribonucleoside) in mRNA + H2O = (N(2),N(2),N(7))-trimethyl-GMP + a 5'-end diphospho-ribonucleoside in mRNA + 2 H(+) The hydrolytic product 7-methylguanosine diphosphate (m7GDP) efficiently inhibits the decapping scavenger activity and acts as a competitive inhibitor in vitro. Belongs to the HIT family. +Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS11 family. +L-histidine = NH4(+) + trans-urocanate Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 1/3. Contains an active site 4-methylidene-imidazol-5-one (MIO), which is formed autocatalytically by cyclization and dehydration of residues Ala-Ser-Gly. Belongs to the PAL/histidase family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +May be involved in a process influencing telomere capping. Belongs to the WD repeat RTC1 family. +Participates in the formation of a gel matrix (sperm coagulum) entrapping the accessory gland secretions and ejaculated spermatozoa. Interacts with SERPINA5. Belongs to the semenogelin family. +Belongs to the universal ribosomal protein uS2 family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes. Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Homodimer and homohexamer; in equilibrium. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrR subfamily. +To C.perfringens pIP404 ORF6. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Negative regulator of FtsZ ring formation; modulates the frequency and position of FtsZ ring formation. Inhibits FtsZ ring formation at polar sites. Interacts either with FtsZ or with one of its binding partners to promote depolymerization. Colocalized with FtsZ to the nascent septal site. Belongs to the EzrA family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 1 subfamily. +Belongs to the PPR family. PCMP-E subfamily. +Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). diphosphate + N-(5-phospho-beta-D-ribosyl)anthranilate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate Binds 2 magnesium ions per monomer. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 2/5. Homodimer. Belongs to the anthranilate phosphoribosyltransferase family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate. AH2 + GTP + S-adenosyl-L-methionine = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + A + H(+) + L-methionine Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate. Cofactor biosynthesis; molybdopterin biosynthesis. Monomer and homodimer. Belongs to the radical SAM superfamily. MoaA family. +Essential component of the Ost-alpha/Ost-beta complex, a heterodimer that acts as the intestinal basolateral transporter responsible for bile acid export from enterocytes into portal blood (PubMed:15563450, PubMed:16317684, PubMed:17650074, PubMed:22535958). The Ost-alpha/Ost-beta complex efficiently transports the major species of bile acids (taurocholate) (PubMed:16317684, PubMed:17650074, PubMed:22535958). Taurine conjugates are transported more efficiently across the basolateral membrane than glycine-conjugated bile acids (PubMed:16317684). Can also transport steroids such as estrone 3-sulfate and dehydroepiandrosterone 3-sulfate, therefore playing a role in the enterohepatic circulation of sterols (By similarity). Able to transport eicosanoids such as prostaglandin E2 (By similarity). Modulates SLC51A glycosylation, membrane trafficking and stability activities (PubMed:15563450). taurocholate(out) = taurocholate(in) tauroursodeoxycholate(out) = tauroursodeoxycholate(in) glycoursodeoxycholate(out) = glycoursodeoxycholate(in) glycocholate(out) = glycocholate(in) taurochenodeoxycholate(out) = taurochenodeoxycholate(in) glycochenodeoxycholate(out) = glycochenodeoxycholate(in) taurodeoxycholate(out) = taurodeoxycholate(in) glycodeoxycholate(out) = glycodeoxycholate(in) prostaglandin E2(out) = prostaglandin E2(in) estrone 3-sulfate(out) = estrone 3-sulfate(in) dehydroepiandrosterone 3-sulfate(out) = dehydroepiandrosterone 3-sulfate(in) Interacts with SLC51A. The Ost-alpha/Ost-beta complex is a heterodimer composed of alpha (SLC51A) and beta (SLC51B) subunit; induces the transport of SLC51A from the reticulum endoplasmic to the plasma membrane. Mainly restricted to the lateral and basal membranes of ileal enterocytes. Present at high level in ileum. In ileum, it is restricted to the apical domain on the mature villus enterocytes with little detectable expression in the goblet cells or crypt enterocytes (at protein level). Expressed in kidney but not in heart, brain, liver, spleen, embryo, lung, thymus, ovary nor testis. Positively regulated via the bile acid-activated nuclear receptor farnesoid X receptor (NR1H4/FXR). The transmembrane domain (TM) is the major site of interaction with SLC51A. The extracellular-membrane interface is absolutely required for transport activity. The intracellular-membrane interface is necessary for establishing the correct membrane orientation that is essential for the heterodimer Ost-alpha/Ost-beta complex formation and transport activity at the cell membrane surface. Belongs to the OST-beta family. Truncated C-terminus. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +Transfers a succinyl group from succinyl-CoA to L-homoserine, forming succinyl-L-homoserine. L-homoserine + succinyl-CoA = CoA + O-succinyl-L-homoserine Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; O-succinyl-L-homoserine from L-homoserine: step 1/1. Belongs to the MetA family. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbK family. +Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 1 subfamily. +Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system. ATP + H2O + phosphate(out) = ADP + H(+) + 2 phosphate(in) The complex is composed of two ATP-binding proteins (PstB), two transmembrane proteins (PstC and PstA) and a solute-binding protein (PstS). Belongs to the ABC transporter superfamily. Phosphate importer (TC 3.A.1.7) family. +Required for formate dehydrogenase (FDH) activity. Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH. Belongs to the FdhD family. +Involved in the aerobic and anaerobic degradation of long-chain fatty acids via beta-oxidation cycle. Catalyzes the formation of 3-oxoacyl-CoA from enoyl-CoA via L-3-hydroxyacyl-CoA. It can also use D-3-hydroxyacyl-CoA and cis-3-enoyl-CoA as substrate. a (3S)-3-hydroxyacyl-CoA + NAD(+) = a 3-oxoacyl-CoA + H(+) + NADH a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O a 4-saturated-(3S)-3-hydroxyacyl-CoA = a (3E)-enoyl-CoA + H2O (3S)-3-hydroxybutanoyl-CoA = (3R)-3-hydroxybutanoyl-CoA a (3Z)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA a (3E)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadB) and two beta chains (FadA). In the N-terminal section; belongs to the enoyl-CoA hydratase/isomerase family. In the C-terminal section; belongs to the 3-hydroxyacyl-CoA dehydrogenase family. +Suppresses apoptosis in a variety of cell systems including factor-dependent lymphohematopoietic and neural cells (PubMed:1508712, PubMed:8183370). Regulates cell death by controlling the mitochondrial membrane permeability (PubMed:11368354). Appears to function in a feedback loop system with caspases (PubMed:11368354). Inhibits caspase activity either by preventing the release of cytochrome c from the mitochondria and/or by binding to the apoptosis-activating factor (APAF-1) (PubMed:11368354). Also acts as an inhibitor of autophagy: interacts with BECN1 and AMBRA1 during non-starvation conditions and inhibits their autophagy function (PubMed:18570871, PubMed:21358617, PubMed:20889974). May attenuate inflammation by impairing NLRP1-inflammasome activation, hence CASP1 activation and IL1B release (PubMed:17418785). Forms homodimers, and heterodimers with BAX, BAD, BAK and Bcl-X(L). Heterodimerization with BAX requires intact BH1 and BH2 motifs, and is necessary for anti-apoptotic activity (PubMed:8183370, PubMed:25609812). Part of a complex composed of SEPTIN4 isoform ARTS, XIAP and BCL2, within the complex interacts (via BH3 domain) with SEPTIN4 isoform ARTS and XIAP, SEPTIN4 isoform ARTS acts as a scaffold protein and stabilizes the complex (PubMed:29020630). Interacts with EI24 (By similarity). Also interacts with APAF1, BBC3, BCL2L1, BNIPL, MRPL41 and TP53BP2. Binding to FKBP8 seems to target BCL2 to the mitochondria and probably interferes with the binding of BCL2 to its targets. Interacts with BAG1 in an ATP-dependent manner. Interacts with RAF1 (the 'Ser-338' and 'Ser-339' phosphorylated form). Interacts (via the BH4 domain) with EGLN3; the interaction prevents the formation of the BAX-BCL2 complex and inhibits the anti-apoptotic activity of BCL2. Interacts with G0S2; this interaction also prevents the formation of the anti-apoptotic BAX-BCL2 complex. Interacts with RTL10/BOP. Interacts with the SCF(FBXO10) complex. Interacts (via the loop between motifs BH4 and BH3) with NLRP1 (via LRR repeats), but not with NLRP2, NLRP3, NLRP4, PYCARD, nor MEFV (PubMed:17418785). Interacts with GIMAP3/IAN4, GIMAP4/IAN1 and GIMAP5/IAN5 (By similarity). Interacts with BCAP31 (PubMed:31206022). Interacts with IRF3; the interaction is inhibited by Sendai virus infection (PubMed:25609812). Interacts with BECN1; thereby inhibiting autophagy in non-starvation conditions (PubMed:18570871, PubMed:21358617). Interacts with AMBRA1; thereby inhibiting autophagy (PubMed:21358617). Expressed in a variety of tissues. BH1 and BH2 domains are required for the interaction with BAX and for anti-apoptotic activity. The BH4 motif is required for anti-apoptotic activity and for interaction with RAF1 and EGLN3. The loop between motifs BH4 and BH3 is required for the interaction with NLRP1. The BH3 domain is required for interaction with SEPTIN4 isoform ARTS and thereby for XIAP-mediated ubiquitination and subsequent induction of apoptosis. Phosphorylation/dephosphorylation on Ser-70 regulates anti-apoptotic activity (PubMed:11368354). Growth factor-stimulated phosphorylation on Ser-70 by PKC is required for the anti-apoptosis activity and occurs during the G2/M phase of the cell cycle (PubMed:11368354). In the absence of growth factors, BCL2 appears to be phosphorylated by other protein kinases such as ERKs and stress-activated kinases (PubMed:11368354). Phosphorylated by MAPK8/JNK1 at Thr-69, Ser-70 and Ser-87, wich stimulates starvation-induced autophag (PubMed:10567572, PubMed:18570871). Dephosphorylated by protein phosphatase 2A (PP2A) (By similarity). Proteolytically cleaved by caspases during apoptosis. The cleaved protein, lacking the BH4 motif, has pro-apoptotic activity, causes the release of cytochrome c into the cytosol promoting further caspase activity. Monoubiquitinated by PRKN, leading to an increase in its stability (PubMed:20889974). Ubiquitinated by SCF(FBXO10), leading to its degradation by the proteasome (PubMed:23431138). Ubiquitinated by XIAP, leading to its degradation by the proteasome (PubMed:29020630). A chromosomal aberration involving BCL2 has been found in chronic lymphatic leukemia. Translocation t(14;18)(q32;q21) with immunoglobulin gene regions. BCL2 mutations found in non-Hodgkin lymphomas carrying the chromosomal translocation could be attributed to the Ig somatic hypermutation mechanism resulting in nucleotide transitions. Belongs to the Bcl-2 family. Bcl-2 entry +Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single-stranded and double-stranded RNA (By similarity). an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]. an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]. Monomer. Belongs to the pancreatic ribonuclease family. +Ribonucleoside-diphosphate reductase holoenzyme provides the precursors necessary for viral DNA synthesis. Allows virus growth in non-dividing cells. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity). [thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-diphosphate Binds 2 iron ions per subunit. Genetic information processing; DNA replication. Heterodimer of a large and a small chain. Belongs to the ribonucleoside diphosphate reductase small chain family. +Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP. an acyl phosphate + sn-glycerol 3-phosphate = a 1-acyl-sn-glycero-3-phosphate + phosphate Lipid metabolism; phospholipid metabolism. Probably interacts with PlsX. Belongs to the PlsY family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). 3-methyl-2-oxobutanoate + acetyl-CoA + H2O = (2S)-2-isopropylmalate + CoA + H(+) Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 1/4. Homotetramer. Belongs to the alpha-IPM synthase/homocitrate synthase family. LeuA type 1 subfamily. +D-glyceraldehyde 3-phosphate + NADP(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADPH D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5. Homotetramer. Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. +Probable neurotoxin with unknown target. Possibly targets ion channels. Expressed by the venom duct. The cysteine framework is I (CC-C-C). Alpha5/5 pattern. Belongs to the conotoxin A superfamily. +Belongs to the UPF0270 family. +Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides. May be an antioxidant enzyme particularly in the developing shoot and photosynthesizing leaf. [thioredoxin]-dithiol + a hydroperoxide = [thioredoxin]-disulfide + an alcohol + H2O Homodimer; disulfide-linked, upon oxidation (By similarity). Interacts with the plastidial thioredoxin CDSP32 (PubMed:12084836). Interacts with the plastidial NADPH-dependent thioredoxin reductase ANTR-C (PubMed:16884685). Down-regulated under highly reduced cellular thiol pool conditions. Down-regulated by ascorbate. Slightly induced by oxidative stress. The active site is a conserved redox-active cysteine residue, the peroxidatic cysteine (C(P)), which makes the nucleophilic attack on the peroxide substrate. The peroxide oxidizes the C(P)-SH to cysteine sulfenic acid (C(P)-SOH), which then reacts with another cysteine residue, the resolving cysteine (C(R)), to form a disulfide bridge. The disulfide is subsequently reduced by an appropriate electron donor to complete the catalytic cycle. In this typical 2-Cys peroxiredoxin, C(R) is provided by the other dimeric subunit to form an intersubunit disulfide. The disulfide is subsequently reduced by thioredoxin CDSP32. Belongs to the peroxiredoxin family. AhpC/Prx1 subfamily. +Ubiquitin-like modifier that increases cell-surface expression of kappa-type opioid receptor through facilitating anterograde intracellular trafficking of the receptor. Involved in formation of autophagosomal vacuoles. While LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation. The precursor molecule is cleaved by ATG4 (atg4a, atg4b, atg4c or atg4d) to expose the glycine at the C-terminus and form the cytosolic form, gabarapl1-I. The processed form is then activated by apg7l/atg7, transferred to atg3 and conjugated to phosphatidylethanolamine (PE) phospholipid to form the membrane-bound form, gabarapl1-II. During non-canonical autophagy, the processed form is conjugated to phosphatidylserine (PS) phospholipid. Atg4 proteins also mediate the delipidation of PE-conjugated forms required for gabarapl1 recycling when autophagosomes fuse with lysosomes. In addition, some atg4 proteins mediate delipidation of ATG8 proteins conjugated to PS during non-canonical autophagy. Belongs to the ATG8 family. +Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate. ATP + shikimate = 3-phosphoshikimate + ADP + H(+) Binds 1 Mg(2+) ion per subunit. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 5/7. Monomer. Belongs to the shikimate kinase family. +Catalytic subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation (By similarity). N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity. This subunit contains the active site and the acceptor peptide and donor lipid-linked oligosaccharide (LLO) binding pockets (By similarity). STT3A is present in the majority of OST complexes and mediates cotranslational N-glycosylation of most sites on target proteins, while STT3B-containing complexes are required for efficient post-translational glycosylation and mediate glycosylation of sites that have been skipped by STT3A (PubMed:12887896). a dolichyl diphosphooligosaccharide + L-asparaginyl-[protein] = a dolichyl diphosphate + H(+) + N(4)-(oligosaccharide-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl)-L-asparaginy-[protein] Protein modification; protein glycosylation. Component of the oligosaccharyltransferase (OST) complex (By similarity). OST exists in two different complex forms which contain common core subunits RPN1, RPN2, OST48, OST4, DAD1 and TMEM258, either STT3A or STT3B as catalytic subunits, and form-specific accessory subunits (PubMed:12887896, PubMed:15835887, PubMed:25135935). STT3A complex assembly occurs through the formation of 3 subcomplexes. Subcomplex 1 contains RPN1 and TMEM258, subcomplex 2 contains the STT3A-specific subunits STT3A, DC2/OSTC, and KCP2 as well as the core subunit OST4, and subcomplex 3 contains RPN2, DAD1, and OST48. The STT3A complex can form stable complexes with the Sec61 complex or with both the Sec61 and TRAP complexes (PubMed:29519914). Despite low primary sequence conservation between eukaryotic catalytic subunits and bacterial and archaeal single subunit OSTs (ssOST), structural comparison revealed several common motifs at spatially equivalent positions, like the DXD motif 1 on the external loop 1 and the DXD motif 2 on the external loop 2 involved in binding of the metal ion cofactor and the carboxamide group of the acceptor asparagine, the conserved Glu residue of the TIXE/SVSE motif on the external loop 5 involved in catalysis, as well as the WWDYG and the DK/MI motifs in the globular domain that define the binding pocket for the +2 Ser/Thr of the acceptor sequon. In bacterial ssOSTs, an Arg residue was found to interact with a negatively charged side chain at the -2 position of the sequon. This Arg is conserved in bacterial enzymes and correlates with an extended sequon requirement (Asp-X-Asn-X-Ser/Thr) for bacterial N-glycosylation. Belongs to the STT3 family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Catalyzes the alpha-1,2 addition of a mannose residue from polyprenol-phosphate-mannose (PPM) to a monoacyl phosphatidylinositol pentamannoside (AcPIM5) to generate a monoacyl phosphatidylinositol hexamannoside (AcPIM6). Phospholipid metabolism; phosphatidylinositol metabolism. Belongs to the glycosyltransferase 87 family. Truncated N-terminus. Extended N-terminus. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Some bacteria have evolved a zinc-coordinating structure that stabilizes the LID domain. Belongs to the adenylate kinase family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Neurotoxin with probable ion channel impairing activity. In vivo, is both paralytic and lethal, when injected into lepidopteran larvae. Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. LD(50) is 1.40 mg/kg by subcutaneous injection. Belongs to the neurotoxin 21 family. +Operates as a K(+)/H(+) antiporter that maintains K(+) homeostasis in guard cells and could regulate pH. Plays a critical role in osmoregulation through the control of stomates opening. Expressed in leaves and stems. Preferentially expressed in guards cells. Impaired light-induced stomatal opening. Belongs to the monovalent cation:proton antiporter 2 (CPA2) transporter (TC 2.A.37) family. CHX (TC 2.A.37.4) subfamily. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +May influence blood pressure by functioning as a GTPase-activating protein for RHOA in vascular smooth muscle. Highly and selectively expressed in smooth muscle cells. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 3 subfamily. +Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Oxidized purine nucleoside triphosphate hydrolase which is a prominent sanitizer of the oxidized nucleotide pool (PubMed:26862114, PubMed:30304478). Catalyzes the hydrolysis of 2-oxo-dATP (2-hydroxy-dATP) into 2-oxo-dAMP (PubMed:26862114). Has also a significant hydrolase activity toward 2-oxo-ATP, 8-oxo-dGTP and 8-oxo-dATP (PubMed:26862114, PubMed:30304478). Through the hydrolysis of oxidized purine nucleoside triphosphates, prevents their incorporation into DNA and the subsequent transversions A:T to C:G and G:C to T:A (PubMed:26862114, PubMed:30304478). Also catalyzes the hydrolysis of methylated purine nucleoside triphosphate preventing their integration into DNA (PubMed:32144205, PubMed:30304478). Through this antimutagenic activity protects cells from oxidative stress (PubMed:32144205, PubMed:26862114, PubMed:30304478). 2-oxo-dATP + H2O = 2-oxo-dAMP + diphosphate + H(+) 2-oxo-ATP + H2O = 2-oxo-AMP + diphosphate + H(+) 8-oxo-dGTP + H2O = 8-oxo-dGMP + diphosphate + H(+) 8-oxo-dATP + H2O = 8-oxo-dAMP + diphosphate + H(+) H2O + O(6)-methyl-dGTP = diphosphate + H(+) + O(6)-methyl-dGMP H2O + N(6)-methyl-dATP = diphosphate + H(+) + N(6)-methyl-dAMP H2O + N(6)-methyl-ATP = diphosphate + H(+) + N(6)-methyl-AMP Binds 2 Mg(2+) ion per subunit. Inhibited by TH588. kcat is 5.4 sec(-1) with 8-oxo-dGTP as substrate (at pH 7.5) (PubMed:26862114). kcat is 12.0 sec(-1) with 2-oxo-dATP as substrate (at pH 7.5) (PubMed:26862114). kcat is 7.6 sec(-1) with dGTP as substrate (at pH 7.5) (PubMed:26862114). Shows the best catalytic efficiency for the 8-oxo-dGTP substrate (PubMed:26862114). Monomer. Belongs to the Nudix hydrolase family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Homodimer. Belongs to the CutC family. Once thought to be involved in copper homeostasis, experiments in E.coli have shown this is not the case. +Binds with high affinity to muscular (alpha-1/CHRNA1) and neuronal (alpha-7/CHRNA7) nicotinic acetylcholine receptor (nAChR) and inhibits acetylcholine from binding to the receptor, thereby impairing neuromuscular and neuronal transmission. Expressed by the venom gland. Belongs to the snake three-finger toxin family. Long-chain subfamily. Type II alpha-neurotoxin sub-subfamily. +May have a role in mesendoderm development during embryogenesis. Expressed in mesendodermal precursor cells of embryos. Tenfold increase in expression between 4-cell and 12-cell embryos. Down-regulated in 12-cell embryos from mutant worms lacking skn-1. +Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA. S-adenosyl-L-methionine + uridine(1939) in 23S rRNA = 5-methyluridine(1939) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily. +Catalyzes the conversion of lactate to pyruvate. (S)-lactate + NAD(+) = H(+) + NADH + pyruvate Allosterically activated by fructose 1,6-bisphosphate (FBP). Fermentation; pyruvate fermentation to lactate; (S)-lactate from pyruvate: step 1/1. Homotetramer. Belongs to the LDH/MDH superfamily. LDH family. +Seems to play a role in the dimerization of PSII. Belongs to the PsbT family. +Belongs to the FAM166C family. +Transports viral genome to neighboring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier. Forms a ribonucleoprotein complex with viral RNA. Binds microtubules and modulates microtubule stability. Can bind double-stranded DNA. Triggers host hypersensitive defense reaction in incompatible plants harboring resistance (R) proteins. Binds to host RBCS at the plasmodesmata; this interaction seems required for viral systemic movement (By similarity). In resistant plants, interacts with host MBP2C at host microtubules; this interaction prevents virus cell to cell movement. In resistant plants, interacts with host resistance (R) protein (e.g. tomato ToMV resistance protein TM-2(2), AC Q71BG9) at the host plasma membrane; this interaction triggers host defense responses leading to programmed cell death (By similarity). Binds to the host cytoskeleton before being transported to the host plasmodesmata. Observed in virus replication complexes (VRCs) of tobamovirus infected host cells (By similarity). In resistant plants, targeted to the host plasma membrane via the interaction with host resistance (R) protein TM-2 (e.g. tomato ToMV resistance protein TM-2(2), AC Q71BG9) (By similarity). Belongs to the tobamovirus movement protein family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL2 family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Plasma membrane osmosensor that activates the high osmolarity glycerol (HOG) MAPK signaling pathway in response to high osmolarity. Forms homooligomers. Belongs to the SHO1 family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Probable cell surface metalloreductase. May be involved in iron or copper homeostasis (By similarity). Belongs to the ferric reductase (FRE) family. AIM14 subfamily. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in general and miRNA-mediated mRNA turnover. PAN specifically shortens poly(A) tails of RNA and the activity is stimulated by poly(A)-binding protein (PABP). PAN deadenylation is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping and subsequent 5'-3' exonucleolytic degradation by XRN1. Exonucleolytic cleavage of poly(A) to 5'-AMP. Binds 2 metal cations per subunit in the catalytic exonuclease domain. Positively regulated by the regulatory subunit PAN3. Forms a heterotrimer with an asymmetric homodimer of the regulatory subunit PAN3 to form the poly(A)-nuclease (PAN) deadenylation complex. Shuttles between nucleus and cytoplasm. Contains a pseudo-UCH domain. This ubiquitin C-terminal hydrolase (UCH)-like or ubiquitin specific protease (USP)-like domain is predicted to be catalytically inactive because it lacks the active site catalytic triad characteristic of thiol proteases, with residues at the equivalent structural positions that are incompatible with catalysis, and it cannot bind ubiquitin. It functions as a structural scaffold for intra- and intermolecular interactions in the complex. The linker, or PAN3 interaction domain (PID), between the WD40 repeats and the pseudo-UCH domain mediates interaction with PAN3. Belongs to the peptidase C19 family. PAN2 subfamily. +Structural protein required for transport of intracellular particles from the assembly sites to the plasma membrane (By similarity). Binds to both ssDNA and dsDNA (By similarity). Suppressed the activation of the cGAS/STING pathway by interfering with the recruitment of IRF3 to TBK1, which in turn suppresses IRF3 phosphorylation, decreasing interferon production (By similarity). Interacts with the major capsid protein (By similarity). Interacts with host IRF3; this interaction interfers with the recruitment of IRF3 to TBK1 (By similarity). Localizes at the surface of the intracellular virion. Expressed in the late phase of the viral replicative cycle. Acetylated. Belongs to the asfivirus structural protein p14.5 family. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Belongs to the UPF0325 family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Catalyzes the hydrolytic deamination of dCMP to yield dUMP, the nucleotide substrate for thymidylate synthetase. dCMP + H(+) + H2O = dUMP + NH4(+) Allosteric enzyme whose activity is greatly influenced by the end products of its metabolic pathway, dCTP and dTTP. Present with 1510 molecules/cell in log phase SD medium. Belongs to the cytidine and deoxycytidylate deaminase family. +A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+). Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis. Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes. Belongs to the type II topoisomerase GyrB family. +Regulatory subunit of a potassium efflux system that confers protection against electrophiles. Required for full activity of KefC. Shows redox enzymatic activity, but this enzymatic activity is not required for activation of KefC. a quinone + H(+) + NADH = a quinol + NAD(+) a quinone + H(+) + NADPH = a quinol + NADP(+) Homodimer. Interacts with KefC. Belongs to the NAD(P)H dehydrogenase (quinone) family. KefF subfamily. +Probable transcription factor that forms a heterodimer with the MADS-box protein AGL104 and is involved in the regulation of pollen maturation at the late stages of pollen development and pollen tube growth. Forms a heterodimer with AGL104. Expressed in pollen. +Involved in the type II arabinogalactan (AG) side chains degradation (PubMed:30564851). Specifically releases the non-reducing terminal beta-1,6-galactobiose (beta-1,6-Gal2) from both dearabinosylated larch AG and polymeric beta-1,6-galactan chains by an exo-mode of action (PubMed:30564851). Shows lower activity with larch AG, and very weak activity with dearabinosylated gum arabic, gum arabic and potato galactan (PubMed:30564851). Can probably release beta-1,6-Gal2 from the internal side chains of type II AG (PubMed:30564851). Hydrolysis of (1->6)-beta-D-galactosidic linkages in arabinogalactan proteins and (1->3):(1->6)-beta-galactans to yield (1->6)-beta-galactobiose as the final product. kcat is 261 sec(-1) with beta-1,6-Gal3 as substrate. Optimum pH is 4.5 with beta-1,6-Gal3 as substrate. Optimum temperature is 40 degrees Celsius with beta-1,6-Gal3 as substrate. Belongs to the glycosyl hydrolase 30 family. +Part of the binding-protein-dependent transport system for D-xylose. Probably responsible for the translocation of the substrate across the membrane (By similarity). Belongs to the binding-protein-dependent transport system permease family. AraH/RbsC subfamily. +Belongs to the UPF0225 family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Cell wall formation. ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) + phosphate Binds 2 magnesium or manganese ions per subunit. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the D-alanine--D-alanine ligase family. +DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. Belongs to the NAD-dependent DNA ligase family. LigA subfamily. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. PetL is important for photoautotrophic growth as well as for electron transfer efficiency and stability of the cytochrome b6-f complex. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the PetL family. +Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions. diphosphate + H2O = H(+) + 2 phosphate Homohexamer. Maximal activity at 95 Celsius degrees. Belongs to the PPase family. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homotetramer; dimer of dimers. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis. phosphate + thymidine = 2-deoxy-alpha-D-ribose 1-phosphate + thymine Pyrimidine metabolism; dTMP biosynthesis via salvage pathway; dTMP from thymine: step 1/2. Homodimer. Belongs to the thymidine/pyrimidine-nucleoside phosphorylase family. +Ligand for members of the frizzled family of seven transmembrane receptors. Probable developmental protein. May be a signaling molecule which affects the development of discrete regions of tissues. Is likely to signal over only few cell diameters. Palmitoleoylation is required for efficient binding to frizzled receptors. Depalmitoleoylation leads to Wnt signaling pathway inhibition. Belongs to the Wnt family. +Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate. (2R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (2S)-2-acetolactate + H(+) + NADPH (2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP(+) = (S)-2-ethyl-2-hydroxy-3-oxobutanoate + H(+) + NADPH Binds 2 magnesium ions per subunit. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 2/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 2/4. Belongs to the ketol-acid reductoisomerase family. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Participates in the degradation of poly-3-hydroxybutyrate (PHB). It works downstream of poly(3-hydroxybutyrate) depolymerase, hydrolyzing D(-)-3-hydroxybutyrate oligomers of various length (3HB-oligomers) into 3HB-monomers. (3R)-hydroxybutanoate dimer + H2O = 2 (R)-3-hydroxybutanoate + H(+) Lipid metabolism; butanoate metabolism. Belongs to the D-(-)-3-hydroxybutyrate oligomer hydrolase family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, HCO(3)(-)/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate. ATP + hydrogencarbonate + L-threonine = diphosphate + H2O + L-threonylcarbamoyladenylate Belongs to the SUA5 family. TsaC subfamily. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. +Catalyzes a trans-dehydration via an enolate intermediate. 3-dehydroquinate = 3-dehydroshikimate + H2O Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 3/7. Homododecamer. Belongs to the type-II 3-dehydroquinase family. +Belongs to the TMEM248 family. +Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue. Belongs to the radical SAM superfamily. RlmN family. +Probable aspartic-type endopeptidase which contributes to virulence. Belongs to the peptidase A1 family. +Catalyzes the formation of the isocyclic ring in chlorophyll biosynthesis. Mediates the cyclase reaction, which results in the formation of divinylprotochlorophyllide (Pchlide) characteristic of all chlorophylls from magnesium-protoporphyrin IX 13-monomethyl ester (MgPMME). 2 H(+) + Mg-protoporphyrin IX 13-monomethyl ester + 3 NADPH + 3 O2 = 3,8-divinyl protochlorophyllide a + 5 H2O + 3 NADP(+) Porphyrin-containing compound metabolism; chlorophyll biosynthesis. Part of the FLU-containing chloroplast membrane complex composed of FLU, CRD1, PORB, PORC, CHLP and HEMA1. A number of isoforms are produced. According to EST sequences. Knock-down mutant (chl27-t) grow slowly with a pale green appearance. confers also severe defects in chloroplast development, including the unstacking of thylakoid membranes (PubMed:18682427). Belongs to the AcsF family. Truncated N-terminus. +Methyltransferase; part of the gene cluster that mediates the biosynthesis of UCS1025A, a member of the pyrrolizidinone family that acts as a strong telomerase inhibitor and displays potent antibacterial and antitumor properties (PubMed:29373009). These compounds share a hemiaminal-containing pyrrolizidinone core fused with a gamma-lactone, giving a furopyrrolizidine that is connected to a decalin fragment (PubMed:29373009). The polyketide synthase module (PKS) of the PKS-NRPS ucsA is responsible for the synthesis of the polyketide backbone via the condensation of an acetyl-CoA starter unit with 6 malonyl-CoA units (PubMed:29373009). The downstream nonribosomal peptide synthetase (NRPS) module then amidates the carboxyl end of the polyketide with a 2S,3S-methylproline derived from L-isoleucine by the 2-oxoglutarate-dependent dioxygenase ucsF which converts L-isoleucine to (4S,5S)-4-methylpyrroline-5-carboxylate that is further converted to 2S,3S-methylproline by the pyrroline-5-carboxylate reductase ucsG (PubMed:29373009). Reductive release of the completed aminoacyl polyketide from the assembly line can form the 3-pyrrolin-2-one structure via an intramolecular Knoevenagel reaction (PubMed:29373009). Because ucsA lacks a designated enoylreductase (ER) domain, the required activity is provided the enoyl reductase ucsL (PubMed:29373009). This keto acyclic precursor is the substrate of the Diels-Alderase ucsH, that catalyzes the Diels-Alder cycloaddition (PubMed:29373009). Oxidation of the 3S-methyl group to a carboxylate by the cytochrome P450 monooxygenase ucsK allows an oxa-Michael cyclization that might involve the reductase/dehydrogenase ucsI and which furnishes the furopyrrolizidine (PubMed:29373009). The oxidase ucsJ likely plays a critical role in stereoselective reduction of the C5-C6 double bond to afford the required R-configured carboxylate group (Probable). Further enolization and oxidation at C5 by an unidentified enzyme affords the last intermediate that can undergo oxa-Michael cyclization to yield UCS1025A (Probable). Mycotoxin biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Mediates the nuclear export of encapsidated genomic RNAs (ribonucleoproteins, RNPs). Acts as an adapter between viral RNPs complexes and the nuclear export machinery of the cell. Possesses no intrinsic RNA-binding activity, but includes a C-terminal M1-binding domain. This domain is believed to allow recognition of RNPs bound to the protein M1. Since protein M1 is not available in large quantities before late stages of infection, such an indirect recognition mechanism probably ensures that genomic RNPs are not exported from the host nucleus until sufficient quantities of viral mRNA and progeny genomic RNA have been synthesized. Furthermore, the RNPs enter the host cytoplasm only when associated with the M1 protein that is necessary to guide them to the plasma membrane. May down-regulate viral RNA synthesis when overproduced. Interacts with protein M1. May interact with host nucleoporin RAB/HRB and exportin XPO1/CRM1. Average number present in a viral particle is estimated to be 130-200 molecules. Belongs to the influenza viruses NEP family. +Multiprotein complex (SCF) with cullin and F-box-containing protein. Capable of undergoing aggregation. Expressed throughout the life cycle. O-linked glycan consists of linear Gal-Gal-Fuc-Gal-GlcNAc. FpaA and fpaB seem to be identically glycosylated. Glycosylation is required for nuclear enrichment. Hydroxylated by phyA. The mass corresponds to the peptide with Ser-2 acetylated, Pro-143 hydroxylated and modified by a GlcNAc residue. There are two genes coding for Skp1, they only differ in a single position in the coding region. Belongs to the SKP1 family. +Repressor involved in the biosynthesis of the osmoprotectant glycine betaine. It represses transcription of the choline transporter BetT and the genes of BetAB involved in the synthesis of glycine betaine (By similarity). Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway [regulation]. +Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Belongs to the Antp homeobox family. Proboscipedia subfamily. +Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids. acetyl-CoA + H(+) + malonyl-[ACP] = 3-oxobutanoyl-[ACP] + CO2 + CoA Lipid metabolism; fatty acid biosynthesis. Homodimer. The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH. Belongs to the thiolase-like superfamily. FabH family. +Exhibits acyltransferase activity (PubMed:21498505, PubMed:18156367). Exhibits acetyltransferase activity (By similarity). Activity is calcium-independent (By similarity). Catalyzes the conversion of lysophosphatidylcholine (1-acyl-sn-glycero-3-phosphocholine or LPC) into phosphatidylcholine (1,2-diacyl-sn-glycero-3-phosphocholine or PC) (PubMed:21498505, PubMed:18156367). Catalyzes the conversion 1-acyl-sn-glycerol-3-phosphate (lysophosphatidic acid or LPA) into 1,2-diacyl-sn-glycerol-3-phosphate (phosphatidic acid or PA) by incorporating an acyl moiety at the sn-2 position of the glycerol backbone (By similarity). Displays a clear preference for saturated fatty acyl-CoAs, and 1-myristoyl or 1-palmitoyl LPC as acyl donors and acceptors, respectively (By similarity). Involved in platelet-activating factor (PAF) biosynthesis by catalyzing the conversion of the PAF precursor, 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF) into 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine (PAF) (By similarity). May synthesize phosphatidylcholine in pulmonary surfactant, thereby playing a pivotal role in respiratory physiology (By similarity). Involved in the regulation of lipid droplet number and size (PubMed:25491198). a 1-acyl-sn-glycero-3-phosphocholine + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phosphocholine + CoA a 1-acyl-sn-glycero-3-phosphate + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phosphate + CoA 1-O-alkyl-sn-glycero-3-phosphocholine + acetyl-CoA = a 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine + CoA 1-O-(1Z-alkenyl)-sn-glycero-3-phosphocholine + an acyl-CoA = 1-O-(1Z-alkenyl)-2-acyl-sn-glycero-3-phosphocholine + CoA 1-acyl-sn-glycero-3-phospho-(1'-sn-glycerol) + an acyl-CoA = 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + CoA (9Z)-octadecenoyl-CoA + 1-hexadecanoyl-sn-glycero-3-phosphocholine = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + CoA 1-hexadecanoyl-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine + CoA 1-O-hexadecyl-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1-O-hexadecyl-2-hexadecanoyl-sn-glycero-3-phosphocholine + CoA 1-O-(1Z-alkenyl)-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1-O-(1Z)-alkenyl-2-hexadecanoyl-sn-glycero-3-phosphocholine + CoA 1-hexadecanoyl-sn-glycero-3-phospho-(1'-sn-glycerol) + hexadecanoyl-CoA = 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1'-sn-glycerol) + CoA 1-dodecanoyl-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1-dodecanoyl-2-hexadecanoyl-sn-glycero-3-phosphocholine + CoA 1-tetradecanoyl-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1-tetradecanoyl-2-hexadecanoyl-sn-glycero-3-phosphocholine + CoA 1-O-octadecyl-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1-O-octadecyl-2-hexadecanoyl-sn-glycero-3-phosphocholine + CoA 1-octadecanoyl-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1-octadecanoyl-2-hexadecanoyl-sn-glycero-3-phosphocholine + CoA 1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1-(9Z-octadecenoyl)-2-hexadecanoyl-sn-glycero-3-phosphocholine + CoA 1-eicosanoyl-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1-eicosanoyl-2-hexadecanoyl-sn-glycero-3-phosphocholine + CoA 1-hexadecanoyl-sn-glycero-3-phosphocholine + hexanoyl-CoA = 1-hexadecanoyl-2-hexanoyl-sn-glycero-3-phosphocholine + CoA 1-hexadecanoyl-sn-glycero-3-phosphocholine + octanoyl-CoA = 1-hexadecanoyl-2-octanoyl-sn-glycero-3-phosphocholine + CoA 1-hexadecanoyl-sn-glycero-3-phosphocholine + decanoyl-CoA = 1-hexadecanoyl-2-decanoyl-sn-glycero-3-phosphocholine + CoA 1-hexadecanoyl-sn-glycero-3-phosphocholine + dodecanoyl-CoA = 1-hexadecanoyl-2-dodecanoyl-sn-glycero-3-phosphocholine + CoA 1-hexadecanoyl-sn-glycero-3-phosphocholine + tetradecanoyl-CoA = 1-hexadecanoyl-2-tetradecanoyl-sn-glycero-3-phosphocholine + CoA (9Z,12Z)-octadecadienoyl-CoA + 1-hexadecanoyl-sn-glycero-3-phosphocholine = 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine + CoA (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA + 1-hexadecanoyl-sn-glycero-3-phosphocholine = 1-hexadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphocholine + CoA 1-hexadecanoyl-sn-glycero-3-phosphocholine + acetyl-CoA = 1-hexadecanoyl-2-acetyl-sn-glycero-3-phosphocholine + CoA 1-hexadecanoyl-sn-glycero-3-phosphocholine + eicosanoyl-CoA = 1-hexadecanoyl-2-eicosanoyl-sn-glycero-3-phosphocholine + CoA 1-O-hexadecyl-sn-glycero-3-phosphocholine + acetyl-CoA = 1-O-hexadecyl-2-acetyl-sn-glycero-3-phosphocholine + CoA a 1-acyl-sn-glycero-3-phosphocholine + hexadecanoyl-CoA = 1-acyl-2-hexadecanoyl-sn-glycero-3-phosphocholine + CoA a 1-acyl-sn-glycero-3-phosphate + hexadecanoyl-CoA = 1-acyl-2-hexadecanoyl-sn-glycero-3-phosphate + CoA 1-acyl-sn-glycero-3-phospho-(1'-sn-glycerol) + hexadecanoyl-CoA = 1-acyl-2-hexadecanoyl-sn-glycero-3-phospho-(1'-sn-glycerol) + CoA Optimum pH is 5.5 and 7.5. Lipid metabolism; phospholipid metabolism. May adopt a monotopic topology when embedded in the lipid monolayer of the lipid droplet, with both termini exposed to the cytoplasm. Erythrocytes. The HXXXXD motif is essential for acyltransferase activity and may constitute the binding site for the phosphate moiety of the glycerol-3-phosphocholine. The di-lysine motif may confer endoplasmic reticulum localization. Belongs to the 1-acyl-sn-glycerol-3-phosphate acyltransferase family. Truncated N-terminus. Truncated N-terminus. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +Seems to play a negative regulatory role in 5-phosphoribose 1-diphosphate synthesis. Binds to PRPS1 and PRPS2. Belongs to the ribose-phosphate pyrophosphokinase family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase C chain family. +Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. This protein is an E3 ubiquitin ligase that interferes with host's ubiquitination pathway. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Secreted via type III secretion system 1 (SPI-1 TTSS), and delivered into the host cell. Ubiquitinated in the presence of host E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme and ubiquitin. Belongs to the SopA E3 ligase family. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +Regulatory subunit of the trehalose synthase complex that catalyzes the production of trehalose from glucose-6-phosphate and UDP-glucose in a two step process. May stabilize the trehalose synthase complex, and confer sensitivity to physiological concentrations of phosphate and to fructose 6-phosphate. The trehalose synthase complex is composed of the two catalytic subunits TPS1 and TPS2, and at least one of the two regulatory subunits TPS3 or TSL1. Repressed by glucose. C-terminal 700 AA are mainly in alpha-helices and beta-sheets. Present with 1960 molecules/cell in log phase SD medium. In the C-terminal section; belongs to the glycosyltransferase 20 family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'-nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Magnesium is required for nucleotidyltransferase activity. Nickel for phosphatase activity. Monomer. Can also form homodimers and oligomers. Comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain associated with both phosphodiesterase and phosphatase activities. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 1 subfamily. +ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys) Binds 3 Mg(2+) ions per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Has endoglucanase activity on substrates containing beta-1,4 glycosidic bonds, like in carboxymethylcellulose (CMC), hydroxyethylcellulose (HEC) and beta-glucan. Involved in the degradation of complex natural cellulosic substrates. Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. Optimum pH is 4.0. Optimum temperature is 57 degrees Celsius. Highly expressed in presence of carboxymethylcellulose (CMC). Belongs to the glycosyl hydrolase 5 (cellulase A) family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Na(+)/H(+) antiporter that extrudes sodium in exchange for external protons. 2 H(+)(out) + Na(+)(in) = 2 H(+)(in) + Na(+)(out) Belongs to the NhaA Na(+)/H(+) (TC 2.A.33) antiporter family. +Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF2. Belongs to the prokaryotic/mitochondrial release factor family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Catalyzes the cleavage of L-arabino-gamma-lactone to L-arabonate. Is involved in a degradation pathway of L-arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. Can also use D-galactono-1,4-lactone as substrate in vitro; however, the enzyme is probably not involved in the metabolism of D-galactose in vivo. H2O + L-arabinono-1,4-lactone = H(+) + L-arabinonate Binds 1 divalent metal cation per subunit. Belongs to the SMP-30/CGR1 family. +Involved in chemotaxis. Part of a chemotaxis signal transduction system that modulates chemotaxis in response to various stimuli. Catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins or MCP) by CheR. Also mediates the irreversible deamidation of specific glutamine residues to glutamic acid. [protein]-L-glutamate 5-O-methyl ester + H2O = H(+) + L-glutamyl-[protein] + methanol H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Contains a C-terminal catalytic domain, and an N-terminal region which modulates catalytic activity. Phosphorylated by CheA. Phosphorylation of the N-terminal regulatory domain activates the methylesterase activity. Belongs to the CheB family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +Belongs to the bacterial ribosomal protein bL33 family. +Belongs to the universal ribosomal protein uL14 family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O H2O + L-histidinol phosphate = L-histidinol + phosphate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 8/9. In the N-terminal section; belongs to the histidinol-phosphatase family. In the C-terminal section; belongs to the imidazoleglycerol-phosphate dehydratase family. +Non-catalytic component of a structure-specific DNA repair endonuclease responsible for the 5'-incision during DNA repair. Responsible, in conjunction with SLX4, for the first step in the repair of interstrand cross-links (ICL). Participates in the processing of anaphase bridge-generating DNA structures, which consist in incompletely processed DNA lesions arising during S or G2 phase, and can result in cytokinesis failure. Also required for homology-directed repair (HDR) of DNA double-strand breaks, in conjunction with SLX4. Not functional in the nucleotide excision repair pathway. Not functional in the nucleotide excision repair pathway. Not functional in the nucleotide excision repair pathway. Heterodimer composed of ERCC1 isoform 1 and ERCC4/XPF (PubMed:16076955, PubMed:16338413, PubMed:24036546, PubMed:25538220, PubMed:32034146). Interacts with USP45 (PubMed:25538220). Does not interact with ERCC4/XPF. Does not interact with ERCC4/XPF. Does not interact with ERCC4/XPF. Ubiquitinated with both 'Lys-48' and 'Lys-63' linkages (PubMed:25538220). Deubiquitinated by USP45 (PubMed:25538220). The disease is caused by variants affecting the gene represented in this entry. Belongs to the ERCC1/RAD10/SWI10 family. +Belongs to the UPF0440 family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Adapter protein which modulates coupling of cell surface receptor kinases with specific signaling pathways. Binds to, and suppresses signals from, the activated insulin receptor (INSR). Potent inhibitor of insulin-stimulated MAPK3 phosphorylation. Plays a critical role regulating PDPK1 membrane translocation in response to insulin stimulation and serves as an adapter protein to recruit PDPK1 to activated insulin receptor, thus promoting PKB/AKT1 phosphorylation and transduction of the insulin signal. Interacts with the cytoplasmic domain of the autophosphorylated insulin receptor (INSR), through the SH2 domain (By similarity). Interacts with GRB14 (via BPS domain); this interaction protects the tyrosines in the activation loop on INSR from dephosphorylation. Binds to the ankyrin repeat region of TNKS2 via its N-terminus. Interacts with activated NRAS. Interacts (via SH2 domain) with TEK/TIE2 (tyrosine phosphorylated). Upon insulin stimulation, translocates to the plasma membrane. Expressed at high levels in the liver, kidney, pancreas, testis, ovary, heart and skeletal muscle. The PH domain binds relatively non-specifically and with low affinity to several phosphoinositides, the best binder being PI(3,4,5)P3. Phosphorylated on serine residues. Phosphorylated on tyrosine residues by TEK/TIE2. Belongs to the GRB7/10/14 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity. adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue. Belongs to the radical SAM superfamily. RlmN family. +Chemotactic-signal transducers respond to changes in the concentration of attractants and repellents in the environment, transduce a signal from the outside to the inside of the cell, and facilitate sensory adaptation through the variation of the level of methylation. TlpQ is a chemoreceptor that binds and mediates chemotaxis to histamine, a key biological signaling molecule. It binds histamine with high affinity, which permits responses to very low histamine concentrations (PubMed:30425146). Chemotaxis to histamine may play a role in the virulence of P.aeruginosa by recruiting cells at the infection site and consequently modulating the expression of quorum-sensing-dependent virulence genes (Probable). TlpQ also binds and mediates chemotaxis to polyamines such as putrescine, spermidine, cadaverine, agmatine and ethylenediamine (PubMed:30425146). In addition, binds the quorum-sensing signal autoinducer 2 (AI-2), thus inducing chemotaxis toward AI-2 and biofilm formation (PubMed:33097715). Homotetramer. The pctABC-tlpQ deletion mutant is devoid of histamine chemotaxis over the entire concentration range (50 nM to 50 mM) (PubMed:30425146). Deletion of the gene significantly reduces chemotaxis to AI-2 (PubMed:33097715). Belongs to the methyl-accepting chemotaxis (MCP) protein family. +Catalyzes carboxymethyl transfer from carboxy-S-adenosyl-L-methionine (Cx-SAM) to 5-hydroxyuridine (ho5U) to form 5-carboxymethoxyuridine (cmo5U) at position 34 in tRNAs. 5-hydroxyuridine(34) in tRNA + carboxy-S-adenosyl-L-methionine = 5-carboxymethoxyuridine(34) in tRNA + H(+) + S-adenosyl-L-homocysteine Homotetramer. Belongs to the class I-like SAM-binding methyltransferase superfamily. CmoB family. +Cell wall formation. ATP + L-alanine + UDP-N-acetyl-alpha-D-muramate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides and as sensor of hydrogen peroxide-mediated signaling events. Preferentially eliminates organic peroxides rather than hydrogen peroxide (PubMed:10391912, PubMed:9988687, PubMed:10681558). Relays alkyl hydroperoxides as a signal to the transcription factor CAD1/YAP2 by inducing the formation of intramolecular disulfide bonds in CAD1, which causes its nuclear accumulation and activation (PubMed:20145245). Involved in cellular Mn(2+) homeostasis (PubMed:10635552). [thioredoxin]-dithiol + a hydroperoxide = [thioredoxin]-disulfide + an alcohol + H2O Optimum pH is 6.5. Homodimer; disulfide-linked, upon oxidation. By H(2)O(2). Conjugated to URM1, a ubiquitin-like protein. The active site is a conserved redox-active cysteine residue, the peroxidatic cysteine (C(P)), which makes the nucleophilic attack on the peroxide substrate. The peroxide oxidizes the C(P)-SH to cysteine sulfenic acid (C(P)-SOH), which then reacts with another cysteine residue, the resolving cysteine (C(R)), to form a disulfide bridge. The disulfide is subsequently reduced by an appropriate electron donor to complete the catalytic cycle. In this typical 2-Cys Prx, C(R) is provided by the other dimeric subunit to form an intersubunit disulfide. The disulfide is subsequently reduced by thioredoxin. Present with 16228 molecules/cell in log phase SD medium. Belongs to the peroxiredoxin family. Prx5 subfamily. Biochemical and mutational analysis assigned Cys-120 as the resolving cysteine (C(R)) (PubMed:9888818). However, crystal structures showed that Cys-120 is deeply buried within the protein and revealed formation of a disulfide bond between the peroxidatic cysteine Cys-62 and the therefore more likely C(R) Cys-31 (PubMed:22474296, Ref.21). +Molecular chaperone capable of stabilizing a range of proteins. Seems to fulfill an ATP-independent, HSP70-like function in archaeal de novo protein folding. Heterohexamer of two alpha and four beta subunits. Belongs to the prefoldin subunit alpha family. +2-methylcitrate dehydratase-like protein; part of the gene cluster that mediates the biosynthesis of oryzines, natural products with an unusual maleidride backbone (PubMed:30104550). The two subunits of the fungal fatty acid synthase oryfasA and oryfasB probably form octenoic acid (Probable). This fatty acid is most likely activated by the acyl-CoA ligase oryP to give octenyl-CoA before the citrate synthase-like protein oryE catalyzes condensation with oxaloacetate to form tricarboxylic acid (Probable). The next steps of the pathways are conjectural, but a favorite possible route has been proposed, beginning with decarboxylation and concomitant dehydration by the decarboxylase oryM, followed by tautomerization, which may lead to the production of a diene intermediate (Probable). Reduction of this diene intermediate could give the known metabolite piliformic acid (Probable). On the pathway to oryzine B and oryzine A, however, hydroxylation of the diene by the alpha-ketoglutarate-dependent dioxygenase oryG and lactonisation by the lactonohydrolases oryH or oryL could give oryzine B directly (Probable). Finally, enoyl reduction by the dehydrogenase oryD would then convert oryzine B into oryzine A (Probable). Secondary metabolite biosynthesis. Belongs to the PrpD family. +Endoribonuclease that initiates mRNA decay. Belongs to the RNase Y family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +Component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in ubiquitin-proteasome systems (By similarity). +By wounding. Belongs to the Bowman-Birk serine protease inhibitor family. +Belongs to the UPF0234 family. +Involved in iron-sulfur (Fe-S) cluster assembly. May act as a regulator of Fe-S biogenesis. Belongs to the frataxin family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +mRNA cap-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. In the eIF-3 complex, eif3d specifically recognizes and binds the 7-methylguanosine cap of a subset of mRNAs. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The RNA gate region regulates mRNA cap recognition to prevent promiscuous mRNA-binding before assembly of eif3d into the full eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the eIF-3 subunit D family. +Has a dual role in the assembly of mitochondrial ATPase. Acts as a protease that removes N-terminal residues of mitochondrial ATPase CF(0) subunit 6 at the intermembrane space side. Also involved in the correct assembly of the membrane-embedded ATPase CF(0) particle, probably mediating association of subunit 6 with the subunit 9 ring (By similarity). Associates loosely with the inner membrane. Belongs to the peptidase M76 family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Belongs to the UPF0735 family. +Catalyzes the formation of 5-oxoproline from gamma-glutamyl dipeptides and plays a significant role in glutathione (GSH) homeostasis. Converts GSH to 5-oxoproline and cysteine-glycine (Cys-Gly) dipeptide in vitro. Possesses low activity towards gamma-glutamyl-L-alanine. Has no activity towards gamma-glutamyl-L-cysteine. an alpha-(gamma-L-glutamyl)-L-amino acid = 5-oxo-L-proline + an L-alpha-amino acid Binds 2 Mn(2+) ions per subunit. Belongs to the gamma-glutamylcyclotransferase family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +Catalyzes the conversion of UDP-4-keto-arabinose (UDP-Ara4O) to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N). The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. 2-oxoglutarate + UDP-4-amino-4-deoxy-beta-L-arabinose = L-glutamate + UDP-beta-L-threo-pentopyranos-4-ulose Nucleotide-sugar biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis; UDP-4-deoxy-4-formamido-beta-L-arabinose from UDP-alpha-D-glucuronate: step 2/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Homodimer. Belongs to the DegT/DnrJ/EryC1 family. ArnB subfamily. +Catalyzes the ATP-dependent phosphorylation of the 3-deoxy-D-manno-octulosonic acid (Kdo) residue in Kdo-lipid IV(A) at the 4-OH position. alpha-Kdo-(2->6)-lipid IVA + ATP = 4-O-phospho-alpha-Kdo-(2->6)-lipid IVA + ADP + H(+) Bacterial outer membrane biogenesis; LPS core biosynthesis. Belongs to the protein kinase superfamily. KdkA/RfaP family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs. Part of the 50S ribosomal subunit. Probably part of the RNase P complex. Belongs to the eukaryotic ribosomal protein eL8 family. +Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX. coproporphyrinogen III + 2 H(+) + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; protoporphyrinogen-IX from coproporphyrinogen-III (O2 route): step 1/1. Homodimer. Belongs to the aerobic coproporphyrinogen-III oxidase family. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +Cytoplasmic adapter regulating receptors of the signaling lymphocytic activation molecule (SLAM) family. In SLAM signaling may cooperate with Sh2d1a/SAP. Plays a role in regulation of effector functions of natural killer (NK) cells by controlling signal transduction through Cd244/2b4. However, conflicting results are reported which may reflect the use of different strain backgrounds. Proposed to act as an inhibitor of Cd244-mediated NK cell function including cytotoxicity and IFN-gamma production, the latter found also by triggering Klra4 and Klrk1 next to Cd244 (PubMed:16127454). Seems to positively regulate Cd244- and Cd84-dependent NK cell functions implicating Cd244-mediated phosphorylation of Vav1 (PubMed:20962259). Interacts with SLAMF1 (phosphorylated). Interacts with CD244. Interacts with Src kinases HCK, LYN, FYN, FGR and LCK (via kinase domains). Expressed in spleen. Expressed in macrophages, CD8(+) T-Cells and NK cells (PubMed:16425036). Conflictingly found only in NK cells (PubMed:16127454). +Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccA family. +Regulates actin polymerization by inhibiting the actin-nucleating activity of the Arp2/3 complex; the function is competitive with nucleation promoting factors. Participates in an incoherent feedforward loop at the lamellipodium tip where it inhibits the ARP2/2 complex in response to Rac signaling and where Rac also stimulates actin polymerization through the WAVE complex. Involved in steering cell migration by controlling its directional persistence (By similarity). Associates with the Arp2/3 complex. Interacts with ARPC2; enhanced by activated RAC1. Interacts with ARPC5; the interaction is dependent on RAC1. Colocalized with the WAVE complex at lamellipodium tip. The acidic C-terminus is necessary and sufficient to inhibit ARP2/3 complex activity. Belongs to the Arpin family. +Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin. di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available. Belongs to the UppP family. +Catalyzes the CTP-dependent phosphorylation of riboflavin (vitamin B2) to form flavin mononucleotide (FMN). CTP + riboflavin = CDP + FMN + H(+) Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; FMN biosynthesis; FMN from riboflavin (CTP route): step 1/1. Belongs to the archaeal riboflavin kinase family. +May control the expression of the integrase and inhibit excision of the mobile element SXT, and regulate the expression of other genes as well. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Scaffold component of the nucleolar structure. Required for localization of DDX21 and NCL to the granular compartment of the nucleolus. Interacts with DDX21, NCL, NOP2 and EBNA1BP2. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +Involved in iron-sulfur (Fe-S) cluster assembly. May act as a regulator of Fe-S biogenesis. Belongs to the frataxin family. +Required for pre-18S rRNA processing. May bind microtubules (By similarity). Belongs to the NOP5/NOP56 family. +Belongs to the XFP family. +Plant-specific protein that interact with microtubules and regulates microtubule dynamics. May play a role in anisotropic cell expansion and organ growth. In association with MAP70.1, is essential for the normal banding pattern of secondary cell wall and for the proper development of xylem tracheary elements and wood formation. Interacts with MAP70.1 and itself. Associated to microtubules in tracheary elements. Induced upon xylem tracheary elements differentiation. Plant silencing MAP70.5 show reduced inflorescence stem length and diameter, and inhibition of cell expansion. Over-expression of MAP70.5 causes epidermal cells to swell, stunted growth and induces right-handed organ twisting. Belongs to the MAP70 family. +Provides the (R)-glutamate required for cell wall biosynthesis. L-glutamate = D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the aspartate/glutamate racemases family. +Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May be part of a complex containing NF2/merlin that participates in cellular signaling to the actin cytoskeleton downstream of tyrosine kinase signaling pathways (By similarity). Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Forms a ternary complex with NF2/merlin and GRB2. Binds to actin (By similarity). May be also cytoplasmic and membrane-associated. Belongs to the Mediator complex subunit 28 family. +Epimerizes UDP-galactose to UDP-glucose. UDP-alpha-D-glucose = UDP-alpha-D-galactose Belongs to the polysaccharide synthase family. +Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol. 2 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) = a cardiolipin + glycerol Belongs to the phospholipase D family. Cardiolipin synthase subfamily. ClsA sub-subfamily. +Bifunctional decaline synthase; part of the gene cluster that mediates the biosynthesis of calbistrin A and related compounds. Calbistrin A is a secondary metabolite with an interesting structure that was recently found to have bioactivity against leukemia cells. It consists of two polyketides linked by an ester bond: a bicyclic decalin containing polyketide and a linear 12 carbon dioic acid structure (PubMed:30598828). The polyketide synthase calA is probably responsible for forming the decalin moiety. Because calA lacks a designated enoylreductase (ER) domain, the required activity is provided by the trans-enoyl reductase calK (PubMed:30598828). Following release from the PKS, calF then probably catalyzes the oxidation and the subsequent Diels Alder cycloisomerization that lead to the formation of the decalin moiety (Probable). The decalin polyketide backbone includes two C-methyl groups, at C7 and C11 in backbone, of which the C7 position is probably methylated by the methyltransferase domain of calA. A candidate for adding the methyl group at C11, if not done by CalA, is the cluster methyltransferase calH (Probable). Several additional tailoring enzymes within the cluster could be involved in the modification of the decalin polyketide product. Those include the 3 cytochrome P450 monooxygenases CalE, CalG and CalL, of which one might be responsible for the introduction of the extra hydroxyl group attached to the backbone of the decalin moiety, at position C9 in the backbone, that allows for attachment of the linear moiety (Probable). One tailoring enzyme activity that is expected to be involved in biosynthesis of calbistrin is an acyltransferase for connecting the two polyketide synthase products, and which could be performed by the cluster acyltransferase calJ (Probable). The enzyme responsible for the biosynthesis of the linear moiety, probably a second PKS, has not been identified yet (Probable). Secondary metabolite biosynthesis. Expression is induced in complex medium (Czapek yeast autolysate medium) supporting calbistrin production (PubMed:30598828). Expression is positively regulated by the calbistrin biosynthesis cluster-specific transcription factor calC (PubMed:30598828). Calbistrin A has been reported to possess a number of interesting bioactivities including antifungal active against Candida albicans and cytotoxic toward both healthy and leukemic human cells. Belongs to the oxygen-dependent FAD-linked oxidoreductase family. +Belongs to the universal ribosomal protein uS9 family. +RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs. Homohexamer. Belongs to the Hfq family. +Catalyzes the transfer of an acetyl group from acetyl coenzyme A (AcCoA) to an acceptor substrate and releases both CoA and the acetylated product. It prefers the antibiotic chloramphenicol. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase delta chain family. +Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Complex I is composed of 45 different subunits. Belongs to the complex I NDUFC1 subunit family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +Plant non-specific lipid-transfer proteins transfer phospholipids as well as galactolipids across membranes (By similarity). May play a role in wax or cutin deposition in the cell walls of expanding epidermal cells and certain secretory tissues (By similarity). Binds to both saturated and unsaturated lipids, with the highest binding efficiency for linoleic acid, followed by linolenic acid (PubMed:33277525). Expressed in seeds (at protein level). Belongs to the plant LTP family. +Geranylgeranyl pyrophosphate synthase; part of the gene cluster that mediates the biosynthesis of lolitrems, indole-diterpene mycotoxins that are potent tremorgens in mammals, and are synthesized by clavicipitaceous fungal endophytes in association with their grass hosts (PubMed:16765617). The geranylgeranyl diphosphate (GGPP) synthase ltmG is proposed to catalyze the first step in lolitremB biosynthesis (PubMed:16765617, PubMed:15991026). LtmG catalyzes a series of iterative condensations of isopentenyl diphosphate (IPP) with dimethylallyl diphosphate (DMAPP), geranyl diphosphate (GPP), and farnesyl diphosphate (FPP), to form GGPP (PubMed:16765617, PubMed:15991026). GGPP then condenses with indole-3-glycerol phosphate to form 3-geranylgeranylindole, an acyclic intermediate, to be incorporated into paxilline (PubMed:16765617). Either ltmG or ltmC could be responsible for this step, as both are putative prenyl transferases (PubMed:16765617). The FAD-dependent monooxygenase ltmM then catalyzes the epoxidation of the two terminal alkenes of the geranylgeranyl moiety, which is subsequently cyclized by ltmB, to paspaline (PubMed:16765617, PubMed:15991026). The cytochrome P450 monooxygenases ltmQ and ltmP can sequentially oxidize paspaline to terpendole E and terpendole F (PubMed:22750140). Alternatively, ltmP converts paspaline to an intermediate which is oxidized by ltmQ to terpendole F (PubMed:22750140). LtmF, ltmK, ltmE and ltmJ appear to be unique to the epichloe endophytes (PubMed:16765617, PubMed:15991026). The prenyltransferase ltmF is involved in the 27-hydroxyl-O-prenylation (PubMed:22750140). The cytochrome P450 monooxygenase ltmK is required for the oxidative acetal ring formation (PubMed:22750140). The multi-functional prenyltransferase ltmE is required for C20- and C21-prenylations of the indole ring of paspalanes and acts together with the cytochrome P450 monooxygenase ltmJ to yield lolitremanes by multiple oxidations and ring closures (PubMed:22750140). The stereoisomer pairs of lolitriol and lolitrem N or lolitrem B and lolitrem F may be attributed to variations in the way in which ring closure can occur under the action of ltmJ (PubMed:22750140). While the major product of this pathway is lolitrem B, the prenyl transferases and cytochrome P450 monooxygenases identified in this pathway have a remarkable versatility in their regio- and stereo-specificities to generate a diverse range of metabolites that are products of a metabolic grid rather than a linear pathway (PubMed:22750140). dimethylallyl diphosphate + isopentenyl diphosphate = (2E)-geranyl diphosphate + diphosphate (2E)-geranyl diphosphate + isopentenyl diphosphate = (2E,6E)-farnesyl diphosphate + diphosphate (2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = (2E,6E,10E)-geranylgeranyl diphosphate + diphosphate Binds 3 Mg(2+) ions per subunit. Secondary metabolite biosynthesis. Expression is down-regulated when the stress-activated mitogen-activated protein kinase (sakA) is deleted (PubMed:20519633). Belongs to the FPP/GGPP synthase family. +Transcription factor that binds to the promoter of target genes (PubMed:20150279). Regulates fate specification and/or differentiation of multiple cell types arising from the embryonic mesodermal (M) lineage and the ABp(l/r)paa precursors (PubMed:20150279, PubMed:16107479). In the postembryonic M lineage, regulates cleavage orientation, cell proliferation and cell fate specification (PubMed:16107479). Regulates hlh-1 expression to specify coelomocyte fate in the mesodermal (M) lineage (PubMed:16107479). In AWC neurons, initiates expression of ceh-36, leading to the expression of terminal differentiation genes (PubMed:20150279). Regulates ventral cephalic sheath (CEPsh) glia differentiation and expression of transcription factor hlh-17 in CEPsh glia (PubMed:18508862). Promotes terminal differentiation and morphogenesis of the epithelial duct and pore cells (PubMed:22537498). In the duct cell, cooperates with the EGF-Ras-ERK pathway in turning on the terminal differentiation gene lin-48 (PubMed:22537498). Expressed in a subset of head neurons, including AIM and ASK (at protein level). First expressed around the 50-cell stage of embryogenesis in proliferating cells that are primarily located at the anterior of the embryo in the early M lineage (at protein level) (PubMed:16107479, PubMed:18316179, PubMed:22537498). During morphogenesis, expression becomes restricted to a small subset of head neuronal precursors, including AIM and ASK (at protein level) (PubMed:16107479, PubMed:18316179). Expressed in precursor cells of the left and right ventral CEPsh glia, ABplpaaapap and ABprpaaapap, respectively and also in precursors of dorsal CEPsh glia (PubMed:18508862). Expressed in the duct and pore lineages, persisting through the stages of ventral enclosure and 1.5-folds of embryonic development, but not detectable by the L1 larval stage, when duct and pore cells achieve mature morphology (PubMed:22537498, PubMed:25738873). Expressed in ABpxp descendants that give rise to the excretory system (PubMed:25738873). Transiently expressed in AWC neurons in L1 larvae until abolished shortly after hatching (PubMed:20150279). During the L2 and L3 larval stages, expressed in a group of proliferating cells surrounding the gonad (PubMed:18316179). Belongs to the HMX homeobox family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Catalyzes the hydrolysis of the adenine ring of phosphoribosyl-AMP. 1-(5-phospho-beta-D-ribosyl)-5'-AMP + H2O = 1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide Binds 1 Mg(2+) ion per subunit. Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 3/9. Homodimer. Belongs to the PRA-CH family. +Involved in the TCA cycle. Catalyzes the stereospecific interconversion of fumarate to L-malate. (S)-malate = fumarate + H2O Carbohydrate metabolism; tricarboxylic acid cycle; (S)-malate from fumarate: step 1/1. Homotetramer. There are 2 substrate-binding sites: the catalytic A site, and the non-catalytic B site that may play a role in the transfer of substrate or product between the active site and the solvent. Alternatively, the B site may bind allosteric effectors. Belongs to the class-II fumarase/aspartase family. Fumarase subfamily. +This protein is involved in the repair of mismatches in DNA. Belongs to the DNA mismatch repair MutL/HexB family. +Catalyzes the reduction of crotonobetainyl-CoA to gamma-butyrobetainyl-CoA. gamma-butyrobetainyl-CoA + H(+) + oxidized [electron-transfer flavoprotein] = crotonobetainyl-CoA + reduced [electron-transfer flavoprotein] Amine and polyamine metabolism; carnitine metabolism. Homotetramer. Belongs to the acyl-CoA dehydrogenase family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +The thioredoxin domain lacks the 2 redox-active cysteines, suggesting that it lacks thioredoxin activity. The di-lysine motif confers endoplasmic reticulum localization for type I membrane proteins. +Binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Plays a role in cytokinesis. Plays important roles in mating and in spore formation. Localizes both to the cortical actin patches and to the medial ring in an F-actin-dependent manner. +Catalyzes the NADPH-dependent reduction of glyoxylate and hydroxypyruvate into glycolate and glycerate, respectively. glycolate + NADP(+) = glyoxylate + H(+) + NADPH (R)-glycerate + NAD(+) = 3-hydroxypyruvate + H(+) + NADH (R)-glycerate + NADP(+) = 3-hydroxypyruvate + H(+) + NADPH Homodimer. Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. GhrB subfamily. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Required for the activation of the NF-kappa-B factor Relish (Rel) by acting as an essential signaling component in transmitting the lipopolysaccharide (LPS) signal leading to cact degradation, which is required for direct activation of Rel (PubMed:10636911, PubMed:11018014, PubMed:11156609, PubMed:30119996). Phosphorylates inhibitors of NF-kappa-B (cact) thus leading to the dissociation of the inhibitor/NF-kappa-B complex and ultimately the degradation of the NF-kappa-B inhibitor (PubMed:10636911, PubMed:11018014, PubMed:11156609). Essential for antibacterial immune response (PubMed:11018014). Also required for antiviral immune response (PubMed:30119996). ATP + L-seryl-[I-kappa-B protein] = ADP + H(+) + O-phospho-L-seryl-[I-kappa-B protein] Interacts with key to form the I-kappa-B kinase complex. In vitro, interacts with cact. Expressed both maternally and zygotically throughout development. Highest expression is in early embryos and third larval instar. Autophosphorylated; upon LPS stimulation it is transiently activated, and can be autophosphorylated. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. I-kappa-B kinase subfamily. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has four main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains (By similarity). Belongs to the ATPase B chain family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I 30 kDa subunit family. +Belongs to the UPF0342 family. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +Binds 1 zinc ion per subunit. Belongs to the eukaryotic ribosomal protein eS27 family. +Exhibits S-adenosyl-L-methionine-dependent methyltransferase activity. Belongs to the UPF0677 family. +Catalyzes the final step of fatty acid oxidation in which acetyl-CoA is released and the CoA ester of a fatty acid two carbons shorter is formed. acetyl-CoA + an acyl-CoA = a 3-oxoacyl-CoA + CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadB) and two beta chains (FadA). Belongs to the thiolase-like superfamily. Thiolase family. +Catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 2/4. Belongs to the GPI family. +Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). diphosphate + N-(5-phospho-beta-D-ribosyl)anthranilate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate Binds 2 magnesium ions per monomer. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 2/5. Homodimer. Belongs to the anthranilate phosphoribosyltransferase family. +Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. 2-oxoglutarate + O-phospho-L-serine = 3-phosphooxypyruvate + L-glutamate 2-oxoglutarate + 4-(phosphooxy)-L-threonine = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate Binds 1 pyridoxal phosphate per subunit. Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 2/3. Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 3/5. Homodimer. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. SerC subfamily. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Belongs to the PPR family. P subfamily. +Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Responsible for energy coupling to the transport system. ATP + H2O + (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran-[AI-2-binding protein]Side 1 = ADP + phosphate + (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuranSide 2 + [AI-2-binding protein]Side 1. The complex is composed of two ATP-binding proteins (LsrA), two transmembrane proteins (LsrC and LsrD) and a solute-binding protein (LsrB). Belongs to the ABC transporter superfamily. AI-2 autoinducer porter (TC 3.A.1.2.8) family. +Essential component of the helicase/primase complex. Unwinds the DNA at the replication forks and generates single-stranded DNA for both leading and lagging strand synthesis. The primase initiates primer synthesis and thereby produces large amount of short RNA primers on the lagging strand that the polymerase elongates using dNTPs. Associates with the helicase and the primase-associated factor to form the helicase-primase factor. Requires the presence of the primase associated factor to properly localize in the host cell nucleus. Belongs to the herpesviridae DNA primase family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Specifically methylates the N(1) position of adenine 1408 in 16S rRNA. Confers resistance to various aminoglycosides, including kanamycin, neomycin, apramycin, ribostamycin and gentamicin. Methylates only fully assembled 30S subunits. adenosine(1408) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(1)-methyladenosine(1408) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. Kanamycin-apramycin resistance family. +Belongs to the UPF0235 family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Involved in protein translation. Together with hbs1, may function in recognizing stalled ribosomes and triggering endonucleolytic cleavage of the mRNA, a mechanism to release non-functional ribosomes and degrade damaged mRNAs. The complex formed by dom34 and hbs1 has ribonuclease activity towards double-stranded RNA substrates, but does not cleave single-stranded RNA. Acts as endonuclease; has no exonuclease activity. Increases the affinity of hbs1 for GTP, but nor for GDP. Promotes G1 progression and differentiation and is involved in mitotic and meiotic cell divisions. Monomer. Interacts with hbs1. The N-terminal domain has the RNA-binding Sm fold. It harbors the endoribonuclease activity. Belongs to the eukaryotic release factor 1 family. Pelota subfamily. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +Component of the propane 2-monooxygenase multicomponent enzyme system which is involved in the degradation of propane via the O2-dependent hydroxylation of propane (PubMed:21183637). Also involved in the degradation of acetone via the O2-dependent hydroxylation of acetone (PubMed:26293913). Also able to catalyze the oxidation of phenol, methylethylketone (2-butanone), 1-propanol and 2-propanol (PubMed:21183637, PubMed:23171424, PubMed:26293913). H(+) + NADH + O2 + propane = H2O + NAD(+) + propan-2-ol acetone + H(+) + NADH + O2 = H2O + hydroxyacetone + NAD(+) butan-2-one + H(+) + NADH + O2 = 1-hydroxy-2-butanone + H2O + NAD(+) H(+) + NADH + O2 + phenol = H2O + hydroquinone + NAD(+) The propane 2-monooxygenase multicomponent enzyme system is composed of an electron transfer component and a monooxygenase component interacting with the effector protein MimD. The electron transfer component is composed of a reductase (MimB), and the monooxygenase component is formed by a large subunit (MimA) and a small subunit (MimC) (PubMed:21183637). Requires the presence of the chaperonin-like protein MimG to ensure a productive folding, resulting of a soluble MimC, which leads to the active form of MimABCD (PubMed:23171424). By acetone (PubMed:21183637). Transcriptionally activated by MimR (PubMed:21856847). Belongs to the TmoE/XamoE family. +Bifunctional enzyme that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP) (IspD), and catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (IspF). 2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-methyl-D-erythritol + diphosphate 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 4/6. In the N-terminal section; belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily. In the C-terminal section; belongs to the IspF family. +May play a role in very early embryogenesis, gastrulation, and the development and subdivision of the diencephalon and the midbrain. Appears at 9 hours of development, and at 12 hours of development significant levels are found in the developing brain posterior to ocular vesicles. Distributed mainly in the midbrain, part of the diencephalon beneath the epiphysis and in the epiphysis at 18 hours of development. Found in the ventral part of the midbrain and in the dorsal part of the diencephalon at 24 hours of development. Belongs to the paired homeobox family. Bicoid subfamily. +Essential for sperm motility and is involved in the regulation of the beating frequency of motile cilia on the epithelial cells of the respiratory tract (By similarity). Required for the establishment of radial spokes in sperm flagella (By similarity). Belongs to the CFAP206 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Belongs to the glycoside hydrolase-like 3 (GHL3) family. +D-arabinose 5-phosphate + H2O + phosphoenolpyruvate = 3-deoxy-alpha-D-manno-2-octulosonate-8-phosphate + phosphate Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate: step 2/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsA family. +Increases the activity of extracellular murein hydrolases possibly by mediating their export via hole formation. Inhibited by the antiholin-like proteins LrgAB. In an unstressed cell, the LrgAB products probably inhibit the function of the CidAB proteins. When a cell is stressed by the addition of antibiotics or by other factors in the environment, the CidAB proteins possibly oligomerize within the bacterial cell membrane, creating lesions that disrupt the proton motive force, which in turn results in loss of cell viability. These lesions are also hypothesized to regulate the subsequent cell lysis by either allowing the murein hydrolases access to the cell wall substrate and/or regulating their activity by a possible change in the cell wall pH that results from loss of membrane potential (By similarity). Belongs to the CidB/LrgB family. CidB subfamily. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription (By similarity). Belongs to the RNA polymerase subunit omega family. +Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn-glycerol 3-phosphate. ATP + glycerol = ADP + H(+) + sn-glycerol 3-phosphate Activity of this regulatory enzyme is affected by several metabolites. Allosterically and non-competitively inhibited by fructose 1,6-bisphosphate (FBP) and unphosphorylated phosphocarrier protein EIIA-Glc (III-Glc), an integral component of the bacterial phosphotransferase (PTS) system. Polyol metabolism; glycerol degradation via glycerol kinase pathway; sn-glycerol 3-phosphate from glycerol: step 1/1. Homotetramer and homodimer (in equilibrium). Heterodimer with EIIA-Glc. Binds 1 zinc ion per glycerol kinase EIIA-Glc dimer. The zinc ion is important for dimerization. Belongs to the FGGY kinase family. +To M.leprae ML2435 and S.coelicolor SCO3349. +Belongs to the UPF0262 family. +Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways (PubMed:25273556, PubMed:26783301). Believed to act as a core component of the putative HOPS and CORVET endosomal tethering complexes which are proposed to be involved in the rab-5-to-rab-7 endosome conversion probably implicating sand-1, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion (By similarity). The HOPS complex is proposed to be recruited to rab-7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes (By similarity). Within the HOPS complex, contributes to the normal development of gut granules in intestinal cells of the embryo, and also promotes the trafficking of embryonic intestinal gut granules away from lysosomes (PubMed:24501423, PubMed:25273556). The CORVET complex is proposed to function as a rab-5 effector to mediate early endosome fusion probably in specific endosome subpopulations (By similarity). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:18923146, PubMed:26783301). Plays a role in the degradation of apoptotic cells during programmed cell death (PubMed:18923146). Probable core component of at least two putative endosomal tethering complexes, the homotypic fusion and vacuole protein sorting (HOPS) complex and the class C core vacuole/endosome tethering (CORVET) complex. Their common core is composed of the class C Vps proteins vps-11, vps-16 and vps-18, which in HOPS further associates with vps-33.1, vps-39 and vps-41 and in CORVET with vps-8 and vps-33.2. In hermaphrodites, expressed in coelomocytes and gonadal sheath cells. Ubiquitously expressed in embryos. In early larvae, expressed in hypodermal cells, seam cells and body wall muscle cells. Temperature-sensitive defects in the formation of gut granules during embryogenesis (PubMed:24501423). At 15 degrees Celsius, pretzel-stage embryos have a reduced number of gut granules in intestinal cells, and at 22 degrees Celsius, pretzel-stage embryos completely lack gut granules in intestinal cells (PubMed:24501423). At 25 degrees Celsius, many embryos arrest by the pre-bean stage before elongation, and 76% of these embryos contain gut granules irregularly distributed throughout the embryo (PubMed:24501423). Defective apoptotic germ cell corpse digestion with delayed degradation of chromatin in late germ cell corpses (PubMed:18923146). This results in increased numbers of germ cell corpses at 20 degrees Celsius during embryogenesis and post the L4 stage of larval development, and furthermore the retention of cell corpses for a longer duration of time (PubMed:18923146). Impaired formation of endosomes and lysosomes in coelomocytes, in particular there is impaired formation of recycling endosomes (PubMed:18923146). In addition, there are endosome/lysosome fusion defects in coelomocytes (PubMed:18923146, PubMed:26783301). RNAi-mediated knockdown results in defective endosome maturation with the accumulation of small vesicles near the gut lumen and large endosomes/lysosomes on the basal side of the cell (PubMed:25273556). Double knockout with either sorf-1 or sorf-2, results in larger endosomes and larger lysosomes and thus suppresses the endosome/lysosome fusion defect in the vps-18 single mutant (PubMed:26783301). +Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex. 4 Fe(2+) + 4 H(+) + O2 = 4 Fe(3+) + 2 H2O Binds 1 heme b (iron(II)-protoporphyrin IX) group per dimer. Binds 2 iron ions per subunit. The catalytic dinuclear iron-binding site within each subunit is known as the ferroxidase center. Homooligomer of 24 subunits, arranged as 12 dimers, that are packed together to form an approximately spherical molecule with a central cavity, in which large amounts of iron can be deposited. Belongs to the bacterioferritin family. +With LigD forms a non-homologous end joining (NHEJ) DNA repair enzyme, which repairs dsDNA breaks with reduced fidelity. Binds linear dsDNA with 5'- and 3'- overhangs but not closed circular dsDNA nor ssDNA. Recruits and stimulates the ligase activity of LigD. Homodimer. Interacts with LigD. Belongs to the prokaryotic Ku family. +Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid (By similarity). H2O + NAD(+) + xanthine = H(+) + NADH + urate H2O + hypoxanthine + NAD(+) = H(+) + NADH + xanthine Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit. Binds 2 [2Fe-2S] clusters per subunit. Homodimer. Belongs to the xanthine dehydrogenase family. +Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids. acetyl-CoA + H(+) + malonyl-[ACP] = 3-oxobutanoyl-[ACP] + CO2 + CoA Lipid metabolism; fatty acid biosynthesis. Homodimer. The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH. Belongs to the thiolase-like superfamily. FabH family. +Promotes the survival of neuronal populations that are all located either in the central nervous system or directly connected to it. Belongs to the NGF-beta family. +Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)). 7-carboxy-7-deazaguanine + ATP + NH4(+) = 7-cyano-7-deazaguanine + ADP + H(+) + H2O + phosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. Belongs to the QueC family. +ATP + D-ribose 5-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + H(+) Belongs to the ribose-phosphate pyrophosphokinase family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP. Can remove uracil from double-stranded DNA containing either a U/G or U/A base pair as well as from single-stranded DNA. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Product-inhibited by both uracil and apurinic/apyrimidinic sites. Optimum pH is around 6.2. Extremely thermostable, maintaining full activity after heating for 1.5 hour at 95 degrees Celsius (PubMed:10777501). Exhibits a broad temperature optimum for activity around 80 degrees Celsius (PubMed:24936520). Contains a pseudo-FCL region, a large solvent-exposed peptide region containing an alpha helix and loop anchored on each end via ligation of two cysteine thiolates to a [4Fe-4S](2+) cluster. This region is involved in DNA binding and catalysis, particularly in duplex DNA contexts. Belongs to the uracil-DNA glycosylase (UDG) superfamily. Type 4 (UDGa) family. +Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process (By similarity). Necessary for extracellular secretion of the pertussis toxin (PTX). Belongs to the thioredoxin family. DsbC subfamily. +Belongs to the UPF0234 family. +May be involved in transcriptional regulation. Belongs to the krueppel C2H2-type zinc-finger protein family. Truncated C-terminus. +Catalyzes the conversion of the 17-keto group of estrone, 4- and 5-androstenes and 5-alpha-androstanes into their 17-beta-hydroxyl metabolites and the conversion of the 3-keto group of 3-, 3,17- and 3,20- diketosteroids into their 3-hydroxyl metabolites. Exhibits reductive 3-beta-hydroxysteroid dehydrogenase activity toward 5-beta-androstanes, 5-beta-pregnanes, 4-pregnenes and bile acids. May also reduce endogenous and exogenous alpha-dicarbonyl compounds and xenobiotic alicyclic ketones. a 3beta-hydroxysteroid + NADP(+) = a 3-oxosteroid + H(+) + NADPH 17beta-estradiol + NAD(+) = estrone + H(+) + NADH 17beta-estradiol + NADP(+) = estrone + H(+) + NADPH Inhibited by flavonoids including apigenin, luteolin, genistein, kaempferol and quercetin and also by carbenoxolone, zearalenone, glycyrrhetinic, curcumin and flufenamic acid. Steroid biosynthesis; estrogen biosynthesis. Homotetramer. Isoform 1: Ubiquitously expressed, with highest levels in testis, small intestine, colon, kidney, brain and heart. Isoform 3: Expressed in brain, heart and skeletal muscle. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway. D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = beta-D-fructose 6-phosphate + D-erythrose 4-phosphate Carbohydrate degradation; pentose phosphate pathway; D-glyceraldehyde 3-phosphate and beta-D-fructose 6-phosphate from D-ribose 5-phosphate and D-xylulose 5-phosphate (non-oxidative stage): step 2/3. Belongs to the transaldolase family. Type 3B subfamily. +High affinity, high specificity proton-dependent sulfate transporter, which mediates sulfate uptake. Provides the sulfur source for the cysteine synthesis pathway. Belongs to the CysZ family. +Putative oxidoreductase. Acts as a tumor suppressor and plays a role in apoptosis. May function synergistically with p53/TP53 to control genotoxic stress-induced cell death. Plays a role in TGFB1 signaling and TGFB1-mediated cell death. Inhibits Wnt signaling, probably by sequestering DVL2 in the cytoplasm (By similarity). May also play a role in tumor necrosis factor (TNF)-mediated cell death. Required for normal bone development. Interacts with TP53, TP73/p73 and MAPK8. Interacts with MAPT/TAU. Forms a ternary complex with TP53 and MDM2 and interacts with ERBB4, LITAF and WBP1. May interact with FAM189B and SCOTIN (By similarity). Interacts with HYAL2 and RUNX2. Interacts with TNK2 (By similarity). Interacts with TMEM207 (By similarity). Partially localizes to the mitochondria (By similarity). Translocates to the nucleus in response to TGFB1 (PubMed:19366691). Translocates to the nucleus upon genotoxic stress or TNF stimulation (PubMed:11058590). Ubiquitous. In the brain, expressed in cortex, striatum, hippocampus and cerebellum (at protein level). Detected in embryonic skeleton, in cranofacial bones, vertebrae and limb bones. Detected in chondrocytes and osteoblasts. Expression starts at 8 dpc in the developing heart. Higher expression in the brain is detected between 12 dpc and 16 dpc. High levels of expression in dorsal root ganglia and spinal nerves were observed throughout all developmental stages. In later developmental stages expression is more prominent in skeletal systems (at protein level). By hyaluronidase. Up-regulated in outer and inner nuclear layers during retinal degeneration. The WW 1 domain mediates interaction with TP73, TFAP2C, LITAF, WBP1 and probably TP53. Phosphorylated upon genotoxic stress. Phosphorylation of Tyr-33 regulates interaction with TP53, TP73 and MAPK8. May also regulate proapoptotic activity. Phosphorylation by TNK2 is associated with polyubiquitination and degradation (By similarity). Ubiquitinated when phosphorylated by TNK2, leading to its degradation. Indistinguishable from wild-type at birth, but die after three weeks due to metabolic syndrome characterized by serum hypoproteinemia, hypoalbuminemia, hypoglycemia, hypocalcemia, hypotriglyceridemia and hypocholesterolemia, growth retardation, decreased bone formation and increased bone resorption. In addition, spontaneous tumor development was observed. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. Belongs to the FlgH family. +ATP-dependent RNA helicase essential for mRNA export from the nucleus. Plays an important role in the positive regulation of CBF/DREB transcription factors. ATP + H2O = ADP + H(+) + phosphate Interacts with NUP214 (via N-terminus). Constitutively expressed. By abscisic acid (ABA). The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis. Belongs to the DEAD box helicase family. DDX19/DBP5 subfamily. +Calcium-dependent lectin that acts as a pattern recognition receptor (PRR) of the innate immune system: recognizes damage-associated molecular patterns (DAMPs) of pathogen-associated molecular patterns (PAMPs) of bacteria and fungi (PubMed:23602766, PubMed:23911656). The PAMPs include alpha-mannans on C.albicans hypheas and mycobacterial trehalose 6,6'-dimycolate (TDM) (PubMed:23602766, PubMed:23911656). Interacts with signaling adapter Fc receptor gamma chain/FCER1G, likely via CLEC4E, to form a functional complex in myeloid cells (By similarity). Binding of mycobacterial TDM or C.albicans alpha-mannans to this receptor complex leads to phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) of FCER1G, triggering activation of SYK, CARD9 and NF-kappa-B, consequently driving maturation of antigen-presenting cells and shaping antigen-specific priming of T-cells toward effector T-helper 1 and T-helper 17 cell subtypes (PubMed:23602766, PubMed:23911656). The heterodimer formed with CLEC6A is active against fungal infection (PubMed:23911656). Functions as an endocytic receptor (PubMed:14971047). May be involved in antigen uptake at the site of infection, either for clearance of the antigen, or for processing and further presentation to T-cells (PubMed:14971047). Heterodimer with CLEC4E; disulfide-linked (By similarity). CLEC4E acts as a bridge for interaction between CLEC4D and FCER1G to form a functional complex (By similarity). Heterodimer with CLEC6A; this heterodimer forms a pattern recognition receptor (PRR) against fungal infection (PubMed:23911656). Expressed weakly in peripheral blood leukocytes, bone marrow and spleen. Expression is confined mostly in monocytes and macrophage and seems to be up-regulated by IL-6, IL-10, TNF-alpha and IFN-gamma. By autocrine inflammatory stimuli. MCL +F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein (By similarity). Homodimer; antiparallel. Ubiquitinated by FBXL22, leading to proteasomal degradation. Belongs to the alpha-actinin family. +Multifunctional serine/threonine kinase that plays a role in several processes including egress of virus particles from the nucleus, modulation of the actin cytoskeleton and regulation of viral and cellular gene expression. Regulates the nuclear localization of viral envelopment factors UL34 and UL31 homologs, by phosphorylating the US3 kinase homolog, indicating a role in nuclear egress. Disrupts host nuclear lamins, including LMNA and LMNB1. Phosphorylates the viral Fc receptor composed of glycoproteins E (gE) and I (gI). Phosphorylation of glycoprotein E (gE) by UL13 homolog alters its subcellular localization, from the host early endosome to the plasma membrane. Participates in the transcriptional regulation of cellular and viral mRNAs mainly by phosphorylating the viral transcriptional regulator ICP22 homolog (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Autophosphorylated. Displays a substrate specificity similar to host CDC2. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvP family. +Cell adhesion, ankyrin-binding protein which may be involved in neurite extension, axonal guidance, synaptogenesis, myelination and neuron-glial cell interactions. Isoform 2/isoform 3 may be responsible for mediating and signaling axon-glial interaction during the early stages of myelination. Horseshoe-shaped homodimer (By similarity). Probable constituent of a NFASC/NRCAM/ankyrin G complex. Associates with the sodium channel beta-1 (SCN1B) and beta-3 (SCN3B) subunits. Associates to subunit beta-1 in developing axons as early as postanatal day 5, during the period that nodes of Ranvier are forming. Isoform 2/isoform 3 is likely to interact with axonal proteins in close association with CNTNAP1. Interacts with GLDN/gliomedin. Interacts with MYOC (By similarity). Isoform 1 colocalizes with ankyrin G at the nodes of Ranvier. Isoform 2/ isoform 3 is a glial component of the paranodal axo-glial junction. Isoform 1 is expressed at Nodes of Ranvier while isoform 2/isoform 3 is expressed in unmyelinated axons. Strongly but transiently up-regulated in oligodendrocytes at the onset of myelinogenesis. Once these last have engaged their target exons, expression declines precipitously. Homophilic adhesion is primarily mediated by the interaction of the second Ig-like domains. Isoform 2/isoform 3 is phosphorylated at P12. Dephosphorylation is required for ankyrin binding. Belongs to the immunoglobulin superfamily. L1/neurofascin/NgCAM family. +D-aminoacyl-tRNA deacylase with broad substrate specificity. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo. a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) Binds 2 Zn(2+) ions per subunit. Monomer. Belongs to the DtdA deacylase family. +Regulates arginine biosynthesis genes. Amino-acid biosynthesis; L-arginine biosynthesis [regulation]. Belongs to the ArgR family. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Catalyzes the NAD(+)-dependent oxidation of L-threonine to 2-amino-3-ketobutyrate. L-threonine + NAD(+) = (2S)-2-amino-3-oxobutanoate + H(+) + NADH Binds 2 Zn(2+) ions per subunit. Amino-acid degradation; L-threonine degradation via oxydo-reductase pathway; glycine from L-threonine: step 1/2. Homotetramer. Belongs to the zinc-containing alcohol dehydrogenase family. +Involved in uptake of hemolymph trehalose into epithelial cells in the midgut of feeding larvae. alpha,alpha-trehalose + H2O = alpha-D-glucose + beta-D-glucose In midgut and Malpighian tubules. Belongs to the glycosyl hydrolase 37 family. +May be involved in proton extrusion. Indirectly promotes efficient inorganic carbon uptake into chloroplasts. Belongs to the Cema family. +Involved in nucleolar processing of pre-18S ribosomal RNA. Involved in ribosome biosynthesis (By similarity). Component of the ribosomal small subunit (SSU) processome. Belongs to the HEATR1/UTP10 family. +Belongs to the UPF0367 family. +May play a role in L-lactate transport. Belongs to the lactate permease family. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Belongs to the cyclin family. Cyclin T subfamily. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit. Binds 1 zinc ion per subunit. Monomer. Associates with 30S ribosomal subunit, binds 16S rRNA. Belongs to the TRAFAC class YlqF/YawG GTPase family. RsgA subfamily. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +Catalyzes the ATP-dependent phosphorylation of N-acetyl-L-glutamate. ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamyl 5-phosphate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 2/4. Belongs to the acetylglutamate kinase family. ArgB subfamily. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +Secreted metalloproteinase probably acting as a virulence factor. Binds 1 zinc ion per subunit. Belongs to the peptidase M36 family. +Short chain dehydrogenase; part of the gene cluster that mediates the biosynthesis of pleosporalin A, ascomycone A, as well as a third cryptic naphthoquinone derived pigment, all responsible for the coloration of conidia (PubMed:28471414, PubMed:35351612). Essential for the production of pleosporalin A, but not the 2 other final products (PubMed:35351612). The pathway begins with the biosynthesis of the cyclized heptaketide 3-acetonyl-1,6,8-trihydroxy-2-naphthaldehyde by the NR-PKS pgmA. The C-6 hydroxyl group is further methylated by the O-methyltransferase pgmB to yield fusarubinaldehyde which is in turn oxidized by the cytochrome P450 monooxygenase pgmC at C-9. The C-1 hydroxyl group is then methylated spontaneously. Although pgmE, pgmD and pgmH are essential for the production of pleosporalin A, it is not the case for the 2 other final products and it remains difficult to assign a specific function to each enzyme. PgmF and pgmG seem not to be involved in pigment biosynthesis although they were regulated by the cluster-specific transcription factor pgmR (PubMed:35351612) (Probable). Pigment biosynthesis. Secondary metabolite biosynthesis. Expression is significantly up-regulated at the end of late growth phase, in the presence of Butyrolactone I (PubMed:28471414). Expression is positively regulated by the pgm cluster-specific transcription factor pgmR (PubMed:35351612). Only abolishes the production of pleosporalin A but not of the 2 other final products. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Mediates the endocytosis of plasma glycoproteins to which the terminal sialic acid residue on their complex carbohydrate moieties has been removed. The receptor recognizes terminal galactose and N-acetylgalactosamine units. After ligand binding to the receptor, the resulting complex is internalized and transported to a sorting organelle, where receptor and ligand are disassociated. The receptor then returns to the cell membrane surface. The functioning ligand-binding unit of this receptor is thought to be at least a dimer. Interacts with LASS2. (Microbial infection) Interacts with hepatitis E virus capsid protein ORF2. Expressed exclusively in hepatic parenchymal cells. Calcium is required for ligand binding. Hepatic asialoglycoprotein receptor subunit 2 +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Has a ubiquitin-protein ligase activity acting as an E3 ubiquitin protein ligase or as an ubiquitin-ubiquitin ligase promoting elongation of ubiquitin chains on substrates. By mediating 'Lys-48'-linked polyubiquitination of proteins could target them for proteasomal degradation (PubMed:11435423). May also function as a chaperone, playing a role in transport to the cell membrane of BSG/Basigin for instance (PubMed:15946952). Probable inactive PPIase with no peptidyl-prolyl cis-trans isomerase activity (PubMed:20676357). S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Interacts with isoform 2 of BSG (PubMed:15946952). Interacts (via the PPIase cyclophilin-type domain) with CRNKL1; they may form a trimeric complex with HSP90. May also localize to the cytoplasm and the cell membrane. Highest expression in thymus, pancreas and testis. Also detected in heart, placenta, lung, liver, skeletal muscle, kidney, spleen, prostate, ovary, small intestine and colon. Poorly detected in brain and leukocytes. Strong protein expression in lymph node (cortical, paracortical and medullar regions), thyroid (follicular epithelial cells), testis (developing spermatozoa), stomach (cells lining the gastric pit), pancreas, kidney (proximal and distal-tubule cells and collecting duct cells but not in glomeruli), endometrium and colon (goblet cells). Moderate protein expression in spleen, prostate (epithelium and squamous cell carcinomas), placenta and adrenal gland. Weak protein expression in liver, heart, breast, ovary, and lung. No protein expression in brain and bladder. High protein expression in most lymphomas and melanomas. Belongs to the cyclophilin-type PPIase family. PPIL2 subfamily. Despite the fact that it belongs to the cyclophilin-type PPIase family, a report has shown that it has probably no peptidyl-prolyl cis-trans isomerase activity due to the presence of a tyrosine instead of a tryptophan at position 389. +Hydrolyzes trehalose to glucose. Could be involved, in cells returning to low osmolarity conditions, in the utilization of the accumulated cytoplasmic trehalose, which was synthesized in response to high osmolarity. alpha,alpha-trehalose + H2O = alpha-D-glucose + beta-D-glucose Glycan degradation; trehalose degradation; D-glucose from alpha,alpha-trehalose: step 1/1. Monomer. Belongs to the glycosyl hydrolase 37 family. +Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS3 family. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP). (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate Cofactor biosynthesis; molybdopterin biosynthesis. Homohexamer; trimer of dimers. Belongs to the MoaC family. +Belongs to the tRNA methyltransferase O family. +Belongs to the UPF0229 family. +DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate. Belongs to the endonuclease V family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system. The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. Belongs to the TatA/E family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A. 3'-dephospho-CoA + ATP = ADP + CoA + H(+) Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 5/5. Belongs to the CoaE family. +Allows intracellular utilization of 4-hydroxyproline, one of the major constituents of host collagen, by converting 4-hydroxy-L-proline to 4-hydroxy-D-proline, which can be further metabolized by intracellular 4-hydroxy-D-proline oxidases. Strong B-cell mitogen. Plays an important role in the regulation of intra- and extracellular amino acid pools, allowing the bacterium to profit from host precursors and enzymatic pathways (By similarity). trans-4-hydroxy-L-proline = cis-4-hydroxy-D-proline Homodimer. Belongs to the proline racemase family. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Belongs to the urease beta subunit family. +Bifunctional enzyme that catalyzes the reactions from geranylgeranyl diphosphate to phytoene (phytoene synthase) and from lycopene to beta-carotene via the intermediate gamma-carotene and from 3,4-didehydrolycopene to torulene (lycopene cyclase). Torulene is further processed to the acidic carotenoid neurosporaxanthin. The cyclase preferentially catalyzes single cyclizations at only one end of the substrate to produce monocyclic carotenoids. all-trans-lycopene = gamma-carotene gamma-carotene = all-trans-beta-carotene 2 (2E,6E,10E)-geranylgeranyl diphosphate = 15-cis-phytoene + 2 diphosphate Carotenoid biosynthesis; beta-carotene biosynthesis. Carotenoid biosynthesis; phytoene biosynthesis; all-trans-phytoene from geranylgeranyl diphosphate: step 1/1. By blue light. In the N-terminal section; belongs to the lycopene beta-cyclase family. In the C-terminal section; belongs to the phytoene/squalene synthase family. +Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde, which spontaneously cyclizes to quinolinate. 3-hydroxyanthranilate + O2 = (2Z,4Z)-2-amino-3-carboxymuconate 6-semialdehyde Binds 2 Fe(2+) ions per subunit. Cofactor biosynthesis; NAD(+) biosynthesis; quinolinate from L-kynurenine: step 3/3. Homodimer. Belongs to the 3-HAO family. +Trancsription activator, when associated with MYB75/PAP1 or MYB90/PAP2. Homodimer (Probable). Interacts with MYB75/PAP1, MYB90/PAP2, MYB4, MYB5, MYB6, MYB23, MYB82, MYB113, MYB114, TT2, MYB0/GL1, and MYB66/WER. A number of isoforms are produced. According to EST sequences. Mostly expressed in developing seeds. Also detected in stems and leaves. By cold, UV, flagellin, jasmonic acid (JA), and salicylic acid (SA) treatments. +Catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde to succinate. Although it has succinate semialdehyde dehydrogenase activity, is likely to act physiologically on a different aldehyde(s) (By similarity). H2O + NADP(+) + succinate semialdehyde = 2 H(+) + NADPH + succinate Belongs to the aldehyde dehydrogenase family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. Can use either ATP or GTP, but prefers ATP. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. ATP + CoA + succinate = ADP + phosphate + succinyl-CoA Binds 1 Mg(2+) ion per subunit. Exhibits two interesting properties: 'substrate synergism', in which the enzyme is most active for the catalysis of its partial reactions only when all the substrate-binding sites are occupied, and 'catalytic cooperativity' between alternating active sites in the tetramer, whereby the interaction of substrates (particularly ATP) at one site is needed to promote catalysis at the other. kcat is 2684 min(-1) with ATP as substrate and 1471 min(-1) with GTP as substrate. Optimum pH is 7.4. Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. Heterotetramer of two alpha and two beta subunits. Succinyl-CoA synthetase (SCS) of E.coli catalyzes its reaction via three steps that involve phosphoryl enzyme and enzyme-bound succinyl phosphate as intermediates. Belongs to the succinate/malate CoA ligase beta subunit family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Could act as an H1-type linker histone. Belongs to the histone H1/H5 family. +Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate. (2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate + CO2 + NADH Binds 1 Mg(2+) or Mn(2+) ion per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4. Homodimer. Belongs to the isocitrate and isopropylmalate dehydrogenases family. LeuB type 1 subfamily. +Belongs to the HesB/IscA family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Component of SEC61 channel-forming translocon complex that mediates transport of signal peptide-containing precursor polypeptides across endoplasmic reticulum (ER) (By similarity). Component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis (By similarity). The SEC61 channel cooperates with the translocating protein TRAM1 to import nascent proteins into the ER (By similarity). The SEC61 channel-forming translocon complex consists of channel-forming core components SEC61A1, SEC61B and SEC61G and different auxiliary components such as SEC62 and SEC63 (By similarity). The ribosome-associated ER translocon complex includes SEC61A1, SEC61B, SEC61G, TMCO1, CCDC47, NCLN/Nicalin, NOMO and TMEM147; in the absence of ribosomes, only the complex forms with NCLN/Nicalin, NOMO and TMEM147 remains intact (By similarity). Belongs to the SecE/SEC61-gamma family. +Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids. acetyl-CoA + H(+) + malonyl-[ACP] = 3-oxobutanoyl-[ACP] + CO2 + CoA Lipid metabolism; fatty acid biosynthesis. Homodimer. The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH. Belongs to the thiolase-like superfamily. FabH family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Shows particularly broad specificity; although bonds involving phenylalanine and leucine are preferred, many others are also cleaved to some extent. Preferential cleavage: hydrophobic, preferably aromatic, residues in P1 and P1' positions. Cleaves 1-Phe-|-Val-2, 4-Gln-|-His-5, 13-Glu-|-Ala-14, 14-Ala-|-Leu-15, 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17, 23-Gly-|-Phe-24, 24-Phe-|-Phe-25 and 25-Phe-|-Tyr-26 bonds in the B chain of insulin. Pepsin A-2 is predominant at the 4-month stage. Pepsin A-3 is predominant at fetal stages. Pepsin A-2 is phosphorylated, but not pepsin A-3. Each pepsinogen is converted to corresponding pepsin at pH 2.0 in part as a result of the release of a 47 AA activation segment and in part as a result of stepwise proteolytic cleavage via an intermediate form(s). The expression of pepsinogen genes is regulated by hormones and related substances. Belongs to the peptidase A1 family. It is not known if this is Pep A-2 or Pep A-3. +Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of replication as well as for processivity of DNA replication. Forms a ring-shaped head-to-tail homodimer around DNA which binds and tethers DNA polymerases and other proteins to the DNA. The DNA replisome complex has a single clamp-loading complex (3 tau and 1 each of delta, delta', psi and chi subunits) which binds 3 Pol III cores (1 core on the leading strand and 2 on the lagging strand) each with a beta sliding clamp dimer. Additional proteins in the replisome are other copies of gamma, psi and chi, Ssb, DNA helicase and RNA primase. Belongs to the beta sliding clamp family. Extended N-terminus. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily. +Receptor that may play a role in the perception of bitterness and is gustducin-linked. May play a role in sensing the chemical composition of the gastrointestinal content. The activity of this receptor may stimulate alpha gustducin, mediate PLC-beta-2 activation and lead to the gating of TRPM5 (By similarity). Most taste cells may be activated by a limited number of bitter compounds; individual taste cells can discriminate among bitter stimuli. Belongs to the G-protein coupled receptor T2R family. +Part of the ABC transporter complex GlnHMPQ involved in glutamine transport. The complex is composed of two ATP-binding proteins (GlnQ), two transmembrane proteins (GlnM and GlnP) and a solute-binding protein (GlnH). Positively regulated by TnrA under nitrogen-limited conditions. Belongs to the bacterial solute-binding protein 3 family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +Pigment protein that is green in color. Has a strong fluorescence emission spectrum which peaks at 486 nm. Tentacle and oral disk. Contains a chromophore consisting of modified amino acid residues. The chromophore is formed by autocatalytic backbone condensation between Xaa-N and Gly-(N+2), oxidation of Tyr-(N+1) to didehydrotyrosine, and formation of a double bond to the alpha-amino nitrogen of residue Xaa-N. Maturation of the chromophore requires nothing other than molecular oxygen. The precise stereochemistry of the tyrosine has not been determined. Fluorescent proteins have become a useful and ubiquitous tool for making chimeric proteins, where they function as a fluorescent protein tag. Typically they tolerate N- and C-terminal fusion to a broad variety of proteins. They have been expressed in most known cell types and are used as a noninvasive fluorescent marker in living cells and organisms. They enable a wide range of applications where they have functioned as a cell lineage tracer, reporter of gene expression, or as a measure of protein-protein interactions. Belongs to the GFP family. +Catalyzes the reversible phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha-D-ribose 1-phosphate a purine 2'-deoxy-D-ribonucleoside + phosphate = 2-deoxy-alpha-D-ribose 1-phosphate + a purine nucleobase Homohexamer; trimer of homodimers. Belongs to the PNP/UDP phosphorylase family. +beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Binds 2 magnesium ions per subunit. Carbohydrate biosynthesis; gluconeogenesis. Homotetramer. Belongs to the FBPase class 1 family. +Guanine nucleotide-binding proteins (G proteins) are involved as a modulator or transducer in various transmembrane signaling systems (Probable). The beta and gamma chains are required for the GTPase activity, for replacement of GDP by GTP, and for G protein-effector interaction (Probable). Involved in the regulation of plant architecture, panicle erectness, panicle and grain length, grain weight, and grain yield (PubMed:19305410, PubMed:19407986, PubMed:19546322). Involved in the regulation of grain size (PubMed:29487318, PubMed:32111163). G proteins are composed of 3 units, alpha, beta and gamma. Expressed in the inflorescence meristem and intercalary meristem (PubMed:19305410). Expressed in the bract primordia of primary and secondary rachis branches (PubMed:19305410). Semi-dwarf phenotype (PubMed:19305410, Ref.2). Dense and erect panicles, and high grain number per panicle (PubMed:19305410, PubMed:32111163). Increased number of spikelets (Ref.2). Increased tolerance to drought, salt and cold stresses (PubMed:32111163). Involved in tolerance to cadmium and copper ions (PubMed:24163402). Seedlings overexpressing DEP1 exhibit enhanced tolerance to cadmium (PubMed:24163402). +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds a dinuclear copper A center per subunit. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Found in a complex with TMEM177, COA6, COX18, COX20, SCO1 and SCO2. Interacts with TMEM177 in a COX20-dependent manner. Interacts with COX20. Interacts with COX16 (By similarity). Belongs to the cytochrome c oxidase subunit 2 family. +Catalyzes the reversible retro-aldol cleavage of 4-hydroxy-2-oxovalerate to pyruvate and acetaldehyde. (S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate Xenobiotic degradation; biphenyl degradation. By growth on ethylbenzene or biphenyl. Belongs to the HpcH/HpaI aldolase family. +Belongs to the UPF0301 (AlgH) family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +By tobacco mosaic virus infection, wounding, UV light, salicylic acid and ethylene. Belongs to the protease inhibitor I13 (potato type I serine protease inhibitor) family. +Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX. (6R)-NADHX = (6S)-NADHX (6R)-NADPHX = (6S)-NADPHX Binds 1 potassium ion per subunit. Belongs to the NnrE/AIBP family. Extended N-terminus. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 2 [4Fe-4S] clusters per subunit. NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I 23 kDa subunit family. +Probable voltage-independent potassium-selective tonoplast ion channel. Homodimer. Expressed in roots, stems, leaves and flowers. Each of the two pore-forming region (also called P-domain or P-loop) is enclosed by two transmembrane segments (2P/4TM) and contains the GYGD signature motif which seems to be involved in potassium selectivity. Belongs to the two pore domain potassium channel (TC 1.A.1.7) family. +Belongs to the UPF0416 family. +Catalyzes the phosphorylation of ribose 1,5-bisphosphate to 5-phospho-D-ribosyl alpha-1-diphosphate (PRPP). alpha-D-ribose 1,5-bisphosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + ADP Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route II): step 3/3. Belongs to the ribose 1,5-bisphosphokinase family. +Belongs to the NXPE family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene). 5-methylsulfanyl-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate Binds 1 Mg(2+) ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 3/6. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 4/6. Monomer. Belongs to the HAD-like hydrolase superfamily. MasA/MtnC family. +Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-terminal L-methionyl-[peptide] Binds 1 Fe(2+) ion. Belongs to the polypeptide deformylase family. +Belongs to the AAE transporter (TC 2.A.81) family. YbjL subfamily. +Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). H2O + O2 + pyridoxamine 5'-phosphate = H2O2 + NH4(+) + pyridoxal 5'-phosphate O2 + pyridoxine 5'-phosphate = H2O2 + pyridoxal 5'-phosphate Binds 1 FMN per subunit. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1. Homodimer. Belongs to the pyridoxamine 5'-phosphate oxidase family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, HCO(3)(-)/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate. ATP + hydrogencarbonate + L-threonine = diphosphate + H2O + L-threonylcarbamoyladenylate Belongs to the SUA5 family. TsaC subfamily. +C-5 sterol desaturase; part of the third module of ergosterol biosynthesis pathway that includes the late steps of the pathway (PubMed:1864507). ERG3 catalyzes the introduction of a C-5 double bond in the B ring to produce 5-dehydroepisterol (PubMed:1864507). The third module or late pathway involves the ergosterol synthesis itself through consecutive reactions that mainly occur in the endoplasmic reticulum (ER) membrane. Firstly, the squalene synthase ERG9 catalyzes the condensation of 2 farnesyl pyrophosphate moieties to form squalene, which is the precursor of all steroids. Squalene synthase is crucial for balancing the incorporation of farnesyl diphosphate (FPP) into sterol and nonsterol isoprene synthesis. Secondly, the squalene epoxidase ERG1 catalyzes the stereospecific oxidation of squalene to (S)-2,3-epoxysqualene, which is considered to be a rate-limiting enzyme in steroid biosynthesis. Then, the lanosterol synthase ERG7 catalyzes the cyclization of (S)-2,3 oxidosqualene to lanosterol, a reaction that forms the sterol core. In the next steps, lanosterol is transformed to zymosterol through a complex process involving various demethylation, reduction and desaturation reactions. The lanosterol 14-alpha-demethylase ERG11 (also known as CYP51) catalyzes C14-demethylation of lanosterol to produce 4,4'-dimethyl cholesta-8,14,24-triene-3-beta-ol, which is critical for ergosterol biosynthesis. The C-14 reductase ERG24 reduces the C14=C15 double bond of 4,4-dimethyl-cholesta-8,14,24-trienol to produce 4,4-dimethyl-cholesta-8,24-dienol. 4,4-dimethyl-cholesta-8,24-dienol is substrate of the C-4 demethylation complex ERG25-ERG26-ERG27 in which ERG25 catalyzes the three-step monooxygenation required for the demethylation of 4,4-dimethyl and 4alpha-methylsterols, ERG26 catalyzes the oxidative decarboxylation that results in a reduction of the 3-beta-hydroxy group at the C-3 carbon to an oxo group, and ERG27 is responsible for the reduction of the keto group on the C-3. ERG28 has a role as a scaffold to help anchor ERG25, ERG26 and ERG27 to the endoplasmic reticulum and ERG29 regulates the activity of the iron-containing C4-methylsterol oxidase ERG25. Then, the sterol 24-C-methyltransferase ERG6 catalyzes the methyl transfer from S-adenosyl-methionine to the C-24 of zymosterol to form fecosterol. The C-8 sterol isomerase ERG2 catalyzes the reaction which results in unsaturation at C-7 in the B ring of sterols and thus converts fecosterol to episterol. The sterol-C5-desaturase ERG3 then catalyzes the introduction of a C-5 double bond in the B ring to produce 5-dehydroepisterol. The C-22 sterol desaturase ERG5 further converts 5-dehydroepisterol into ergosta-5,7,22,24(28)-tetraen-3beta-ol by forming the C-22(23) double bond in the sterol side chain. Finally, ergosta-5,7,22,24(28)-tetraen-3beta-ol is substrate of the C-24(28) sterol reductase ERG4 to produce ergosterol (PubMed:32679672). episterol + 2 Fe(II)-[cytochrome b5] + 2 H(+) + O2 = 5-dehydroepisterol + 2 Fe(III)-[cytochrome b5] + 2 H2O Steroid metabolism; ergosterol biosynthesis; ergosterol from zymosterol: step 3/5. Interacts with ERG28. The ERG3 promoter contains 2 upstream activation sequences, UAS1 and UAS2 (PubMed:8772195). UAS1 regulates gene expression but does not affect sterol regulation (PubMed:8772195). UAS2 is required for sterol regulation (PubMed:8772195). The absence of sterol esterification leads to a decrease of ERG3 expression (PubMed:8772195). The histidine box domains may contain the active site and/or be involved in metal ion binding. Present with 36200 molecules/cell in log phase SD medium. Belongs to the sterol desaturase family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Factor B which is part of the alternate pathway of the complement system is cleaved by factor D into 2 fragments: Ba and Bb. Bb, a serine protease, then combines with complement factor 3b to generate the C3 or C5 convertase. It has also been implicated in proliferation and differentiation of preactivated B-lymphocytes, rapid spreading of peripheral blood monocytes, stimulation of lymphocyte blastogenesis and lysis of erythrocytes. Ba inhibits the proliferation of preactivated B-lymphocytes (By similarity). Cleavage of Arg-|-Ser bond in complement component C3 alpha-chain to yield C3a and C3b, and Arg-|-Xaa bond in complement component C5 alpha-chain to yield C5a and C5b. Monomer (By similarity). Part of the C3-convertase enzyme complex comprised of Complement C3 beta chain (C3b) and Complement factor B Bb fragment (Bb) and CFP (By similarity). Interacts to C3b; this interaction is dependent on the presence of Mg2+ (By similarity). Interacts to CFP; this interaction contributes to the stabilization of the active C3-convertase enzyme complex (By similarity). The unliganded VWA domain has an inactive 'locked' conformation whereby the scissile Arg-259|Lys-260 bond is protected from proteolytic activation. Belongs to the peptidase S1 family. +ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein] This protein is synthesized as a Gag-Fes polyprotein. Belongs to the protein kinase superfamily. Tyr protein kinase family. Fes/fps subfamily. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Catalyzes the NADPH-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5-carboxylate. L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 2/2. Belongs to the gamma-glutamyl phosphate reductase family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the LeuD family. LeuD type 2 subfamily. +Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-aspartyl-tRNA(Asx) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +Involved in both the assembly of spliceosomal snRNPs and the methylation of Sm proteins (By similarity). Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome, and thereby plays an important role in the splicing of cellular pre-mRNAs (By similarity). Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP (Sm core) (By similarity). In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP (By similarity). Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus (By similarity). Component of the methylosome, a 20S complex containing at least PRMT5/SKB1, WDR77/MEP50 and CLNS1A/pICln. May mediate SNRPD1 and SNRPD3 methylation. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP. Interacts with LSM10 and LSM11. A small fraction is also associated with the cytoskeleton. Belongs to the pICln (TC 1.A.47) family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Involved in peptidoglycan biosynthesis. Transports lipid-linked peptidoglycan precursors from the inner to the outer leaflet of the cytoplasmic membrane. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurJ/MviN family. +Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. ATP + cytidine(34) in tRNA(Ile2) + L-lysine = AMP + diphosphate + H(+) + lysidine(34) in tRNA(Ile2) The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a P-loop motif involved in ATP binding. Belongs to the tRNA(Ile)-lysidine synthase family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a, b, b' and c. Belongs to the ATPase A chain family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseB family. +Nonribosomal peptide synthetase; part of the gene cluster that mediates the biosynthesis of aspulvinones (PubMed:29305695, PubMed:23841722, PubMed:28791090). The nonribosomal peptide synthetase apvA is responsible for the production of aspulvinone E, the core structure of aspulvinones (PubMed:29305695, PubMed:23841722, PubMed:28791090). ApvA first activates 4-hydroxyphenylpyruvate (HPPA) through its A domain to AMP-HPPA (Probable). The HPPA unit is then loaded to the T domain and eventually transferred to the TE domain (Probable). Upon loading of another HPPA unit to the T domain, the TE domain promotes the enolate formation on the unit attached (Probable). The next step involves head to tail Claisen condensation, followed by the keto-enol tautermerization and a nucleophilic attack on the carbonyl carbon to yield the furanone partial structure (Probable). A spontaneous oxidation at the beta-carbon of the thioester might occur in aerobic condition (Probable). The TE domain then catalyzes the hydrolysis of the thioester, followed by spontaneous decarboxylation, dehydroxylation and keto-enol tautermerization to give the aspulvinone core (Probable). Aspulvinone E is highly unstable and converted to isoaspulvinone E in the presence of light (PubMed:29305695). The structural diversity of the aspulvinones suggests that other tailoring enzymes are involved and have still to be identified (Probable). 2 3-(4-hydroxyphenyl)pyruvate = aspulvinone E + H2O Secondary metabolite biosynthesis. ApvA specifically produces aspulvinone E in hyphea, in contrast to melA which produces aspulvinone E in conidia where it is converted to UV-protective Asp-melanin. ApvA has an A-T-TE domain architecture (Probable). The adenylation (A) domain recognizes and activates the aryl acid substrates, and loads them onto the thiolation (T) domain (Probable). The thioesterase (TE) domain shares the missing condensation (C) domain function, and is responsible for condensation and final product release (Probable). Abolishes the production of aspulvinone E in hyphae, but not in conidia. Belongs to the NRP synthetase family. +Belongs to the SfsA family. +Catalyzes the methylation of C-1 in cobalt-precorrin-5B to form cobalt-precorrin-6A. Co-precorrin-5B + S-adenosyl-L-methionine = Co-precorrin-6A + S-adenosyl-L-homocysteine Cofactor biosynthesis; adenosylcobalamin biosynthesis; cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route): step 6/10. Belongs to the CbiD family. +Major component of the virus occlusion bodies, which are large proteinaceous structures (polyhedra), that protect the virus from the outside environment for extended periods until they are ingested by insect larvae. Belongs to the polyhedrin family. +Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. Homodimer. Belongs to the transketolase family. DXPS subfamily. +Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34. 5-aminomethyl-2-thiouridine(34) in tRNA + S-adenosyl-L-methionine = 5-methylaminomethyl-2-thiouridine(34) in tRNA + H(+) + S-adenosyl-L-homocysteine In the N-terminal section; belongs to the methyltransferase superfamily. tRNA (mnm(5)s(2)U34)-methyltransferase family. In the C-terminal section; belongs to the DAO family. +Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline. carbamoyl phosphate + L-ornithine = H(+) + L-citrulline + phosphate Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 1/3. Homotrimer. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. OTCase family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Belongs to the universal ribosomal protein uL29 family. +Catalyzes the formation of methylglyoxal from dihydroxyacetone phosphate. dihydroxyacetone phosphate = methylglyoxal + phosphate Belongs to the methylglyoxal synthase family. +Probably catalyzes the deacetylation of acetylated carbohydrates an important step in the degradation of oligosaccharides. Homodimer. Belongs to the YdjC deacetylase family. +Plays an important role in the final stage of carbohydrate digestion. Isomaltase activity is specific for both alpha-1,4- and alpha-1,6-oligosaccharides (By similarity). Hydrolysis of sucrose and maltose by an alpha-D-glucosidase-type action. Hydrolysis of (1->6)-alpha-D-glucosidic linkages in some oligosaccharides produced from starch and glycogen by alpha-amylase, and in isomaltose. The resulting sucrase and isomaltase subunits stay associated with one another in a complex by non-covalent linkages. Brush border. The precursor is proteolytically cleaved when exposed to pancreatic proteases in the intestinal lumen. Sulfated. Belongs to the glycosyl hydrolase 31 family. +Catalyzes the ATP- as well as the pyrophosphate-dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK/P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P-Ser-HPr). The two antagonistic activities of HprK/P are regulated by several intracellular metabolites, which change their concentration in response to the absence or presence of rapidly metabolisable carbon sources (glucose, fructose, etc.) in the growth medium. Also phosphorylates/dephosphorylates the HPr-like catabolite repression protein crh on a specific serine residue. Therefore, by controlling the phosphorylation state of HPr and crh, HPrK/P is a sensor enzyme that plays a major role in the regulation of carbon metabolism and sugar transport: it mediates carbon catabolite repression (CCR), and regulates PTS-catalyzed carbohydrate uptake and inducer exclusion. [HPr protein]-L-serine + ATP = [HPr protein]-O-phospho-L-serine + ADP + H(+) [HPr protein]-O-phospho-L-serine + H(+) + phosphate = [HPr protein]-L-serine + diphosphate Homohexamer. The Walker A ATP-binding motif also binds Pi and PPi. Both phosphorylation and phosphorolysis are carried out by the same active site and suggest a common mechanism for both reactions. Belongs to the HPrK/P family. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. ATP + CoA + succinate = ADP + phosphate + succinyl-CoA Binds 1 Mg(2+) ion per subunit. Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. Heterotetramer of two alpha and two beta subunits. Belongs to the succinate/malate CoA ligase beta subunit family. +Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA. a fatty acyl-[ACP] + phosphate = an acyl phosphate + holo-[ACP] Lipid metabolism; phospholipid metabolism. Homodimer. Probably interacts with PlsY. Associated with the membrane possibly through PlsY. Belongs to the PlsX family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Regulator of the DNA damage response (DDR). Part of the TTT complex that is required to stabilize protein levels of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family proteins. The TTT complex is involved in the cellular resistance to DNA damage stresses, like ionizing radiation (IR), ultraviolet (UV) and mitomycin C (MMC). Together with the TTT complex and HSP90 may participate in the proper folding of newly synthesized PIKKs. Promotes assembly, stabilizes and maintains the activity of mTORC1 and mTORC2 complexes, which regulate cell growth and survival in response to nutrient and hormonal signals (By similarity). Component of the TTT complex composed of TELO2, TTI1 and TTI2. Interacts with ATM, ATR, MTOR, PRKDC, SMG1, TELO2, TRRAP AND TTI2. Component of the mTORC1 and mTORC2 complexes. Interacts with WAC; WAC positively regulates MTOR activity by promoting the assembly of the TTT complex and the RUVBL complex composed of RUVBL1 and RUVBL2 into the TTT-RUVBL complex which leads to the dimerization of the mTORC1 complex and its subsequent activation. Phosphorylated at Ser-823 by CK2 following growth factor deprivation, leading to its subsequent ubiquitination by the SCF(FBXO9) complex. Phosphorylation by CK2 only takes place when TELO2 is bound to mTORC1, not mTORC2; leading to selective ubiquitination of mTORC1-associated protein (By similarity). Ubiquitinated by the SCF(FBXO9) complex following phosphorylation by CK2 in response to growth factor deprivation, leading to its degradation by the proteasome. Only mTORC1-associated protein is ubiquitinated and degraded, leading to selective inactivation of mTORC1 to restrain cell growth and protein translation, while mTORC2 is activated due to the relief of feedback inhibition by mTORC1 (By similarity). Belongs to the tti1 family. +Rod linker protein, associated with phycocyanin. Linker polypeptides determine the state of aggregation and the location of the disk-shaped phycobiliprotein units within the phycobilisome and modulate their spectroscopic properties in order to mediate a directed and optimal energy transfer. Associated with the phycobilisome, a hemidiscoidal structure that is composed of two distinct substructures: a core complex and a number of rods radiating from the core. This protein occurs in the rod, it is associated with phycocyanin. Belongs to the phycobilisome linker protein family. +Belongs to the bacterial ribosomal protein bL34 family. +Binds to the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the eukaryotic ribosomal protein eL43 family. Putative zinc-binding subfamily. Extended N-terminus. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Reversible hydration of carbon dioxide (PubMed:14729686). Essential for photosynthetic carbon dioxide fixation, supplies CO(2) to RuBisCO (ribulose bisphosphate carboxylase, cbbL-cbbS) in the carboxysome (Probable). H(+) + hydrogencarbonate = CO2 + H2O Binds 1 Zn(2+) per monomer. Homodimer. This cyanobacterium makes alpha-type carboxysomes. Belongs to the beta-class carbonic anhydrase family. CsoSCA subfamily. +Stimulates the secretion of gonadotropins. Olfactory bulbs, hypothalamus and telencephalon, midbrain and posterior brain areas. Belongs to the GnRH family. +IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. Monomer. Belongs to the IF-3 family. +Belongs to the MEMO1 family. +Belongs to the SWM2 family. +Transcriptional repressor that plays a role in various developmental processes. Specifically binds the consensus DNA sequence 5'-[AC]ACATCTG[GT][AC]-3' which contains the E box core, and acts by recruiting chromatin remodeling multiprotein complexes (By similarity). Belongs to the krueppel C2H2-type zinc-finger protein family. ZBTB18 subfamily. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Involved in cardenolide biosynthesis. Catalyzes the stereospecific conversion of progesterone to 5-beta-pregnane-3,20-dione. Can use progesterone, testosterone, 4-androstene-3,17-dione, cortisol and cortisone as substrates, but not pregnenolone, 21-OH-pregnenolone or isoprogesterone. NADPH could not be replaced by NADH. 5beta-cholestan-3-one + NADP(+) = cholest-4-en-3-one + H(+) + NADPH 4,5beta-dihydrocortisone + NADP(+) = cortisone + H(+) + NADPH Optimum pH is 7.8. Optimum temperature is 40 degrees Celsius. Homodimer. Belongs to the short-chain dehydrogenases/reductases (SDR) family. Highly divergent. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +As part of the MCIA complex, involved in the assembly of the mitochondrial complex I. Participates in constructing the membrane arm of complex I. Part of the mitochondrial complex I assembly/MCIA complex that comprises at least the core subunits TMEM126B, NDUFAF1, ECSIT and ACAD9 and complement subunits such as COA1 and TMEM186. Associates with the intermediate 370 kDa subcomplex of incompletely assembled complex I. Interacts with TMEM70 (By similarity). Belongs to the TMEM126 family. +Cytosolic aldo-keto reductase that catalyzes the NADH and NADPH-dependent reduction of ketosteroids to hydroxysteroids. Acts as a NAD(P)(H)-dependent 3-, 17- and 20-ketosteroid reductase on the steroid nucleus and side chain and regulates the metabolism of androgens, estrogens and progesterone (PubMed:10622721, PubMed:11165022, PubMed:7650035, PubMed:9415401, PubMed:9927279). Displays the ability to catalyze both oxidation and reduction in vitro, but most probably acts as a reductase in vivo since the oxidase activity measured in vitro is inhibited by physiological concentration of NADPH (PubMed:14672942, PubMed:11165022). Acts preferentially as a 17-ketosteroid reductase and has the highest catalytic efficiency of the AKR1C enzyme for the reduction of delta4-androstenedione to form testosterone (PubMed:20036328). Reduces prostaglandin (PG) D2 to 11beta-prostaglandin F2, progesterone to 20alpha-hydroxyprogesterone and estrone to 17beta-estradiol (PubMed:15047184, PubMed:20036328, PubMed:10622721, PubMed:11165022, PubMed:10998348, PubMed:19010934). Catalyzes the transformation of the potent androgen dihydrotestosterone (DHT) into the less active form, 5-alpha-androstan-3-alpha,17-beta-diol (3-alpha-diol) (PubMed:10998348, PubMed:14672942, PubMed:11165022, PubMed:7650035, PubMed:9415401, PubMed:10557352). Also displays retinaldehyde reductase activity toward 9-cis-retinal (PubMed:21851338). a 3alpha-hydroxysteroid + NADP(+) = a 3-oxosteroid + H(+) + NADPH a 3alpha-hydroxysteroid + NAD(+) = a 3-oxosteroid + H(+) + NADH NADP(+) + prostaglandin F2alpha = H(+) + NADPH + prostaglandin D2 NADP(+) + prostaglandin F2alpha = H(+) + NADPH + prostaglandin H2 H(+) + NADPH + prostaglandin D2 = 11beta-prostaglandin F2 + NADP(+) H(+) + NADPH + prostaglandin D2-ethanolamide = 11beta-prostaglandin F2-ethanolamide + NADP(+) NAD(+) + testosterone = androst-4-ene-3,17-dione + H(+) + NADH NADP(+) + testosterone = androst-4-ene-3,17-dione + H(+) + NADPH 17beta-estradiol + NADP(+) = estrone + H(+) + NADPH 17beta-estradiol + NAD(+) = estrone + H(+) + NADH (20S)-hydroxypregn-4-en-3-one + NADP(+) = H(+) + NADPH + progesterone (20S)-hydroxypregn-4-en-3-one + NAD(+) = H(+) + NADH + progesterone 5alpha-androstane-3alpha,17beta-diol + NADP(+) = 17beta-hydroxy-5alpha-androstan-3-one + H(+) + NADPH 5alpha-androstane-3alpha,17beta-diol + NAD(+) = 17beta-hydroxy-5alpha-androstan-3-one + H(+) + NADH 3alpha-hydroxy-5alpha-androstan-17-one + H(+) + NADPH = 5alpha-androstane-3alpha,17beta-diol + NADP(+) 5alpha-androstane-3alpha,17beta-diol + NAD(+) = 3alpha-hydroxy-5alpha-androstan-17-one + H(+) + NADH 5alpha-androstane-3beta,17beta-diol + NADP(+) = 17beta-hydroxy-5alpha-androstan-3-one + H(+) + NADPH 9-cis-retinol + NADP(+) = 9-cis-retinal + H(+) + NADPH Strongly inhibited by nonsteroidal anti-inflammatory drugs (NSAID) including flufenamic acid and indomethacin. Also inhibited by the flavinoid, rutin, and by selective serotonin inhibitors (SSRIs) (PubMed:14979715, PubMed:14996743, PubMed:10557352). The oxidation reaction is inhibited by low micromolar concentrations of NADPH (PubMed:14672942). kcat is 0.044 min(-1) for testosterone oxydation (PubMed:10998348). kcat is 13 min(-1) for 9-cis-retinal as substrate (PubMed:21851338). kcat is 4.18 min(-1) for 17beta-hydroxy-5alpha-androstan-3-one reduction (PubMed:10998348). kcat is 0.37 min(-1) for 3alpha-hydroxy-5alpha-androstan-17-one reduction (PubMed:10998348). kcat is 0.046 min(-1) for 17beta-hydroxy-5alpha-androstan-3-one oxydation (PubMed:10998348). Steroid metabolism. Expressed in many tissues including adrenal gland, brain, kidney, liver, lung, mammary gland, placenta, small intestine, colon, spleen, prostate and testis. High expression in prostate and mammary gland. In the prostate, higher levels in epithelial cells than in stromal cells. In the brain, expressed in medulla, spinal cord, frontotemporal lobes, thalamus, subthalamic nuclei and amygdala. Weaker expression in the hippocampus, substantia nigra and caudate. Belongs to the aldo/keto reductase family. Truncated N-terminus. +Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser) ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec) Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. Homodimer. The tRNA molecule binds across the dimer. Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily. +Glyoxalase domain-containing protein; part of the gene cluster that mediates the biosynthesis of itaconic acid and 2-hydroxyparaconate (PubMed:26639528, PubMed:27750034). Cis-aconitate is secreted by the mitochondrial tricarboxylate transporter MTT1. In the cytosol cis-aconitate is converted into trans-aconitate via isomerization by the aconitate-delta-isomerase ADI1 (PubMed:26639528). Decarboxylation of trans-aconitate by the trans-aconitate decarboxylase TAD1 then leads then to the production of itaconic acid (PubMed:26639528). The cytochrome P450 monooxygenase CYP3 further converts itaconate to 2-hydroxyparaconate via oxidation of the double bond, leading to a transient epoxide, which can subsequently be lactonized to produce 2-hydroxyparaconate (PubMed:27750034). Secretion of itaconate and possibly 2-hydroxyparaconate into the medium is mediated by the major facilitator ITP1 (PubMed:26639528, PubMed:27750034). The glyoxalase domain-containing protein RDO1 is not involved in the biosynthesis of itaconate and 2-hydroxyparaconate, however, it might play a role in the further conversion of 2-hydroxyparaconate to itatartarate (PubMed:27750034). Secondary metabolite biosynthesis. Does not affect the itaconic acid nor 2-hydroxyparaconate production (PubMed:26639528, PubMed:27750034). Belongs to the glyoxalase I family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a(1), b(1), b'(1) and c(9-12) (By similarity). Belongs to the ATPase alpha/beta chains family. +ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 2/3. Homotetramer. Belongs to the argininosuccinate synthase family. Type 2 subfamily. +Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery. ATP-dependent cleavage of peptide bonds with broad specificity. Allosterically activated by HslU binding. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the peptidase T1B family. HslV subfamily. +Belongs to the plant self-incompatibility (S1) protein family. +Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell. Homopentamer. Belongs to the MscL family. +Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III. 4 H(+) + uroporphyrinogen III = 4 CO2 + coproporphyrinogen III Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 4/4. Homodimer. Belongs to the uroporphyrinogen decarboxylase family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Component of the spliceosomal U1 snRNP, which is essential for recognition of the pre-mRNA 5' splice-site and the subsequent assembly of the spliceosome. U1-C is directly involved in initial 5' splice-site recognition for both constitutive and regulated alternative splicing. The interaction with the 5' splice-site seems to precede base-pairing between the pre-mRNA and the U1 snRNA. Stimulates commitment or early (E) complex formation by stabilizing the base pairing of the 5' end of the U1 snRNA and the 5' splice-site region. U1 snRNP is composed of the 7 core Sm proteins B/B', D1, D2, D3, E, F and G that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP, and at least 3 U1 snRNP-specific proteins U1-70K, U1-A and U1-C. U1-C interacts with U1 snRNA and the 5' splice-site region of the pre-mRNA. Belongs to the U1 small nuclear ribonucleoprotein C family. +D-aminoacyl-tRNA deacylase with broad substrate specificity. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo. a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) Binds 2 Zn(2+) ions per subunit. Monomer. Belongs to the DtdA deacylase family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Receptor component of the CCM signaling pathway which is a crucial regulator of heart and vessel formation and integrity. May act through the stabilization of endothelial cell junctions. Interacts with CCM2 and KRIT1; KRIT1 markedly facilitates interaction with CCM2. Expressed in the endocardium of developing heart. Death at embryonic stages due to heart growth defects. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. +Regulates arginine biosynthesis genes. Amino-acid biosynthesis; L-arginine biosynthesis [regulation]. Belongs to the ArgR family. +Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF2. Belongs to the prokaryotic/mitochondrial release factor family. +Catalyzes the prenylation of para-hydroxybenzoate (PHB) with an all-trans polyprenyl group. Mediates the second step in the final reaction sequence of ubiquinone-8 (UQ-8) biosynthesis, which is the condensation of the polyisoprenoid side chain with PHB, generating the first membrane-bound Q intermediate 3-octaprenyl-4-hydroxybenzoate. 4-hydroxybenzoate + all-trans-octaprenyl diphosphate = 4-hydroxy-3-all-trans-octaprenylbenzoate + diphosphate Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the UbiA prenyltransferase family. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5. Homotetramer. Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +This protein is an aporepressor. When complexed with L-tryptophan it binds the operator region of the trp operon and prevents the initiation of transcription. Homodimer. Belongs to the TrpR family. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +May be involved in heavy metals transport. Belongs to the cornifelin family. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Required for efficient primary cilium formation. Belongs to the WD repeat WDR90/POC16 family. +Catalyzes the hydrolysis of N(2)-succinylarginine into N(2)-succinylornithine, ammonia and CO(2). 2 H(+) + 2 H2O + N(2)-succinyl-L-arginine = CO2 + N(2)-succinyl-L-ornithine + 2 NH4(+) Amino-acid degradation; L-arginine degradation via AST pathway; L-glutamate and succinate from L-arginine: step 2/5. Homodimer. Belongs to the succinylarginine dihydrolase family. +Belongs to the GAGE family. +Probable cyclin-dependent protein kinase (CDK) inhibitor that functions as a repressor of mitosis in the endoreduplication cell cycle. Extended C-terminus. +Regulates G protein-coupled receptor signaling cascades, including signaling downstream of the muscarinic acetylcholine receptor CHRM2. Inhibits signal transduction by increasing the GTPase activity of G protein alpha subunits, thereby driving them into their inactive GDP-bound form (PubMed:8774883, PubMed:10608901, PubMed:9353196, PubMed:11443111, PubMed:18434541). Modulates the activity of potassium channels that are activated in response to CHRM2 signaling (PubMed:11443111). Activity on GNAZ is inhibited by palmitoylation of the G-protein (PubMed:9353196). Interacts with GNAZ, GNAI1 and GNAI3 (PubMed:8774883, PubMed:11443111, PubMed:18434541). Associates specifically with the activated, GTP-bound forms of GNAZ and GNAI3 (PubMed:8774883). Forskolin treatment promotes phosphorylation and translocation to the nucleus. +Chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Has a low intrinsic ATPase activity which is markedly stimulated by HscB. Belongs to the heat shock protein 70 family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +Catalyzes the conversion of GTP to GDP through hydrolysis of the gamma-phosphate bond in GTP. When hydroxylated at C-3 of 'Lys-21' by JMJD7, may bind to RNA and play a role in translation. GTP + H2O = GDP + H(+) + phosphate Interacts with RWDD1; this interaction confers protection to polyubiquitination and proteolytic degradation (By similarity). Interacts with JMJD7; this interaction is direct (By similarity). Polyubiquitinated. Hydroxylated (with S stereochemistry) at C-3 of Lys-21 by JMJD7. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Transcription factor that regulates specifically the terrein biosynthesis gene cluster (PubMed:24816227, PubMed:26173180, PubMed:25852654). Recognizes CGG direct repeat consensus sequences in the terrein cluster forming the high affinity consensus motif TCGGHHWYHCGGH (PubMed:25852654). Expression is induced by methionine (PubMed:26173180). Nitrogen starvation induces expression of terR and promotes terrein production during fruit infection, via regulation by areA and atfA (PubMed:26173180). Iron limitation acts as a third independent signal for terrein cluster induction via the iron response regulator hapX (PubMed:26173180). Impairs the expression of the terrein gene cluster and subsequent production of terrein (PubMed:24816227, PubMed:25852654). Terrein shows anticancer activity on various tumors including cervical carcinoma, ovarian cancer, and head and neck cancer (PubMed:23417151, PubMed:25318762, PubMed:27127118, PubMed:25592371). The secondary metabolite acts as angiogenesis inhibitors through the inhibition of angiogenin secretion (PubMed:18776656, PubMed:27127118). Terrein has also anti-inflammatory activity (PubMed:18358890). It shows an alleviative function of age-related inflammation characterized as an anti-oxidant and might therefore be a useful nutraceutical compound for anti-aging (PubMed:26416516). Terrein may enhance osseointegration by decreasing the level of ROS and has a potentially synergistic effect on osteoblast differentiation (PubMed:21104936). Terrein has also been shown to act as a melanogenesis inhibitor (PubMed:15558216, PubMed:15603975, PubMed:19493001). +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Zinc-dependent endoprotease with a unique preference for proline residues surrounding the scissile bond, which cleaves in a PLP-|-PVP motif. Cleaves the cell surface protein encoded by an adjacent gene, which contains two PPEP-2 cleaving sites and putative extracellular matrix-binding domains. Thereby, may have a role in the regulation of P.alvei adhesion. Is not able to cleave within the PVP-|-PVQ motif, and only shows a very poor cleavage of the VNP-|-PVP motif in vitro, which is the optimal substrate peptide for PPEP-1 from P.difficile. The enzyme catalyzes the hydrolytic cleavage of peptide bonds between two proline residues. Binds 1 zinc ion per subunit. kcat is 8 sec(-1) with a FRET peptide containing PLPPVP as substrate. kcat is 3 sec(-1) with a FRET peptide containing VLPPVP as substrate. Monomer. Belongs to the peptidase M34 family. Pro-Pro endopeptidase subfamily. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase C chain family. +Dephosphorylates several organic phosphate monoesters including monophosphate nucleotides (NMPs), coenzyme A (CoA), nicotinamide adenine dinucleotide phosphate (NADP), flavin mononucleotide (FMN) and phosphorylated 5-6 carbon sugars in vitro (PubMed:25848029). Also has a phosphotransferase activity catalyzing the transfer of low-energy phosphate groups from organic phosphate monoesters to free hydroxyl groups of various organic compounds (By similarity). a phosphate monoester + H2O = an alcohol + phosphate Binds 1 Mg(2+) ion per subunit. Homotetramer. Belongs to the class B bacterial acid phosphatase family. +Removes the pyruvyl group from chorismate, with concomitant aromatization of the ring, to provide 4-hydroxybenzoate (4HB) for the ubiquinone pathway. chorismate = 4-hydroxybenzoate + pyruvate Cofactor biosynthesis; ubiquinone biosynthesis. Monomer. Belongs to the UbiC family. +Activates KDO8N (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in the Shewanella genus. 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate + CTP = CMP-8-amino-3,8-dideoxy-alpha-D-manno-oct-2-ulosonate + diphosphate Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsB family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ). 5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphooxyethyl)-thiazole + ADP + H(+) Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-methyl-5-(2-phosphoethyl)-thiazole from 5-(2-hydroxyethyl)-4-methylthiazole: step 1/1. Belongs to the Thz kinase family. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Bifunctional serine/threonine kinase and phosphorylase involved in the regulation of the phosphoenolpyruvate synthase (PEPS) by catalyzing its phosphorylation/dephosphorylation. [pyruvate, water dikinase] + ADP = [pyruvate, water dikinase]-phosphate + AMP + H(+) [pyruvate, water dikinase]-phosphate + H(+) + phosphate = [pyruvate, water dikinase] + diphosphate Belongs to the pyruvate, phosphate/water dikinase regulatory protein family. PSRP subfamily. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Bradykinin-potentiating peptide (PubMed:28670326). Shows poor inhibition over ACE (Ki=1 mM) (PubMed:28670326). In vivo, potentiates bradykinin activity by increasing its edema-inducing activity in rat paw (PubMed:28670326). May also potentiate the hypotensive effects of bradykinin (Probable). Expressed by the venom gland. Belongs to the bradykinin-potentiating peptide family. +Belongs to the UPF0246 family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 1 subfamily. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +Strongly expressed in brain, cerebellum, skeletal muscle, testis. High expression also found in fetal brain, fetal retinal pigmentary epithelium, and fetal retina. Highly expressed in retinal ganglion cells. The disease is caused by variants affecting the gene represented in this entry. Belongs to the TMEM126 family. +Catalyzes the formation of methylglyoxal from dihydroxyacetone phosphate. dihydroxyacetone phosphate = methylglyoxal + phosphate Belongs to the methylglyoxal synthase family. +Moderately inhibits voltage-gated sodium channels and weakly inhibits voltage-gated potassium channel (PubMed:17150181, PubMed:17618665, PubMed:23246579, PubMed:26721415). Inhibits the inactivation of rat Nav1.2/SCN2A (IC(50)=870 nM), rat Nav1.3/SCN3A (IC(50)=845 nM), rat Nav1.4/SCN4A (IC(50)=339 nM), human Nav1.5/SCN5A (IC(50)=335 nM) and human Nav1.7/SCN9A sodium channels (IC(50)=348 nM) (PubMed:26721415). The toxin delays the inactivation of sodium channels without affecting the activation and steady-state inactivation kinetics in the physiological range of voltages (PubMed:26721415). Site-directed mutagenesis of the sodium channel indicates that the toxin interacts with site 3 located at the extracellular S3-S4 linker of domain IV (PubMed:26721415). On potassium channels, it inhibits activation of channels with an IC(50) of 8.05 uM through a voltage sensor-trapping mechanism (PubMed:23246579). It increases muscle contraction in several assays (mouse phrenic nerve-diaphragm, toad heart, rat vas deferens) and is suggested to act both presynaptically and postsynaptically (PubMed:17618665). Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 10 (Hwtx-1) family. 33 (Jztx-1) subfamily. +Assembly factor required for Rieske Fe-S protein RIP1 incorporation into the cytochrome b-c1 (CIII) complex. Functions as a chaperone, binding to this subunit within the mitochondrial matrix and stabilizing it prior to its translocation and insertion into the late CIII dimeric intermediate within the mitochondrial inner membrane. Modulates the mitochondrial matrix zinc pool (By similarity). Interacts with RIP1. Belongs to the complex I LYR family. MZM1 subfamily. +Almost completely overlaps SEL1. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Catalyzes the NAD(P)H-dependent reduction of dihydroxyacetonephosphate (DHAP or glycerone phosphate) to glycerol 1-phosphate (G1P). The G1P thus generated is used as the glycerophosphate backbone of phospholipids in the cellular membranes of Archaea. NAD(+) + sn-glycerol 1-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 1-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Binds 1 zinc ion per subunit. Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the glycerol-1-phosphate dehydrogenase family. +Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily. +Cell wall formation. ATP + L-alanine + UDP-N-acetyl-alpha-D-muramate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Regulates centrosome duplication, probably by inhibiting the kinase activity of ROCK2. Proposed to act as co-chaperone for HSP90. May play a role in the regulation of NOD1 via a HSP90 chaperone complex. In vitro, has intrinsic chaperone activity. This function may be achieved by inhibiting association of ROCK2 with NPM1. Plays a role in ensuring the localization of the tyrosine kinase receptor EGFR to the plasma membrane, and thus ensures the subsequent regulation of EGFR activity and EGF-induced actin cytoskeleton remodeling (By similarity). Involved in stress response. Prevents tumorigenesis (By similarity). Interacts with HSP90AA1, HSP90AB1, PPP5C, ROCK1 and ROCK2. +Participates in cysteine desulfuration mediated by SufS. Cysteine desulfuration mobilizes sulfur from L-cysteine to yield L-alanine and constitutes an essential step in sulfur metabolism for biosynthesis of a variety of sulfur-containing biomolecules. Functions as a sulfur acceptor for SufS, by mediating the direct transfer of the sulfur atom from the S-sulfanylcysteine of SufS, an intermediate product of cysteine desulfuration process. Cofactor biosynthesis; iron-sulfur cluster biosynthesis. Homodimer. Interacts with SufS. Belongs to the SufE family. +Probably required for replication-independent chromatin assembly. Required for transcriptional silencing in the outer repeat (otr) centromeric repeats and the Tf2 long terminal repeat retrotransposons. Repressor of histone gene transcription in G1 arrested cells. Required for repression of htb1 gene expression outside of S phase. Interacts with his3 and slm9. Belongs to the WD repeat HIR1 family. +DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Part of the RNA polymerase complex. Belongs to the archaeal Rpo11/eukaryotic RPB11/RPC19 RNA polymerase subunit family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit. Belongs to the RnpA family. +Mitochondrial electrogenic aspartate/glutamate antiporter that favors efflux of aspartate and entry of glutamate and proton within the mitochondria as part of the malate-aspartate shuttle (PubMed:4436323). Also mediates the uptake of L-cysteinesulfinate by mitochondria in exchange of L-glutamate and proton. Can also exchange L-cysteinesulfinate with aspartate in their anionic form without any proton translocation (PubMed:486467). H(+)(out) + L-aspartate(in) + L-glutamate(out) = H(+)(in) + L-aspartate(out) + L-glutamate(in) 3-sulfino-L-alanine(out) + H(+)(in) + L-glutamate(in) = 3-sulfino-L-alanine(in) + H(+)(out) + L-glutamate(out) 3-sulfino-L-alanine(out) + L-aspartate(in) = 3-sulfino-L-alanine(in) + L-aspartate(out) L-aspartate and 3-sulfino-L-alanine uptake are both inhibited by glisoxepide. Homodimer (via N-terminus). The EF-hand 2 domain within the regulatory N-terminal domain binds one calcium in the mitochondrial intermembrane space. Calcium triggers the binding of the regulatory N-terminal domain to the C-terminal domain, opening a vestibule which allows the substrates to be translocated through the carrier domain (By similarity). In the absence of calcium, the linker loop domain may close the vestibule and prevent substrates from entering the carrier domain (By similarity). Belongs to the mitochondrial carrier (TC 2.A.29) family. +Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Capsid protein VP1 mainly forms the vertices of the capsid (By similarity). Capsid protein VP1 interacts with host cell receptor to provide virion attachment to target host cells (By similarity). This attachment induces virion internalization (By similarity). Tyrosine kinases are probably involved in the entry process (By similarity). After binding to its receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP1 N-terminus (that contains an amphipathic alpha-helix) and capsid protein VP4 are externalized (By similarity). Together, they shape a pore in the host membrane through which viral genome is translocated to host cell cytoplasm (By similarity). Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Lies on the inner surface of the capsid shell (By similarity). After binding to the host receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP4 is released, Capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm (By similarity). Component of immature procapsids, which is cleaved into capsid proteins VP4 and VP2 after maturation (By similarity). Allows the capsid to remain inactive before the maturation step (By similarity). Cysteine protease that cleaves viral polyprotein and specific host proteins (By similarity). It is responsible for the autocatalytic cleavage between the P1 and P2 regions, which is the first cleavage occurring in the polyprotein (By similarity). Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation (By similarity). Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores (By similarity). Counteracts stress granule formation probably by antagonizing its assembly or promoting its dissassembly (By similarity). Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host reticulum endoplasmic and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cytoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication. Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3. Localizes the viral replication complex to the surface of membranous vesicles. Together with protein 3CD binds the Cis-Active RNA Element (CRE) which is involved in RNA synthesis initiation. Acts as a cofactor to stimulate the activity of 3D polymerase, maybe through a nucleid acid chaperone activity. Localizes the viral replication complex to the surface of membranous vesicles (By similarity). It inhibits host cell endoplasmic reticulum-to-Golgi apparatus transport and causes the disassembly of the Golgi complex, possibly through GBF1 interaction (By similarity). This would result in depletion of MHC, trail receptors and IFN receptors at the host cell surface (By similarity). Plays an essential role in viral RNA replication by recruiting ACBD3 and PI4KB at the viral replication sites, thereby allowing the formation of the rearranged membranous structures where viral replication takes place (By similarity). Acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU (By similarity). The oriI viral genomic sequence may act as a template for this. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome (By similarity). Following genome release from the infecting virion in the cytoplasm, the VPg-RNA linkage is probably removed by host TDP2 (By similarity). During the late stage of the replication cycle, host TDP2 is excluded from sites of viral RNA synthesis and encapsidation, allowing for the generation of progeny virions (By similarity). Involved in the viral replication complex and viral polypeptide maturation. It exhibits protease activity with a specificity and catalytic efficiency that is different from protease 3C. Protein 3CD lacks polymerase activity. Protein 3CD binds to the 5'UTR of the viral genome. Replicates the viral genomic RNA on the surface of intracellular membranes. May form linear arrays of subunits that propagate along a strong head-to-tail interaction called interface-I. Covalently attaches UMP to a tyrosine of VPg, which is used to prime RNA synthesis. The positive stranded RNA genome is first replicated at virus induced membranous vesicles, creating a dsRNA genomic replication form. This dsRNA is then used as template to synthesize positive stranded RNA genomes. ss(+)RNA genomes are either translated, replicated or encapsidated. Major viral protease that mediates proteolytic processing of the polyprotein (By similarity). Cleaves host EIF5B, contributing to host translation shutoff (By similarity). Cleaves also host PABPC1, contributing to host translation shutoff (By similarity). Cleaves host NLRP1, triggers host N-glycine-mediated degradation of the autoinhibitory NLRP1 N-terminal fragment (By similarity). a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. Binds 2 magnesium ions that constitute a dinuclear catalytic metal center (By similarity). The magnesium ions are not prebound but only present for catalysis (By similarity). Requires the presence of 3CDpro or 3CPro (By similarity). Replication or transcription is subject to high level of random mutations by the nucleotide analog ribavirin. Interacts with capsid protein VP1 and capsid protein VP3 to form heterotrimeric protomers. Interacts with capsid protein VP0, and capsid protein VP3 to form heterotrimeric protomers (By similarity). Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid (By similarity). Interacts with capsid protein VP2, capsid protein VP3 and capsid protein VP4 following cleavage of capsid protein VP0 (By similarity). Interacts with capsid protein VP1 and capsid protein VP3 in the mature capsid. Interacts with capsid protein VP0 and capsid protein VP1 to form heterotrimeric protomers (By similarity). Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid (By similarity). Interacts with capsid protein VP4 in the mature capsid (By similarity). Interacts with protein 2C; this interaction may be important for virion morphogenesis (By similarity). Interacts with capsid protein VP1 and capsid protein VP3. Homodimer. Homohexamer; forms a hexameric ring structure with 6-fold symmetry characteristic of AAA+ ATPases (By similarity). Interacts (via N-terminus) with host RTN3 (via reticulon domain); this interaction is important for viral replication (By similarity). Interacts with capsid protein VP3; this interaction may be important for virion morphogenesis (By similarity). Interacts with protein 3CD. Homodimer (By similarity). Interacts with host GBF1 (By similarity). Interacts (via GOLD domain) with host ACBD3 (via GOLD domain); this interaction allows the formation of a viral protein 3A/ACBD3 heterotetramer with a 2:2 stoichiometry, which will stimulate the recruitment of host PI4KB in order to synthesize PI4P at the viral RNA replication sites (By similarity). Interacts with RNA-directed RNA polymerase. Interacts with protein 3AB and with RNA-directed RNA polymerase. Interacts with Viral protein genome-linked and with protein 3CD. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. The N-terminus has membrane-binding (By similarity). The N-terminus also displays RNA-binding properties (By similarity). The N-terminus is involved in oligomerization (By similarity). The central part contains an ATPase domain and a degenerate C4-type zinc-finger with only 3 cysteines (By similarity). The C-terminus is involved in RNA-binding (By similarity). The extreme C-terminus contains a region involved in oligomerization (By similarity). Specific enzymatic cleavages in vivo by the viral proteases yield processing intermediates and the mature proteins. Myristoylation is required for the formation of pentamers during virus assembly. Further assembly of 12 pentamers and a molecule of genomic RNA generates the provirion. During virion maturation, immature virions are rendered infectious following cleavage of VP0 into VP4 and VP2. This maturation seems to be an autocatalytic event triggered by the presence of RNA in the capsid and it is followed by a conformational change infectious virion. Myristoylation is required during RNA encapsidation and formation of the mature virus particle. VPg is uridylylated by the polymerase into VPg-pUpU. This acts as a nucleotide-peptide primer for the genomic RNA replication. Belongs to the picornaviruses polyprotein family. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Binds to the muscarinic acetylcholine receptor (CHRM). Monomer. Expressed by the venom gland. Is classified as a P-type cytotoxin, since a proline residue stands at position 54 (Pro-31 in standard classification). Belongs to the snake three-finger toxin family. Short-chain subfamily. Aminergic toxin sub-subfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Belongs to the V-ATPase D subunit family. +putrescine + S-adenosyl 3-(methylsulfanyl)propylamine = H(+) + S-methyl-5'-thioadenosine + spermidine Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1. Belongs to the spermidine/spermine synthase family. +Major connective tissue mitoattractant secreted by vascular endothelial cells. Promotes proliferation and differentiation of chondrocytes (By similarity). Mediates heparin- and divalent cation-dependent cell adhesion in many cell types including fibroblasts, myofibroblasts, endothelial and epithelial cells (By similarity). Enhances fibroblast growth factor-induced DNA synthesis (By similarity). Monomer (By similarity). Interacts with TSKU (PubMed:30232710). Testis, spleen, kidney, lung, heart, and brain (lowest level in testis and highest in lung). By growth factors. Belongs to the CCN family. +Inhibition of exopolysaccharide synthesis (EPS) and nodulation ability (NOD). Glycan metabolism; exopolysaccharide biosynthesis. +H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; UDP-N-acetyl-alpha-D-glucosamine from N-acetyl-alpha-D-glucosamine 1-phosphate: step 1/1. Belongs to the UDPGP type 1 family. +Transcription factor that plays a positive role in salt stress tolerance. Interacts with TIFY11A/JAZ9 and binds to the promoter of some potassium ion transporter genes to regulate potassium homeostasis during salt stress. Interacts with TIFY11A/JAZ9. Belongs to the bHLH protein family. Contains a degenerate basic motif not likely to bind DNA. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Part of the ABC transporter complex PhnCDE involved in phosphonates import. Responsible for energy coupling to the transport system. ATP + H2O + phosphonate(out) = ADP + H(+) + phosphate + phosphonate(in) The complex is composed of two ATP-binding proteins (PhnC), two transmembrane proteins (PhnE) and a solute-binding protein (PhnD). Belongs to the ABC transporter superfamily. Phosphonates importer (TC 3.A.1.9.1) family. +Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate. AH2 + GTP + S-adenosyl-L-methionine = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + A + H(+) + L-methionine Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate. Cofactor biosynthesis; molybdopterin biosynthesis. Monomer and homodimer. Belongs to the radical SAM superfamily. MoaA family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. Binds 1 lipoyl cofactor covalently. The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvH family. +Transcription factor which regulates nonfermentable carbon utilization. Activator of gluconeogenetic genes (By similarity). Belongs to the ERT1/acuK family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Although this protein is a class I aminoacyl-tRNA synthetase, it displays a class II mode of tRNA recognition. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 2 subfamily. +Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore. Homotrimer of disulfide-linked HA1-HA2. Targeted to the apical plasma membrane in epithelial polarized cells through a signal present in the transmembrane domain. Associated with glycosphingolipid- and cholesterol-enriched detergent-resistant lipid rafts. In natural infection, inactive HA is matured into HA1 and HA2 outside the cell by one or more trypsin-like, arginine-specific endoprotease secreted by the bronchial epithelial cells. One identified protease that may be involved in this process is secreted in lungs by Clara cells (By similarity). Palmitoylated. Major glycoprotein, comprises over 80% of the envelope proteins present in virus particle. The extent of infection into host organism is determined by HA. Influenza viruses bud from the apical surface of polarized epithelial cells (e.g. bronchial epithelial cells) into lumen of lungs and are therefore usually pneumotropic. The reason is that HA is cleaved by tryptase clara which is restricted to lungs. However, HAs of H5 and H7 pantropic avian viruses subtypes can be cleaved by furin and subtilisin-type enzymes, allowing the virus to grow in other organs than lungs. The influenza A genome consist of 8 RNA segments. Genetic variation of hemagglutinin and/or neuraminidase genes results in the emergence of new influenza strains. The mechanism of variation can be the result of point mutations or the result of genetic reassortment between segments of two different strains. Belongs to the influenza viruses hemagglutinin family. +Catalyzes the exchange of L-carnitine for gamma-butyrobetaine. (R)-carnitine(out) + 4-(trimethylamino)butanoate(in) = (R)-carnitine(in) + 4-(trimethylamino)butanoate(out) Amine and polyamine metabolism; carnitine metabolism. Homotrimer. Belongs to the BCCT transporter (TC 2.A.15) family. CaiT subfamily. +Involved in the biogenesis of peroxisomes. Belongs to the peroxin-16 family. +DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. Belongs to the NAD-dependent DNA ligase family. LigA subfamily. +Catalyzes the reversible reduction of NADP(+) by F420H(2). In this reaction the proS hydrogen at C5 of F420 is transferred into the proS position at C4 of NADPH. NADP(+) + reduced coenzyme F420-(gamma-L-Glu)(n) = 2 H(+) + NADPH + oxidized coenzyme F420-(gamma-L-Glu)(n) Optimum pH is 8.0 for NADP reduction with F420H(2). Optimum pH is 5.5 for F420 reduction with NADPH. Optimum temperature is 80 degrees Celsius. Is highly thermostable. Homodimer. Belongs to the F420-dependent NADP reductase family. +Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate. 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 6/7. Monomer. Belongs to the EPSP synthase family. +Involved in disease resistance. Required for resistance conferred by multiple R genes recognizing different bacterial and oomycete pathogen isolates like avirulent P.syringae or H.parasitica (downy mildew). Required for the establishment of hypersensitive response (HR) and systemic acquired resistance (SAR) after infection with the bacterial pathogen P.syringae DC3000 carrying avrRpt2. Required for resistance to the soilborne fungus V.longisporum. Interaction with RIN4 is required for the activation of the R gene RPS2 and RPS2-mediated resistance. Interacts with RIN4 (via C-terminus). N-glycosylated. No visible phenotype under normal growth condition. In case of infection, plants loose R gene resistance mediated by RPM1, RPS2, RPS5. Plants overexpressing NDR1 show enhanced resistance against the virulent strain of the bacterial pathogen Pst DC3000. +Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). 3-methyl-2-oxobutanoate + acetyl-CoA + H2O = (2S)-2-isopropylmalate + CoA + H(+) Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 1/4. Homotetramer. Belongs to the alpha-IPM synthase/homocitrate synthase family. LeuA type 1 subfamily. +Regulatory subunit of the slx1-slx4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Forms a heterodimer with slx1. Phosphorylated in response to DNA damage. Belongs to the SLX4 family. +Plays important roles in the innate immune response as effector of glucocorticoid-mediated responses and regulator of the inflammatory process. Has anti-inflammatory activity (PubMed:8425544). Plays a role in glucocorticoid-mediated down-regulation of the early phase of the inflammatory response (By similarity). Contributes to the adaptive immune response by enhancing signaling cascades that are triggered by T-cell activation, regulates differentiation and proliferation of activated T-cells (PubMed:17008549). Promotes the differentiation of T-cells into Th1 cells and negatively regulates differentiation into Th2 cells (PubMed:17008549). Has no effect on unstimulated T cells (PubMed:17008549). Negatively regulates hormone exocytosis via activation of the formyl peptide receptors and reorganization of the actin cytoskeleton (PubMed:19625660). Has high affinity for Ca(2+) and can bind up to eight Ca(2+) ions (By similarity). Displays Ca(2+)-dependent binding to phospholipid membranes (PubMed:2532504, PubMed:8557678). Plays a role in the formation of phagocytic cups and phagosomes. Plays a role in phagocytosis by mediating the Ca(2+)-dependent interaction between phagosomes and the actin cytoskeleton (By similarity). Functions at least in part by activating the formyl peptide receptors and downstream signaling cascades (PubMed:22879591, PubMed:15187149, PubMed:25664854). Promotes chemotaxis of granulocytes and monocytes via activation of the formyl peptide receptors (PubMed:15187149). Promotes rearrangement of the actin cytoskeleton, cell polarization and cell migration (PubMed:15187149). Promotes resolution of inflammation and wound healing (PubMed:25664854). Acts via neutrophil N-formyl peptide receptors to enhance the release of CXCL2 (PubMed:22879591). Homodimer; non-covalently linked (By similarity). Homodimer; linked by transglutamylation (PubMed:2532504). Homodimers linked by transglutamylation are observed in placenta, but not in other tissues (PubMed:2532504). Interacts with S100A11 (PubMed:8557678, PubMed:10673436). Heterotetramer, formed by two molecules each of S100A11 and ANXA1 (PubMed:10673436). Interacts with DYSF (By similarity). Interacts with EGFR (By similarity). Secreted, at least in part via exosomes and other secretory vesicles. Detected in exosomes and other extracellular vesicles (PubMed:25664854). Alternatively, the secretion is dependent on protein unfolding and facilitated by the cargo receptor TMED10; it results in the protein translocation from the cytoplasm into ERGIC (endoplasmic reticulum-Golgi intermediate compartment) followed by vesicle entry and secretion (PubMed:32272059). Detected in gelatinase granules in resting neutrophils (PubMed:10772777). Secretion is increased in response to wounding and inflammation (PubMed:25664854). Secretion is increased upon T-cell activation (PubMed:17008549). Neutrophil adhesion to endothelial cells stimulates secretion via gelatinase granules, but foreign particle phagocytosis has no effect (PubMed:10772777). Colocalizes with actin fibers at phagocytic cups (By similarity). Displays calcium-dependent binding to phospholipid membranes (PubMed:2532504, PubMed:8557678). Detected in resting neutrophils (PubMed:10772777). Detected in peripheral blood T-cells (PubMed:17008549). Detected in extracellular vesicles in blood serum from patients with inflammatory bowel disease, but not in serum from healthy donors (PubMed:25664854). Detected in placenta (at protein level) (PubMed:2532504). Detected in liver. The full-length protein can bind eight Ca(2+) ions via the annexin repeats. Calcium binding causes a major conformation change that modifies dimer contacts and leads to surface exposure of the N-terminal phosphorylation sites; in the absence of Ca(2+), these sites are buried in the interior of the protein core. The N-terminal region becomes disordered in response to calcium-binding. Phosphorylated by protein kinase C, EGFR and TRPM7 (PubMed:2457390, PubMed:15485879). Phosphorylated in response to EGF treatment (PubMed:2532504). Sumoylated. Proteolytically cleaved by cathepsin CTSG to release the active N-terminal peptide Ac2-26. Peptides based on the N-terminal sequence might be used for the treatment of inflammation, e.g. in chronic bowel diseases and in rheumatoid arthritis. Was originally identified as calcium and phospholipid binding protein that displays Ca(2+)-dependent binding to phospholipid membranes and can promote membrane aggregation in vitro. Was initially identified as inhibitor of phospholipase A2 activity (in vitro) (PubMed:2936963, PubMed:8425544). Inhibition of phospholipase activity is mediated via its phospholipid binding activity that limits the access of phospholipase to its substrates. Belongs to the annexin family. +Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. 2 H2O2 = 2 H2O + O2 Homotetramer. Belongs to the catalase family. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTGTCCACA-3'. DnaA binds to ATP and to acidic phospholipids. Can form a dimer when binding to a single dnaA box. Belongs to the DnaA family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The L component serves as a unique electron donor to the NB-component of the complex, and binds Mg-ATP. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per dimer. Porphyrin-containing compound metabolism; chlorophyll biosynthesis (light-independent). Homodimer. Protochlorophyllide reductase is composed of three subunits; ChlL, ChlN and ChlB. Belongs to the NifH/BchL/ChlL family. +an acyl-CoA + sn-glycerol 3-phosphate = a 1-acyl-sn-glycero-3-phosphate + CoA Phospholipid metabolism; CDP-diacylglycerol biosynthesis; CDP-diacylglycerol from sn-glycerol 3-phosphate: step 1/3. The HXXXXD motif is essential for acyltransferase activity and may constitute the binding site for the phosphate moiety of the glycerol-3-phosphate. Belongs to the GPAT/DAPAT family. +Component of the thioredoxin-thioredoxin reductase system. Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions (By similarity). Belongs to the thioredoxin family. +Mediates sugar transport across membranes. Belongs to the SWEET sugar transporter family. +Inactivates MAP kinases. Has a specificity for the ERK family. H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Belongs to the protein-tyrosine phosphatase family. Non-receptor class dual specificity subfamily. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Belongs to the MG439/MG440 family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Homodimer. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In contrast to form I RuBisCO, the form II RuBisCO are composed solely of large subunits. Belongs to the RuBisCO large chain family. Type II subfamily. +Belongs to the transferase hexapeptide repeat family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Displays ATPase and GTPase activities. Belongs to the RapZ-like family. +Redox-active protein probably involved in electron transport. Binds 1 FMN per subunit. Binds 1 [4Fe-4S] cluster. Homodimer. Belongs to the SsuE family. Isf subfamily. +Probably plays an important role in intracellular peptide degradation. Release of an N-terminal amino acid, Xaa, from a peptide or arylamide. Xaa is preferably Glu or Asp but may be other amino acids, including Leu, Met, His, Cys and Gln. Binds 2 manganese ions per subunit. Homohexamer. Belongs to the peptidase M17 family. +Component of the ubiquinol-cytochrome c oxidoreductase, a multisubunit transmembrane complex that is part of the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. The cytochrome b-c1 complex catalyzes electron transfer from ubiquinol to cytochrome c, linking this redox reaction to translocation of protons across the mitochondrial inner membrane, with protons being carried across the membrane as hydrogens on the quinol. In the process called Q cycle, 2 protons are consumed from the matrix, 4 protons are released into the intermembrane space and 2 electrons are passed to cytochrome c. Component of the ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), a multisubunit enzyme composed of 3 respiratory subunits cytochrome b, cytochrome c1 and Rieske protein, 2 core protein subunits, and additional low-molecular weight protein subunits. The complex exists as an obligatory dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with cytochrome c oxidase (complex IV, CIV). Belongs to the UQCRB/QCR7 family. +Acts as a neurotoxin by inhibiting an ion channel. Expressed by the venom duct. The cysteine framework is VI/VII (C-C-CC-C-C). The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. +ADP-ribosylates double-stranded DNA by targeting the N2 amino group of dG residues; 10-fold less active on tRNA. Induces apoptosis in a range of human cell lines (PubMed:10485873, PubMed:11592983). May play a role in removing unnecessary or harmful cells during pupation (PubMed:15528160) (Probable). May play a role in defense against parasitic wasps; its habitual predator Cotesia glomerata is only susceptible after removal of its eggshell or the surface of the larval caudal vesicle, while other wasps are damaged by this protein (PubMed:23637752) (Probable). The wild-type catalytic domain (residues 1-233) cannot be expressed in E.coli as it is unstable probably due to its toxicity. A catalytic domain fragment (Glu-165 mutated to Gln) binds dsDNA but not ssDNA; the presence of the linker inhibits DNA-binding (PubMed:28765284). a 2'-deoxyguanosine in DNA + NAD(+) = an N(2)-(ADP-L-ribosyl)-2'-deoxyguanosine in DNA + H(+) + nicotinamide Within late stage larvae and pupal stages most protein is found in fat bodies. Highest expression is found in fifth instar larvae, decreasing through prepupae, early-phase pupae (1 day after pupation) and late-phase pupae (at protein level). Much lower levels present in adult. The N-terminus (residues 1-233) has the ADP-ribosylation catalytic domain. NAD(+)-binding or the presence of the linker do not alter the structure of the catalytic domain, however in vitro the presence of the linker masks the DNA- and NAD(+)-binding regions and thus prevents dsDNA-binding by the catalytic domain. Belongs to the pierisin ADP-ribosyltransferase family. +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Binds 2 nickel ions per subunit. Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Carboxylation allows a single lysine to coordinate two nickel ions. Belongs to the metallo-dependent hydrolases superfamily. Urease alpha subunit family. +Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. 2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl 1-phosphate + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine = H(+) + lipid A disaccharide (E. coli) + UDP a lipid X + a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a lipid A disaccharide + H(+) + UDP Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 5/6. Belongs to the LpxB family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Transports natural purines (adenine and guanine) as well as purine analogs. Confers sensitivity to 8-azaadenine and 8-azaguanine (8-azg). Resistance to 8-azaadenine and 8-azaguanine but not to other toxic nucleobase analogs. Deficiency in the uptake of adenine and guanine. Belongs to the nucleobase:cation symporter-2 (NCS2) (TC 2.A.40) family. Azg-like subfamily. +Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. Binds 2 magnesium ions per monomer. Binds 1 sodium ion per monomer. Homotetramer. Belongs to the glycosyl hydrolase 2 family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Belongs to the ferlin family. +Part of a potassium transport system. The RCK N-terminal domain binds NAD and possibly other effectors. This is expected to cause a conformation change that regulates potassium transport (By similarity). +Might take part in the signal recognition particle (SRP) pathway. This is inferred from the conservation of its genetic proximity to ftsY/ffh. May be a regulatory protein. Belongs to the UPF0122 family. +With EXP1, the specific cargo receptor protein for the plasma membrane ATPase PMA1, is involved in the transport and/or maturation of PMA1 (PubMed:28727280). EXP1 and PSG1 probably act sequentially to promote PMA1 sorting between the ER and the Golgi, with EXP1 promoting PMA1 export from the ER to the Golgi while PSG1 has a role in PMA1 maturation or quality control in the Golgi (PubMed:28727280). PSG1 might also couple PMA1 sorting and maturation in the early secretory pathway with the glycosylation machinery (Probable). PSG1 is cleaved by KEX2 in two stable peptides, PSG1-N' and PSG1-C', the former supporting a role in maturation quality control, the latter having a role in modulating vesicular trafficking. Interacts with EXP1 (PubMed:28727280). PSG1-N' interacts with ERAD-related proteins involved in PMA1 quality control including EPS1, CDC48, UBX2 and SSM4 (PubMed:28727280). PSG1-C' interacts with the TLG1/2 SNARE complex proteins TLG1, TLG2 and VTI1 (PubMed:28727280). The precursor protein is cleaved into two polypeptide chains, PSG1-N' and PSG1-C'. The cleavage is performed in the Golgi apparatus by Ca(+)-dependent serine protease KEX2 between Arg-229 and Asp-230. PSG1-N' is highly O-mannosylated. Leads to enhanced degradation of PMA1 in the vacuole. Present with 606 molecules/cell in log phase SD medium. +Transport of potassium into the cell. Belongs to the HAK/KUP transporter (TC 2.A.72) family. +Neurotoxin. In vivo, elicits 'spasmodic' symptomatology. Expressed by the venom duct. The cysteine framework is IX (C-C-C-C-C-C). Belongs to the conotoxin P superfamily. +Protein phosphatase which regulates actin filament dynamics. Dephosphorylates and activates the actin binding/depolymerizing factor cofilin, which subsequently binds to actin filaments and stimulates their disassembly. Inhibitory phosphorylation of cofilin is mediated by LIMK1, which may also be dephosphorylated and inactivated by this protein. H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Interacts with the 14-3-3 proteins YWHAB, YWHAG, YWHAQ, and YWHAZ. Interaction with 14-3-3 proteins inhibits phosphatase activity and also blocks recruitment to lamellipodia and stimulation by actin (By similarity). Interacts with actin and this stimulates phosphatase activity. Interacts with LIMK1. Localized to the cleavage furrow and the midbody during cytokinesis (By similarity). Also colocalizes with F-actin in the cytoplasm and the cell periphery, which may allow local control of actin dynamics at sites of cell locomotion. Expressed in brain, heart, kidney and thymus. Also expressed at lower levels in liver, skeletal muscle, small intestine and spleen. Ubiquitously expressed in the embryo at 14.5 dpc. Phosphorylated. Inhibitory phosphorylation by PAK4 promotes binding to YWHAZ. Phosphorylation at Ser-970 is decreased by stimuli which promote actin reorganization and lamellipodia formation. Can be dephosphorylated and activated by PPP3CA/calcineurin A. Phosphorylation decreases immediately prior to telophase (By similarity). Tyrosine phosphatase activity has not been demonstrated for this protein to date. Belongs to the protein-tyrosine phosphatase family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit. Belongs to the RnpA family. +Catalyzes the formation of 5-methyl-uridine at position 747 (m5U747) in 23S rRNA. S-adenosyl-L-methionine + uridine(747) in 23S rRNA = 5-methyluridine(747) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmC subfamily. Could be the product of a pseudogene. The N-terminus is much shorter than in related proteins. +Cleaves proteins, imported into the mitochondrion, to their mature size. Release of an N-terminal octapeptide as second stage of processing of some proteins imported into the mitochondrion. Binds 1 zinc ion. Activity is divalent cation-dependent. It is stimulated by manganese, magnesium or calcium ions and reversibly inhibited by zinc, cobalt and iron (By similarity). Monomer. Belongs to the peptidase M3 family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Retinol dehydrogenase with a clear preference for NADP. Converts all-trans-retinol to all-trans-retinal. Has no detectable activity towards 11-cis-retinol, 9-cis-retinol and 13-cis-retinol (By similarity). all-trans-retinol + NADP(+) = all-trans-retinal + H(+) + NADPH Cofactor metabolism; retinol metabolism. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Regulatory subunit of the cAMP-dependent protein kinases involved in cAMP signaling in cells. Type II regulatory chains mediate membrane association by binding to anchoring proteins, including the MAP2 kinase. The inactive form of the enzyme is composed of two regulatory chains and two catalytic chains. Activation by cAMP produces two active catalytic monomers and a regulatory dimer that binds four cAMP molecules. Interacts with PRKACA and PRKACB. Interacts with the phosphorylated form of PJA2. Forms a complex composed of PRKAR2B, GSK3B and GSKIP through GSKIP interaction; facilitates PKA-induced phosphorylation and regulates GSK3B activity. Colocalizes with PJA2 in the cytoplasm and at the cell membrane. Four types of regulatory chains are found: I-alpha, I-beta, II-alpha, and II-beta. Their expression varies among tissues and is in some cases constitutive and in others inducible. Brain. Present in a few pyramidal neurons and mostly in mossy fibers. Colocalizes with PJA2 in dentate granule cells and at postsynaptic sites of primary hippocampal neurons. Phosphorylated by the activated catalytic chain. Belongs to the cAMP-dependent kinase regulatory chain family. +Belongs to the GRP transporter (TC 2.A.7.5) family. +Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. Belongs to the glycosyl hydrolase 9 (cellulase E) family. Truncated C-terminus. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O H2O + L-histidinol phosphate = L-histidinol + phosphate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 8/9. In the N-terminal section; belongs to the histidinol-phosphatase family. In the C-terminal section; belongs to the imidazoleglycerol-phosphate dehydratase family. +One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA. Homotetramer, a dimer of dimers. One homotetramer interacts with 1 SecA dimer. Belongs to the SecB family. +Protein and nucleotide deglycase that catalyzes the deglycation of the Maillard adducts formed between amino groups of proteins or nucleotides and reactive carbonyl groups of glyoxals. Thus, functions as a protein deglycase that repairs methylglyoxal- and glyoxal-glycated proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteine, arginine and lysine residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of Schiff bases and advanced glycation endproducts (AGE). Also functions as a nucleotide deglycase able to repair glycated guanine in the free nucleotide pool (GTP, GDP, GMP, dGTP) and in DNA and RNA. Is thus involved in a major nucleotide repair system named guanine glycation repair (GG repair), dedicated to reversing methylglyoxal and glyoxal damage via nucleotide sanitization and direct nucleic acid repair. Plays an important role in protecting cells from carbonyl stress. H2O + N(omega)-(1-hydroxy-2-oxopropyl)-L-arginyl-[protein] = H(+) + L-arginyl-[protein] + lactate H2O + N(6)-(1-hydroxy-2-oxopropyl)-L-lysyl-[protein] = H(+) + L-lysyl-[protein] + lactate H2O + S-(1-hydroxy-2-oxopropyl)-L-cysteinyl-[protein] = H(+) + L-cysteinyl-[protein] + lactate H2O + N(omega)-(1-hydroxy-2-oxoethyl)-L-arginyl-[protein] = glycolate + H(+) + L-arginyl-[protein] H2O + N(6)-(1-hydroxy-2-oxoethyl)-L-lysyl-[protein] = glycolate + H(+) + L-lysyl-[protein] H2O + S-(1-hydroxy-2-oxoethyl)-L-cysteinyl-[protein] = glycolate + H(+) + L-cysteinyl-[protein] H2O + N(2)-(1-hydroxy-2-oxopropyl)-dGTP = dGTP + H(+) + lactate H2O + N(2)-(1-hydroxy-2-oxopropyl)-GTP = GTP + H(+) + lactate H2O + N(2)-(1-hydroxy-2-oxopropyl)-GDP = GDP + H(+) + lactate H2O + N(2)-(1-hydroxy-2-oxopropyl)-GMP = GMP + H(+) + lactate H2O + N(2)-(1-hydroxy-2-oxoethyl)-dGTP = dGTP + glycolate + H(+) H2O + N(2)-(1-hydroxy-2-oxoethyl)-GTP = glycolate + GTP + H(+) H2O + N(2)-(1-hydroxy-2-oxoethyl)-GDP = GDP + glycolate + H(+) H2O + N(2)-(1-hydroxy-2-oxoethyl)-GMP = glycolate + GMP + H(+) an N(2)-(1-hydroxy-2-oxopropyl)-guanosine in RNA + H2O = a guanosine in RNA + H(+) + lactate an N(2)-(1-hydroxy-2-oxopropyl)-2'-deoxyguanosine in DNA + H2O = a 2'-deoxyguanosine in DNA + H(+) + lactate an N(2)-(1-hydroxy-2-oxoethyl)-guanosine in RNA + H2O = a guanosine in RNA + glycolate + H(+) an N(2)-(1-hydroxy-2-oxoethyl)-2'-deoxyguanosine in DNA + H2O = a 2'-deoxyguanosine in DNA + glycolate + H(+) Homodimer. By heat shock. Belongs to the peptidase C56 family. HchA subfamily. +Catalyzes the reversible oxidation of malate to oxaloacetate. (S)-malate + NAD(+) = H(+) + NADH + oxaloacetate Homodimer. Belongs to the LDH/MDH superfamily. MDH type 1 family. +Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). 5,6-dimethylbenzimidazole + nicotinate beta-D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate Nucleoside biosynthesis; alpha-ribazole biosynthesis; alpha-ribazole from 5,6-dimethylbenzimidazole: step 1/2. Homodimer. Belongs to the CobT family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 1 family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The NB-protein (ChlN-ChlB) is the catalytic component of the complex. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per heterodimer. The cluster is bound at the heterodimer interface by residues from both subunits. Porphyrin-containing compound metabolism; chlorophyll biosynthesis (light-independent). Protochlorophyllide reductase is composed of three subunits; ChlL, ChlN and ChlB. Forms a heterotetramer of two ChlB and two ChlN subunits. Belongs to the ChlB/BchB/BchZ family. +Belongs to the UPF0434 family. +Specifically methylates position 8 of adenine 2503 in 23S rRNA. Can also methylate position 2 of A2503 after the primary methylation at position 8 is complete, to form 2,8-dimethyladenosine; however, C8 is its preferred target. Confers resistance to several classes of antibiotics such as phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A. The antibiotic resistance conferred by Cfr is provided by methylation at the 8 position and is independent of methylation at the 2 position of A2503. adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 5'-deoxyadenosine + 8-methyladenosine(2503) in 23S rRNA + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue. Belongs to the radical SAM superfamily. RlmN family. Cfr subfamily. +Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). 2-oxoglutarate + H(+) + isochorismate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2 Binds 1 thiamine pyrophosphate per subunit. Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 2/7. Quinol/quinone metabolism; menaquinone biosynthesis. Homodimer. Belongs to the TPP enzyme family. MenD subfamily. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Belongs to the UPF0391 family. +DNA helicase which participates in several chromatin remodeling complexes, including the SWR1 and the INO80 complexes. The SWR1 complex mediates the ATP-dependent exchange of histone H2A for the H2A variant H2A.Z leading to transcriptional regulation of selected genes by chromatin remodeling. The INO80 complex remodels chromatin by shifting nucleosomes and is involved in DNA repair. Also involved in pre-rRNA processing (By similarity). ATP + H2O = ADP + H(+) + phosphate May form heterododecamers with hel-2/rvb2. Component of the SWR1 chromatin remodeling complex, the INO80 chromatin remodeling complex, and of the R2TP complex (By similarity). Belongs to the RuvB family. +May be involved in zinc transport from the cytoplasm to either intracellular organelles or extracellular spaces. Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family. SLC30A subfamily. +The heterodimer glycoprotein H-glycoprotein L is required for the fusion of viral and plasma membranes leading to virus entry into the host cell. Following initial binding to host receptor, membrane fusion is mediated by the fusion machinery composed of gB and the heterodimer gH/gL. May also be involved in the fusion between the virion envelope and the outer nuclear membrane during virion morphogenesis (By similarity). In human cytomegalovirus, forms two distincts complexes to mediate viral entry, a trimer and a pentamer at the surface of the virion envelope. The gH-gL-gO trimer is required for infection in fibroblasts by interacting with host PDGFRA. The gH-gL-UL128-UL130-UL131A pentamer is essential for viral entry in epithelial, endothelial and myeloid cells via interaction with host NRP2 (By similarity). Interacts with glycoprotein L (gL); this interaction is necessary for the correct processing and cell surface expression of gH. The heterodimer gH/gL seems to interact with gB trimers during fusion (By similarity). Forms the envelope pentamer complex (PC) composed of gH, gL, UL128, UL130, and UL131A. The pentamer interacts with host NRP2. Forms the envelope trimer complex composed of gH, gL, and gO (PubMed:9733861). The trimer interacts with host PDGFRA (By similarity). Interacts with UL116 (By similarity). During virion morphogenesis, this protein probably accumulates in the endosomes and trans-Golgi where secondary envelopment occurs. It is probably transported to the cell surface from where it is endocytosed and directed to the trans-Golgi network (TGN). N-glycosylated, O-glycosylated, and sialylated. Belongs to the herpesviridae glycoprotein H family. +Belongs to the HesB/IscA family. +Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate. S-adenosyl-L-methionine + trans-aconitate = (E)-3-(methoxycarbonyl)pent-2-enedioate + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. Tam family. +Nucleoside triphosphate pyrophosphatase that hydrolyzes 7-methyl-GTP (m(7)GTP). May have a dual role in cell division arrest and in preventing the incorporation of modified nucleotides into cellular nucleic acids. H2O + N(7)-methyl-GTP = diphosphate + H(+) + N(7)-methyl-GMP Belongs to the Maf family. YceF subfamily. +Belongs to the ABC transporter superfamily. +Catalyzes the hydrolysis of UDP-3-O-myristoyl-N-acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate, the committed step in lipid A biosynthesis. a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 2/6. Belongs to the LpxC family. +H2O + L-glutamate + NADP(+) = 2-oxoglutarate + H(+) + NADPH + NH4(+) Homohexamer. Belongs to the Glu/Leu/Phe/Val dehydrogenases family. +This protein plays a role in synthesis of starch. It catalyzes the synthesis of the activated glycosyl donor, ADP-glucose from Glc-1-P and ATP. alpha-D-glucose 1-phosphate + ATP + H(+) = ADP-alpha-D-glucose + diphosphate Activated by 3'phosphoglycerate, inhibited by orthophosphate. Allosteric regulation. Glycan biosynthesis; starch biosynthesis. Heterotetramer. Belongs to the bacterial/plant glucose-1-phosphate adenylyltransferase family. +Cleaves proteins, imported into the mitochondrion, to their mature size. While most mitochondrial precursor proteins are processed to the mature form in one step by mitochondrial processing peptidase (MPP), the sequential cleavage by MIP of an octapeptide after initial processing by MPP is a required step for a subgroup of nuclear-encoded precursor proteins destined for the matrix or the inner membrane (By similarity). Release of an N-terminal octapeptide as second stage of processing of some proteins imported into the mitochondrion. Binds 1 zinc ion. Belongs to the peptidase M3 family. +Belongs to the HflD family. +As part of a SNARE complex may be involved in endoplasmic reticulum membranes fusion and be required for the maintenance of endoplasmic reticulum organization. Also plays a role in apoptosis. It is for instance required for endoplasmic reticulum stress-induced apoptosis. As a substrate of RNF185 interacting with SQSTM1, might also be involved in mitochondrial autophagy. Component of a SNARE complex consisting of STX18, USE1L, BNIP1/SEC20L and SEC22B. Interacts directly with STX18, RINT1/TIP20L and NAPA. Interacts with ZW10 through RINT1. Interacts with BCL2. Interacts with RNF186. Interacts with RNF185. Interacts with SQSTM1; increased by 'Lys-63'-linked polyubiquitination of BNIP1. Localization to the mitochondrion is regulated by RNF186. Polyubiquitinated. 'Lys-63'-linked polyubiquitination by RNF185 increases the interaction with the autophagy receptor SQSTM1. Undergoes 'Lys-29'- and 'Lys-63'-linked polyubiquitination by RNF186 that may regulate BNIP1 localization to the mitochondrion. Belongs to the SEC20 family. +May act either alone or in interaction with glutaredoxin as a redox-regulated transcriptional regulator, or as a factor regulating Fe-S cluster biogenesis. Interacts in vitro with GRXS14, GRXS15, GRXS16 and GRXS17, but not with GRXC5 (PubMed:24203231). Interacts in vivo only with GRXS14, GRXS15 and GRXS16 (PubMed:24203231). Belongs to the bolA/yrbA family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair (By similarity). Component of the SWR1 chromatin-remodeling complex and of the NuA4 histone acetyltransferase complex. Belongs to the SWC4 family. +An anti-sigma factor for extracytoplasmic function (ECF) sigma factor SigD. ECF sigma factors are held in an inactive form by an anti-sigma factor until released by regulated intramembrane proteolysis (RIP). RIP occurs when an extracytoplasmic signal triggers a concerted proteolytic cascade to transmit information and elicit cellular responses. The membrane-spanning regulatory substrate protein is first cut extracytoplasmically (site-1 protease, S1P), then within the membrane itself (site-2 protease, S2P), while cytoplasmic proteases finish degrading the regulatory protein, liberating the sigma factor (By similarity). Interacts with ECF RNA polymerase sigma factor SigD; this should inhibit the interaction of SigD with the RNA polymerase catalytic core. The cytosolic domain interacts with sigma factor SigD. +Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits. The heterotrimers can form oligomers, although 1 heterotrimer is thought to be able to translocate proteins. Interacts with the ribosome. Interacts with SecDF, and other proteins may be involved. Interacts with SecA. Belongs to the SecE/SEC61-gamma family. +Involved in the synthesis of tocopherol (vitamin E). Methylates gamma- and delta-tocopherol to form beta- and alpha-tocopherol, respectively. gamma-tocopherol + S-adenosyl-L-methionine = (+)-alpha-tocopherol + H(+) + S-adenosyl-L-homocysteine delta-tocotrienol + S-adenosyl-L-methionine = beta-tocotrienol + H(+) + S-adenosyl-L-homocysteine gamma-tocotrienol + S-adenosyl-L-methionine = alpha-tocotrienol + H(+) + S-adenosyl-L-homocysteine delta-tocopherol + S-adenosyl-L-methionine = beta-tocopherol + H(+) + S-adenosyl-L-homocysteine Cofactor biosynthesis; tocopherol biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. gTMT family. +Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II. Binds 1 heme c group covalently per subunit. The oxygen-evolving complex in red algae is composed of psbO (OEC33), psbQ', cytochrome c-550 and psbU. Associated with photosystem II at the lumenal side of the thylakoid membrane. Belongs to the cytochrome c family. PsbV subfamily. +ATP-binding RNA helicase involved in mitochondrial RNA metabolism. Required for maintenance of mitochondrial DNA (By similarity). ATP + H2O = ADP + H(+) + phosphate The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis. Belongs to the DEAD box helicase family. MRH4 subfamily. +Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. [sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Monomer. Belongs to the methylthiotransferase family. MiaB subfamily. +Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction. acetate + ATP = acetyl phosphate + ADP Mg(2+). Can also accept Mn(2+). Metabolic intermediate biosynthesis; acetyl-CoA biosynthesis; acetyl-CoA from acetate: step 1/2. Homodimer. Belongs to the acetokinase family. +Plays an important role in the elongation step of protein synthesis. P1 and P2 exist as dimers at the large ribosomal subunit. Belongs to the eukaryotic ribosomal protein P1/P2 family. +Catalyzes the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH 5,10-methenyltetrahydrofolate + H2O = (6S)-10-formyltetrahydrofolate + H(+) One-carbon metabolism; tetrahydrofolate interconversion. Homodimer. Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family. +Catalyzes the circularization of gamma-N-acetyl-alpha,gamma-diaminobutyric acid (ADABA) to ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid), which is an excellent osmoprotectant. (2S)-4-acetamido-2-aminobutanoate = H2O + L-ectoine Amine and polyamine biosynthesis; ectoine biosynthesis; L-ectoine from L-aspartate 4-semialdehyde: step 3/3. Belongs to the ectoine synthase family. +Solute-binding protein that binds (R)-pantoate and D-erythronate (in vitro) (PubMed:25540822). Probably part of a tripartite ATP-independent periplasmic (TRAP) transport system that mediates solute transport into the cytoplasm. The complex is comprised of an extracytoplasmic solute-binding protein and a heteromeric permease formed by two transmembrane proteins. Belongs to the bacterial solute-binding protein 7 family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Catalyzes the transfer of the AMP portion of ATP to flavin mononucleotide (FMN) to produce flavin adenine dinucleotide (FAD) coenzyme. ATP + FMN + H(+) = diphosphate + FAD Cofactor biosynthesis; FAD biosynthesis; FAD from FMN: step 1/1. Homodimer. Belongs to the archaeal FAD synthase family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Involved in pyrimidine catabolism. May facilitate the hydrolysis of carbamate, a reaction that can also occur spontaneously. carbamate + 2 H(+) = CO2 + NH4(+) Belongs to the AB hydrolase superfamily. Hydrolase RutD family. +Monoterpene synthase involved in the biosynthesis of volatile compounds widely used in aromatherapy and folk medicine, and present in culinary herbs (PubMed:24943828). Mediates the conversion of (2E)-geranyl diphosphate (GPP) into alpha fenchol, limonene and alpha-pinene and, as minor compounds, into beta-myrcene, alpha-terpinolene and alpha-phellandrene (PubMed:24943828). (2E)-geranyl diphosphate = alpha-pinene + diphosphate (2E)-geranyl diphosphate + H2O = (1S,2S,4R)-endo-fenchol + diphosphate (2E)-geranyl diphosphate = diphosphate + limonene Binds 3 Mg(2+) or Mn(2+) ions per subunit. Secondary metabolite biosynthesis; terpenoid biosynthesis. Expressed at high levels in leaves. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg(2+). Belongs to the terpene synthase family. Tpsa subfamily. +Participates in the translocation of lipoproteins from the inner membrane to the outer membrane. Only forms a complex with a lipoprotein if the residue after the N-terminal Cys is not an aspartate (The Asp acts as a targeting signal to indicate that the lipoprotein should stay in the inner membrane). Monomer. Belongs to the LolA family. +Catalyzes the first step in the D-alanylation of lipoteichoic acid (LTA), the activation of D-alanine and its transfer onto the D-alanyl carrier protein (Dcp) DltC. In an ATP-dependent two-step reaction, forms a high energy D-alanyl-AMP intermediate, followed by transfer of the D-alanyl residue as a thiol ester to the phosphopantheinyl prosthetic group of the Dcp. D-alanylation of LTA plays an important role in modulating the properties of the cell wall in Gram-positive bacteria, influencing the net charge of the cell wall. ATP + D-alanine + holo-[D-alanyl-carrier protein] = AMP + D-alanyl-[D-alanyl-carrier protein] + diphosphate Cell wall biogenesis; lipoteichoic acid biosynthesis. Belongs to the ATP-dependent AMP-binding enzyme family. DltA subfamily. +Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of the pseudouridine corresponding to position 914 in M.jannaschii 16S rRNA (By similarity). a pseudouridine in 16S/18S rRNA + S-adenosyl-L-methionine = an N(1)-methylpseudouridine in 16S/18S rRNA + H(+) + S-adenosyl-L-homocysteine Homodimer. Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase NEP1 family. +Belongs to the UPF0607 family. Could be the product of a pseudogene. +K(+)/H(+) antiporter that extrudes potassium in exchange for external protons and maintains the internal concentration of potassium under toxic levels. H(+)(out) + K(+)(in) = H(+)(in) + K(+)(out) Belongs to the monovalent cation:proton antiporter 1 (CPA1) transporter (TC 2.A.36) family. NhaP2 subfamily. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +Belongs to the UPF0235 family. +Component of TORC1, which regulates multiple cellular processes to control cell growth in response to environmental signals. Tor2 is essential for growth. Nutrient limitation and environmental stress signals cause inactivation of TORC1. Active TORC1 positively controls cell growth and ribosome biogenesis by regulating ribosomal protein gene expression. TORC1 negatively controls G1 cell-cycle arrest, sexual development and amino acid uptake. Represses mating, meiosis and sporulation efficiency by interfering with the functions of the transcription factor ste11 and the meiosis-promoting RNA-binding protein mei2. The target of rapamycin complex 1 (TORC1) is composed of at least mip1, pop3/wat1, tco89, toc1 and tor2. Localizes at the barrier septum. Either Thr-10, Ser-11, Ser-12, Ser-13 or Thr-14 and Ser-214 or Ser-215 and Ser-247 or Ser-249 are phosphorylated as well. Belongs to the TORC subunit TCO89 family. +Activates expression of the rhaBAD and rhaT operons. Binds DNA as a dimer. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system. The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. Belongs to the TatA/E family. +With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS5 family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseB family. +Belongs to the UPF0260 family. +Fibrillar structure, part of fimbriae, necessary for full virulence. Forms a homomer composed of subunits assembled in a large structure. Expressed inside macrophages under acidic pH and at 37 degrees Celsius. +ATP + L-asparagine + tRNA(Asn) = AMP + diphosphate + H(+) + L-asparaginyl-tRNA(Asn) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and/or repair of Fe-S clusters in biosynthetic enzymes. Monomer. Belongs to the Fe(2+)-trafficking protein family. +Important for reducing fluoride concentration in the cell, thus reducing its toxicity. Belongs to the CrcB (TC 9.B.71) family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'-nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Magnesium is required for nucleotidyltransferase activity. Nickel for phosphatase activity. Monomer. Can also form homodimers and oligomers. Comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain associated with both phosphodiesterase and phosphatase activities. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 1 subfamily. +Cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. CTDK-I phosphorylates 'Ser-5' if the CTD substrate is not phosphorylated at 'Ser-5', but will phosphorylate 'Ser-2' of a CTD substrate if 'Ser-5' is already phosphorylated. CTDK-I is also more reactive toward substrates that are prephosphorylated at 'Ser-2' or 'Ser-5' compared with an unphosphorylated CTD substrate, therefore efficiently creating doubly phosphorylated CTD repeats. Involved in RNA polymerase II transcriptional elongation, and as part of the CTDK-I complex, pre-mRNA 3'-end processing and SET2 mediated H3K36 methylation. Together with CTK3, required for CTK1 CTD kinase activation. Required for DNA damage induced transcription. Involved in the adaptation to alternative carbon sources, including galactose, glycerol and ethanol, but not raffinose. Required for the integrity of the rDNA locus. CTDK-I consists of three subunits, CTK1, CTK2 and CTK3 (also called alpha, beta and gamma). Interacts with CTK1. Heterodimerization with CTK3 is required to protect this subunit from degradation. Phosphorylated. Ubiquitinated. Phosphorylation and ubiquitination lead to degradation in growth-related way by the ubiquitin-proteasome pathway. Neither phosphorylation nor degradation requires association with CTK1. Null mutants are viable, but grow more slowly than wild-type cells at 30 degrees Celsius. They are cold-sensitive, failing to grow at 12 degrees Celsius. They display flocculent growth in liquid media and they show abnormal cell morphologies, for example, a significant fraction of the cells are greatly enlarged. Deletion mutant is sensitive to the DNA synthesis inhibitor hydroxyurea (HU) and UV irradiation. Present with 1590 molecules/cell in log phase SD medium. Belongs to the cyclin family. +Heterodimeric electron transfer flavoprotein that accepts electrons from several mitochondrial dehydrogenases, including acyl-CoA dehydrogenases, glutaryl-CoA and sarcosine dehydrogenase. It transfers the electrons to the main mitochondrial respiratory chain via ETF-ubiquinone oxidoreductase. Required for normal mitochondrial fatty acid oxidation and normal amino acid metabolism. ETFB binds an AMP molecule that probably has a purely structural role. Heterodimer composed of ETFA and ETFB. Identified in a complex that contains ETFA, ETFB and ETFRF1. Interacts with ACADM. The recognition loop recognizes a hydrophobic patch at the surface of interacting dehydrogenases and acts as a static anchor at the interface. Methylated. Trimethylation at Lys-200 and Lys-203 may negatively regulate the activity in electron transfer from acyl-CoA dehydrogenases. Belongs to the ETF beta-subunit/FixA family. +hexadecanoyl-CoA + L-cysteinyl-[protein] = CoA + S-hexadecanoyl-L-cysteinyl-[protein] The DHHC domain is required for palmitoyltransferase activity. Belongs to the DHHC palmitoyltransferase family. The gene for this protein is duplicated in strains AX3 and AX4. These strains contain a duplication of a segment of 750 kb of chromosome 2 compared to the corresponding sequence in strain AX2. +Probable transporter involved in the regulation of zinc homeostasis. Interacts with cis4. Leads to sensitivity to camptothecin and DNA-damaging agents. Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family. SLC30A subfamily. +Mitogen-activated protein kinase kinase; part of the MCK1-MKK2-MPS1 MAP kinase (MAPK) signal transduction cascade that is essential for appressorium formation, penetration and invasive growth (PubMed:28244240). Beside its role in pathogenesis, the MPS1 cascade is active in conidiation and cellular stress responses (By similarity). Targets downstream of the the MPS1-MAPK pathway include transcription factors MIG1 and SWI6, as well as GSK1 and MPG1 (PubMed:28244240). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts with the adapter protein MST50. Belongs to the protein kinase superfamily. STE Ser/Thr protein kinase family. MAP kinase kinase subfamily. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Belongs to the UPF0412 family. +Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors. [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H(+) Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 51 family. +Expressed by the venom gland. Belongs to the neurotoxin 19 (CSTX) family. 01 subfamily. +Substrate recognition and binding subunit of the essential mitochondrial processing protease (MPP), which cleaves the mitochondrial sequence off newly imported precursors proteins. Heterodimer of mas2 (alpha) and mas1 (beta) subunits, forming the mitochondrial processing protease (MPP) in which mas2 is involved in substrate recognition and binding and mas1 is the catalytic subunit. Belongs to the peptidase M16 family. Does not seem to have a protease activity as it lack the zinc-binding site. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL30 family. +V region of the variable domain of immunoglobulin light chains that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268). Immunoglobulins are composed of two identical heavy chains and two identical light chains; disulfide-linked. There are several alleles. The sequence shown is that of IMGT allele IGLV4-3*01. For an example of a full-length immunoglobulin lambda light chain see AC P0DOX8. +ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 2/3. Homotetramer. Belongs to the argininosuccinate synthase family. Type 1 subfamily. +RNA-binding protein that associates with the RNA exosome complex. Involved in the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and play a role in recruiting the RNA exosome complex to pre-rRNA; this function may include C1D. Associates with the RNA exosome complex, probably mediated by EXOSC10 (PubMed:29906447). Interacts with ARHGAP18, EXOSC10 and MTREX. Cytoplasmic in M phase. Phosphorylated in M (mitotic) phase. Belongs to the MPP6 family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Master enzyme that delivers sulfur to a number of partners involved in Fe-S cluster assembly, tRNA modification or cofactor biosynthesis. Catalyzes the removal of elemental sulfur atoms from cysteine to produce alanine. Functions as a sulfur delivery protein for Fe-S cluster synthesis onto IscU, an Fe-S scaffold assembly protein, as well as other S acceptor proteins. [sulfur carrier]-H + L-cysteine = [sulfur carrier]-SH + L-alanine Cofactor biosynthesis; iron-sulfur cluster biosynthesis. Homodimer. Forms a heterotetramer with IscU, interacts with other sulfur acceptors. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. NifS/IscS subfamily. +Catalyzes the reversible oxidation of malate to oxaloacetate. (S)-malate + NAD(+) = H(+) + NADH + oxaloacetate Belongs to the LDH/MDH superfamily. MDH type 2 family. +May be required for neuronal cell differentiation. Interacts with DYSF; the interaction is direct and Ca(2+)-independent. Truncated N-terminus. +Histone deubiquitinating component of the transcription regulatory histone acetylation (HAT) complex SAGA. Catalyzes the deubiquitination of both histones H2A and H2B, thereby acting as a coactivator. Recruited to specific gene promoters by activators, where it is required for transcription (By similarity). Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Component of some SAGA transcription coactivator-HAT complexes. Belongs to the peptidase C19 family. UBP8 subfamily. +Involved in the negative regulation of the K(+) potassium channel AKT1 by its dephosphorylation, antagonistically to CIPK proteins (e.g. CIPK23) (PubMed:17898163). Functions as positive regulator of abscisic acid-mediated cell signaling during seedling growth (PubMed:22404835). Involved in the regulation of seed dormancy (PubMed:23378449). Acts as negative regulator of seed dormancy by inhibiting abscisic signaling and subsequently activating gibberellic acid signaling (PubMed:23378449). H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 magnesium or manganese ions per subunit. Part of a K(+)-channel calcium-sensing kinase/phosphatase complex composed by a calcium sensor CBL (CBL1, CBL2, CBL3 or CBL9), a kinase CIPK (CIPK6, CIPK16 or CIPK23), a phosphatase PP2C (AIP1) and a K(+)-channel (AKT1) (PubMed:17898163). Interacts with AKT1 and CIPK23 (PubMed:17898163). Interacts with PYL8/RCAR3 in an abscisic acid-independent (PubMed:22404835). Interacts with PYR1/RCAR11 in an abscisic acid-dependent manner (PubMed:23378449). Probably associated to the plasma membrane when interacting with AKT1 and CIPK23 (Probable). Localizes to nucleus when interacting with PYL8/RCAR3 (PubMed:22404835). Expressed in shoot meristem, vascular tissues of cotyledons, and in primary roots surrounding the root meristem (PubMed:22404835). Highly expressed in seeds (PubMed:23378449). Induced by abscisic acid (ABA). No visible phenotype under normal growth conditions, but mutant plants exhibit reduced sensitivity to abscisic acid (ABA) and glucose during seed germination and seedling stage (PubMed:22404835). Freshly harvested seeds of mutant plants exhibit increased seed dormancy (PubMed:23378449). Honsu means abnormal drowsiness in Korean. Belongs to the PP2C family. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. Belongs to the NAD-dependent DNA ligase family. LigB subfamily. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. Binds 2 heme groups. One heme group is bound covalently by a single cysteine link, the other one non-covalently. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Heme 1 (or BH or b566) is high-potential and absorbs at about 566 nm, and heme 2 (or BL or b562) is low-potential and absorbs at about 562 nm. Belongs to the cytochrome b family. PetB subfamily. +Probable transcription factor. Expressed in seedlings, stems, leaf sheaths and blades and panicles. Belongs to the HD-ZIP homeobox family. Class I subfamily. Truncated N-terminus. Intron retention. +Sulfotransferase involved in dorsoventral axis patterning in early embryos. Required for the specific ventral activation of a series of proteases acting in the perivitelline space between the embryonic membrane and the eggshell. Probably acts by mediating the sulfation of some glycoprotein or glycosaminoglycan stably deposited in the egg, whose ventrally localized modification leads to spatially restricted activation of the protease cascade. Interacts directly with windbeutel (wbl). Wbl is required for its processing into the Golgi. Isoform 4 is ovary-specific. Isoform 4 and isoform 5 are specifically expressed in the ventral follicle cells of the egg chamber. Expressed from stage 12 embryos and continues throughout development. Isoform 4 is expressed from stage 14 in the somatic component of the embryonic ovary. Down-regulated by gurken (grk) and EGF receptor signaling, preventing its expression in dorsal follicle cells. Belongs to the sulfotransferase 3 family. Truncated N-terminus. Truncated N-terminus. Wrong choice of frame. Intron retention. Wrong choice of frame. +Modifies, by uridylylation and deuridylylation, the PII regulatory proteins (GlnB and homologs), in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen assimilation and metabolism. [protein-PII]-L-tyrosine + UTP = [protein-PII]-uridylyl-L-tyrosine + diphosphate [protein-PII]-uridylyl-L-tyrosine + H2O = [protein-PII]-L-tyrosine + H(+) + UMP Uridylyltransferase (UTase) activity is inhibited by glutamine, while glutamine activates uridylyl-removing (UR) activity. Has four distinct domains: an N-terminal nucleotidyltransferase (NT) domain responsible for UTase activity, a central HD domain that encodes UR activity, and two C-terminal ACT domains that seem to have a role in glutamine sensing. Belongs to the GlnD family. +Involved in chemotaxis. Part of a chemotaxis signal transduction system that modulates chemotaxis in response to various stimuli. Catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins or MCP) by CheR. Also mediates the irreversible deamidation of specific glutamine residues to glutamic acid. [protein]-L-glutamate 5-O-methyl ester + H2O = H(+) + L-glutamyl-[protein] + methanol H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Contains a C-terminal catalytic domain, and an N-terminal region which modulates catalytic activity. Phosphorylated by CheA. Phosphorylation of the N-terminal regulatory domain activates the methylesterase activity. B.japonicum does not have a chemotaxis group 1 operon. Belongs to the CheB family. +Hormone involved in the regulation of erythrocyte proliferation and differentiation and the maintenance of a physiological level of circulating erythrocyte mass. Binds to EPOR leading to EPOR dimerization and JAK2 activation thereby activating specific downstream effectors, including STAT1 and STAT3. Produced by kidney or liver of adult mammals and by liver of fetal or neonatal mammals. Belongs to the EPO/TPO family. +Specifically methylates the adenine in position 37 of tRNA(1)(Val) (anticodon cmo5UAC). adenosine(37) in tRNA1(Val) + S-adenosyl-L-methionine = H(+) + N(6)-methyladenosine(37) in tRNA1(Val) + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. tRNA (adenine-N(6)-)-methyltransferase family. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. +Belongs to the UPF0297 family. +Belongs to the bacterial ribosomal protein bS16 family. +Catalyzes the ATP-dependent phosphorylation of N-acetyl-L-glutamate. ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamyl 5-phosphate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 2/4. Belongs to the acetylglutamate kinase family. ArgB subfamily. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +General factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Binds specifically to the TATA box promoter element which lies close to the position of transcription initiation. Belongs to the TBP family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Degrades polypeptides processively (By similarity). Homohexamer. Organized in a ring with a central cavity (By similarity). Belongs to the peptidase S16 family. Archaeal LonB subfamily. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr). L-histidyl-[protein] + phosphoenolpyruvate = N(pros)-phospho-L-histidyl-[protein] + pyruvate Homodimer. Transcription of ptsI appears to be regulated in response to sugars supplied, i.e. is four-fold lower when cells were grown on lactose than when grown on glucose. The N-terminal domain contains the HPr binding site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the pyruvate binding site. The reaction takes place in three steps, mediated by a phosphocarrier histidine residue located on the surface of the central domain. The two first partial reactions are catalyzed at an active site located on the N-terminal domain, and the third partial reaction is catalyzed at an active site located on the C-terminal domain. For catalytic turnover, the central domain swivels from the concave surface of the N-terminal domain to that of the C-terminal domain. Belongs to the PEP-utilizing enzyme family. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity. (R)-N(6)-dihydrolipoyl-L-lysyl-[lipoyl-carrier protein] + a hydroperoxide = (R)-N(6)-lipoyl-L-lysyl-[lipoyl-carrier protein] + an alcohol + H2O Belongs to the AhpD family. +Required maternally for germline survival and embryogenesis. Forms a complex with gls-1 which promotes the oogenic cell fate by freeing the translational repressor fbf to repress sperm promoting factors. Promotes maturation of primary spermatocytes to mature sperm. Required during hermaphrodite development to promote sperm fate, which is critical for determining the normal number of sperm. Promotion of sperm fate is at the expense of oogenesis, possibly through the negative regulation of fbf. Required during male development for the continued production of sperm and inhibition of oogenesis. Together with gld-2, promotes the transition from mitosis to meiosis. Interacts (via its KH1 domain) with gld-2. Isoform A but not isoform B interacts specifically with fbf-1 and fbf-2 in an RNA-independent manner. Isoform A interacts with gls-1 isoform C. Localizes to P granules. Found also in particles near but not coincident with P granules. Additional isoforms seem to exist. Experimental confirmation may be lacking for some isoforms. Expressed in the germline (at protein level). In adult hermaphrodites, first detected in the transition zone (TZ), weakly expressed in the early mitotic region and in pachytene germ cells, and becomes more abundantly expressed as germ cells enter diakinesis (at protein level). Expressed in primary spermatocytes, but not in secondary spermatocytes or adult sperm (at protein level). Expressed both maternally and zygotically throughout development and in adult hermaphrodites and males (at protein level). Loss of both maternal and zygotic expression causes variable lethality, ranging from arrest during embryonic development to soon after hatching, and sterility due to early germline defects. In these animals the germline precursor cells Z2 and Z3 are smaller, divide more slowly and their descendants remain small and indistinct compared to their wild-type counterparts. In addition, some of these animals show somatic defects, including a protruding vulva, multiple vulvae or a reduction in animal size. In zygotic mutant adult hermaphrodites, most spermatogenic cells are blocked as primary spermatocytes, the number of spermatocytes appears lower than normal and spermatogenesis is delayed by several hours. Zygotic mutant homozygous adult males produce some spermatogenic cells, although these sperm are less well defined morphologically than normal. In addition, loss of maternal and zygotic expression results in adult males that produce enlarged granular cells that appear oocyte-like and show chromosomal bivalents typical of oocytes. In zygotic mutants the mitotic region is longer and has more nuclei than normal, the mitotic region/TZ boundary is shifted from 20 to an average of 27 or 28 nuclei and the boundaries between mitotic region and TZ and TZ and pachytene region are not sharp as in wild-type. The deletion mutant gld-3 (q730) makes no detectable GLD-3; it is predicted to generate an mRNA with a premature stop codon, which should be subject to NMD. The deletion mutant gld-3 (q741) removes the fbf-binding site from isoform A, but leaves the gld-2-binding site intact. Animals homozygous for gld-3 (7q41) enter meiosis, but are feminized. In addition, gld-3 protein that retains its gld-2-binding region, does not have the dramatic mitosis/meiosis delay seen in gld-3 null mutants. By contrast, sex determination was not normal; gld-3 (q741) males produced oocytes. Therefore, promotes meiosis primarily via its interaction with gld-2 whereas the sperm/oocyte decision relies on its interaction with fbf. +Zinc phosphodiesterase, which has both exoribonuclease and endoribonuclease activities. Binds 2 Zn(2+) ions. Homodimer. Belongs to the RNase Z family. RNase BN subfamily. Extended N-terminus. Extended N-terminus. +One of the components of the core complex of photosystem II (PSII), required for its stability and/or assembly. PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbI family. +Part of the 30S ribosomal subunit. Belongs to the bacterial ribosomal protein bS18 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits. The heterotrimers can form oligomers, although 1 heterotrimer is thought to be able to translocate proteins. Interacts with the ribosome. Interacts with SecDF, and other proteins may be involved. Interacts with SecA. Belongs to the SecE/SEC61-gamma family. +PPIase that acts as a histone chaperone. Histone proline isomerase that increases the rate of cis-trans isomerization at prolines on the histone H3 N-terminal tail. Proline isomerization influences H3 methylation thereby regulating gene expression. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Inhibited by both FK506 and rapamycin. Binds to histones H3 and H4. Belongs to the FKBP-type PPIase family. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Belongs to the FPG family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Interacts with Eb1 via the two SxIP motifs; the interaction is not required for kebab kinetochore localization. During metaphase expressed in the kinetochores. During anaphase expression in the kinetochores progressively increases, and at late anaphase it is also expressed in the microtubules, specifically in the central spindle and centrosomal region. During telophase expression increases in the microtubules, and it is associated with residual spindle microtubules between chromosomes that have separated. At interphase it is expressed in the cytoplasm particularly around the nucleus. No visible phenotype. Flies are viable and fertile. RNAi-mediated knockdown does not affect mitotic progression. +Catalyzes the oxidation of sulfoquinovose to 6-deoxy-6-sulfo-D-glucono-1,5-lactone, with a strong preference for NAD(+) as the electron acceptor. Is involved in a degradation pathway of sulfoquinovose (SQ) that allows P.putida SQ1 to use SQ as the sole carbon and energy source for growth. 6-sulfo-D-quinovose + NAD(+) = 6-deoxy-6-sulfo-D-glucono-1,5-lactone + H(+) + NADH kcat is 33.8 sec(-1) for sulfoquinovose oxidation with NAD(+). kcat is 1.4 sec(-1) for sulfoquinovose oxidation with NADP(+). Optimum pH is 8-9. Is highly up-regulated during growth on sulfoquinovose, compared to growth on glucose or succinate (at protein level). Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Catalyzes the methylation of C-1 in cobalt-precorrin-5B to form cobalt-precorrin-6A. Co-precorrin-5B + S-adenosyl-L-methionine = Co-precorrin-6A + S-adenosyl-L-homocysteine Cofactor biosynthesis; adenosylcobalamin biosynthesis; cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route): step 6/10. Belongs to the CbiD family. +Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. [thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-diphosphate Binds 2 iron ions per subunit. Genetic information processing; DNA replication. Heterodimer of a large and a small subunit. Belongs to the ribonucleoside diphosphate reductase small chain family. +Component of the replication protein A complex (RPA) required for DNA recombination, repair and replication. The activity of RPA is mediated by single-stranded DNA binding and protein interactions (By similarity). Probably involved in repair of double-strand DNA breaks (DSBs) induced by genotoxic stresses (By similarity). Heterotrimer of RPA1, RPA2 and RPA3 (canonical replication protein A complex). No visible phenotype under normal growth conditions, but mutant plants have increased sensitivity to genotoxic stresses and agents that damage DNA bases (UV and methyl methanesulfonate, MMS). Belongs to the replication factor A protein 1 family. +Factor involved in transcription-coupled nucleotide excision repair (TC-NER) in response to UV damage. TC-NER allows RNA polymerase II-blocking lesions to be rapidly removed from the transcribed strand of active genes (By similarity). Accumulates at UV DNA damage sites. Belongs to the UVSSA family. +Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly (By similarity). May play a role in spermatogenesis or folliculogenesis (By similarity). Homodimer. Interacts with E2F1 and with histone H4 acetylated at 'Lys-13' (By similarity). Detected on chromatin and nucleosomes. +Belongs to the bacterial ribosomal protein bL32 family. +Possesses microtubule stabilizing properties. Involved in regulating aneuploidy, cell cycling, and cell death in a p53/TP53-dependent manner (By similarity). Associates with alpha- and beta-tubulins. Belongs to the CKAP2 family. +The B regulatory subunit might modulate substrate selectivity and catalytic activity, and also might direct the localization of the catalytic enzyme to a particular subcellular compartment. The PP2A-PPP2R5C holoenzyme may specifically dephosphorylate and activate TP53 and play a role in DNA damage-induced inhibition of cell proliferation. PP2A-PPP2R5C may also regulate the ERK signaling pathway through ERK dephosphorylation. PP2A consists of a common heterodimeric core enzyme, composed of PPP2CA a 36 kDa catalytic subunit (subunit C) and PPP2R1A a 65 kDa constant regulatory subunit (PR65 or subunit A), that associates with a variety of regulatory subunits. Proteins that associate with the core dimer include three families of regulatory subunits B (the R2/B/PR55/B55, R3/B''/PR72/PR130/PR59 and R5/B'/B56 families), the 48 kDa variable regulatory subunit, viral proteins, and cell signaling molecules. Interacts with PPP2CA AND PPP2R1A; the interaction is direct. Interacts with SGO1; the interaction is direct. Isoform 1 and isoform 2 interact with TP53 (phosphorylated at Ser-15 by ATM); increased upon DNA damage it drives PP2A-mediated dephosphorylation of TP53 at Thr-55. Interacts with IER3 and/or ERK kinases; regulates ERK dephosphorylation. Interacts with CIP2A; this interaction stabilizes CIP2A (PubMed:28174209). Highest levels in heart, skeletal muscle and brain. Lower levels in pancreas, kidney, lung and placenta. Very low levels in liver. Up-regulated upon DNA damage. Isoform Gamma-3 is phosphorylated on serine residues. Isoform Gamma-1 phosphorylation by ERK2 is IER3-dependent and inhibits ERK dephosphorylation by PP2A-PPP2R5C. Belongs to the phosphatase 2A regulatory subunit B56 family. Truncated N-terminus. Truncated N-terminus. +Minor protein of the capsid that localizes along the inner surface of the virion, within the central cavities beneath the L1 pentamers. Plays a role in capsid stabilization through interaction with the major capsid protein L1. Once the virion enters the host cell, L2 escorts the genomic DNA into the nucleus by promoting escape from the endosomal compartments and traffic through the host Golgi network. Mechanistically, the C-terminus of L2 possesses a cell-penetrating peptide that protudes from the host endosome, interacts with host cytoplasmic retromer cargo and thereby mediates the capsid delivery to the host trans-Golgi network. Plays a role through its interaction with host dynein in the intracellular microtubule-dependent transport of viral capsid toward the nucleus. Mediates the viral genome import into the nucleus through binding to host importins. Once within the nucleus, L2 localizes viral genomes to host PML bodies in order to activate early gene expression for establishment of infection. Later on, promotes late gene expression by interacting with the viral E2 protein and by inhibiting its transcriptional activation functions. During virion assembly, encapsidates the genome by direct interaction with the viral DNA. Interacts with major capsid protein L1. Interacts with E2; this interaction inhibits E2 transcriptional activity but not the DNA replication function E2. Interacts with host GADD45GIP1. Interacts with host HSPA8; this interaction is required for L2 nuclear translocation. Interacts with host importins KPNB2 and KPNB3. Forms a complex with importin alpha2-beta1 heterodimers via interaction with the importin alpha2 adapter. Interacts with host DYNLT1; this interaction is essential for virus intracellular transport during entry. Interacts (via C-terminus) with host retromer subunits VPS35 AND VPS29. Highly phosphorylated. Belongs to the papillomaviridae L2 protein family. +Belongs to the bacterial ribosomal protein bS16 family. +Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis. ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4 (By similarity). Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III). ESCRT-III components are thought to multimerize to form a flat lattice on the perimeter membrane of the endosome. Several assembly forms of ESCRT-III may exist that interact and act sequentially. Interacts with VTA1. Interacts with CHMP2A. Interacts with VTA1; the interaction involves soluble CHMP5 (By similarity). Interacts with NOD2 (By similarity). Localizes to the midbody of dividing cells. Localized in two distinct rings on either side of the Flemming body. ISGylated. Isgylation inhibits its interaction with VTA1 (By similarity). Belongs to the SNF7 family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Glycerol-1-phosphate phosphohydrolase involved in glycerol biosynthesis. Plays a role in osmoadaptation. H2O + sn-glycerol 1-phosphate = glycerol + phosphate H2O + sn-glycerol 3-phosphate = glycerol + phosphate Optimum pH is 6.5. Monomer. By osmotic stress (at protein level). Present with 5000 molecules/cell in log phase SD medium. Belongs to the HAD-like hydrolase superfamily. DOG/GPP family. +Removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. Type 4 (UDGa) family. +May be involved in a process influencing telomere capping. Belongs to the RTC5 family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Component of the nuclear pore complex that has a direct role in nuclear protein import (PubMed:20016008). Actively displaces NLSs from importin-alpha, and facilitates disassembly of the importin-alpha:beta-cargo complex and importin recycling (PubMed:20016008). Interacts with regulatory proteins of cell cycle progression including CDKN1B (By similarity). This interaction is required for correct intracellular transport and degradation of CDKN1B (By similarity). Interacts with Importin alpha-2, Importin beta, Importin beta-2, NUP153, Ran binding protein 7, CDKN1B and itself (By similarity). Does not interact with TPR. Localizes to the nucleoplasmic fibrils of the nuclear pore complex (By similarity). Dissociates from the NPC structure early during prophase of mitosis (PubMed:12802065). Associates with the newly formed nuclear membrane during telophase (PubMed:12802065). In the testis, the localization changes during germ cell differentiation from the nuclear surface in spermatocytes to the whole nucleus (interior) in spermatids and back to the nuclear surface in spermatozoa (By similarity). Ubiquitous. Highest levels in testis, peripheral blood leukocytes and fetal liver. Contains FG repeats. FG repeats are interaction sites for karyopherins (importins, exportins) and form probably an affinity gradient, guiding the transport proteins unidirectionally with their cargo through the NPC. FG repeat regions are highly flexible and lack ordered secondary structure. The overall conservation of FG repeats regarding exact sequence, spacing, and repeat unit length is limited. Contrarily to Npap60L, Npap60S does not displaces NLSs, but stabilizes their binding to importin-alpha. +E2-like enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy and nucleophagy. Acts as an E2-like enzyme that catalyzes the conjugation of ATG12 to ATG5. ATG12 conjugation to ATG5 is required for proper localization of ATG8 to the preautophagosomal structure (PAS). Likely serves as an ATG5-recognition molecule (By similarity). Forms homooligomers. Expression is decreased upon fluphenazine treatment. Belongs to the ATG10 family. +To E.coli YifN. +Belongs to the WD repeat LST8 family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +M-factor is a mating pheromone produced by M-type mating cells. All three mfm genes contribute to the production of M-factor. By nitrogen starvation. It is further induced by a pheromone signal. Its transcription is limited to M cells. +Multifunctional protein that plays a role in silencing host antiviral defenses and promoting viral transcription. Does not seem to be essential for HBV infection. May be directly involved in development of cirrhosis and liver cancer (hepatocellular carcinoma). Most of cytosolic activities involve modulation of cytosolic calcium. The effect on apoptosis is controversial depending on the cell types in which the studies have been conducted. May induce apoptosis by localizing in mitochondria and causing loss of mitochondrial membrane potential. May also modulate apoptosis by binding host CFLAR, a key regulator of the death-inducing signaling complex (DISC). Promotes viral transcription by using the host E3 ubiquitin ligase DDB1 to target the SMC5-SMC6 complex to proteasomal degradation. This host complex would otherwise bind to viral episomal DNA, and prevents its transcription. Moderately stimulates transcription of many different viral and cellular transcription elements. Promoters and enhancers stimulated by HBx contain DNA binding sites for NF-kappa-B, AP-1, AP-2, c-EBP, ATF/CREB, or the calcium-activated factor NF-AT. May form homodimer. May interact with host CEBPA, CFLAR, CREB1, DDB1, E4F1, HBXIP, HSPD1/HSP60, NFKBIA, POLR2E and SMAD4. Interacts with host SMC5-SMC6 complex and induces its degradation. Mainly cytoplasmic as only a fraction is detected in the nucleus. In cytoplasm, a minor fraction associates with mitochondria or proteasomes. A fraction may be phosphorylated in insect cells and HepG2 cells, a human hepatoblastoma cell line. Phosphorylated in vitro by host protein kinase C or mitogen-activated protein kinase. N-acetylated in insect cells. Belongs to the orthohepadnavirus protein X family. Transcriptional activities should be taken with a grain of salt. As of 2007, all studies demonstrating in vivo interaction between protein X and transcriptional components were performed with significant overexpression of both proteins and in the absence of viral infection. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +Peptidoglycan-recognition protein probably involved in innate immunity by binding to peptidoglycans (PGN) of bacteria and activating the prophenoloxidase (proPO) cascade immune response. Binds to 1,3-beta-D-glucan and PGN (By similarity). Belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +ATP-dependent RNA helicase. Involved in pre-mRNA splicing as component of the spliceosome. Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. The EJC marks the position of the exon-exon junction in the mature mRNA for the gene expression machinery and the core components remain bound to spliced mRNAs throughout all stages of mRNA metabolism thereby influencing downstream processes including nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH-RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH-RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed. Involved in the splicing modulation of BCL2L1/Bcl-X (and probably other apoptotic genes); specifically inhibits formation of proapoptotic isoforms; the function is different from the established EJC assembly. Involved in craniofacial development. ATP + H2O = ADP + H(+) + phosphate The ATPase activity is increased some 4-fold in the presence of RNA. Identified in the spliceosome C complex. Core component of the mRNA splicing-dependent exon junction complex (EJC); the core complex contains CASC3, EIF4A3, MAGOH or MAGOHB, and RBM8A. Interacts with CASC3, MAGOH, NXF1, RBM8A and ALYREF/THOC4. May interact with NOM1. Interacts with POLDIP3. Interacts with CWC22 and PRPF19 in an RNA-independent manner. Direct interaction with CWC22 is mediated by the helicase C-terminal domain. Full interaction with CWC22 occurs only when EIF4A3 is not part of the EJC and prevents EIF4A3 binding to RNA. Identified in a complex composed of the EJC core, UPF3B and UPF2. The EJC core can also interact with UPF3A (in vitro). Interacts with NCBP3 (By similarity). Interacts with NRDE2 (By similarity). Interacts with DHX34; the interaction is RNA-independent (By similarity). Nucleocytoplasmic shuttling protein. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRNA. Detected in dendritic layer as well as the nuclear and cytoplasmic (somatic) compartments of neurons. Colocalizes with STAU1 and FMR1 in dendrites. Belongs to the DEAD box helicase family. eIF4A subfamily. +Required for the maintenance of phospholipid turnover within the photoreceptor. a 1,2-diacyl-sn-glycerol + ATP = a 1,2-diacyl-sn-glycero-3-phosphate + ADP + H(+) Expressed specifically in adult eye. Flies exhibit photoreceptor cells that degenerate within a week after eclosion. Belongs to the eukaryotic diacylglycerol kinase family. Intron retention. +Cotranslationally removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides. Binds 2 divalent metal cations per subunit. Has a high-affinity and a low affinity metal-binding site. The true nature of the physiological cofactor is under debate. The enzyme is active with cobalt, zinc, manganese or divalent iron ions. Most likely, methionine aminopeptidases function as mononuclear Fe(2+)-metalloproteases under physiological conditions, and the catalytically relevant metal-binding site has been assigned to the histidine-containing high-affinity site. Associates with the 60S ribosomal subunit of the 80S translational complex. Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Catalyzes the cleavage of L-kynurenine (L-Kyn) and L-3-hydroxykynurenine (L-3OHKyn) into anthranilic acid (AA) and 3-hydroxyanthranilic acid (3-OHAA), respectively. H2O + L-kynurenine = anthranilate + H(+) + L-alanine 3-hydroxy-L-kynurenine + H2O = 3-hydroxyanthranilate + H(+) + L-alanine Amino-acid degradation; L-kynurenine degradation; L-alanine and anthranilate from L-kynurenine: step 1/1. Cofactor biosynthesis; NAD(+) biosynthesis; quinolinate from L-kynurenine: step 2/3. Homodimer. Belongs to the kynureninase family. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. STE Ser/Thr protein kinase family. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. +The physiological role of BioH is to remove the methyl group introduced by BioC when the pimeloyl moiety is complete. It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway through the hydrolysis of the ester bonds of pimeloyl-ACP esters. 6-carboxyhexanoyl-[ACP] methyl ester + H2O = 6-carboxyhexanoyl-[ACP] + H(+) + methanol Cofactor biosynthesis; biotin biosynthesis. Monomer. Belongs to the AB hydrolase superfamily. Carboxylesterase BioH family. +Mediates calcium-independent ATP release, suggesting activity as a hemichannel. Does not form functional gap junctions. A connexon is composed of a hexamer of connexins. Not detected in lens or retina. Belongs to the connexin family. Beta-type (group I) subfamily. Could be the product of a pseudogene. There is no mRNA or EST support for this sequence, and GJE1 is a pseudogene in most other primate species. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Monoubiquitination of Lys-119 by BRE1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation. Phosphorylated during apoptosis; which facilitates apoptotic chromatin condensation. GlcNAcylation at Ser-111 promotes monoubiquitination of Lys-119 It fluctuates in response to extracellular glucose, and associates with transcribed genes. Belongs to the histone H2B family. +Exhibits antiviral activity against influenza virus. GTP + H2O = GDP + H(+) + phosphate Heterodimer with other family members, including GBP1, GBP2 and GBP5 (PubMed:21151871). Dimerization regulates subcellular location. Heterodimers with GBP1, GBP2 and GBP5 localize in the compartment of the prenylated GBPs: with GBP1 in a vesicle-like compartment, with GBP2, around the nucleus and with GBP-5, at the Golgi apparatus. Shows the most prominent antiviral activity in epithelial cells. Belongs to the TRAFAC class dynamin-like GTPase superfamily. GB1/RHD3 GTPase family. GB1 subfamily. Contaminating sequence. Potential poly-A sequence. Unlikely isoform. Aberrant splice sites. +Self assembles to form an icosahedral capsid. Most capsids appear to be large particles with an icosahedral symmetry of T=4 and consist of 240 copies of capsid protein, though a fraction forms smaller T=3 particles consisting of 180 capsid proteins. Entering capsids are transported along microtubules to the nucleus. Phosphorylation of the capsid is thought to induce exposure of nuclear localization signal in the C-terminal portion of the capsid protein that allows binding to the nuclear pore complex via the importin (karyopherin-) alpha and beta. Capsids are imported in intact form through the nuclear pore into the nuclear basket, where it probably binds NUP153. Only capsids that contain the mature viral genome can release the viral DNA and capsid protein into the nucleoplasm. Immature capsids get stuck in the basket. Capsids encapsulate the pre-genomic RNA and the P protein. Pre-genomic RNA is reverse-transcribed into DNA while the capsid is still in the cytoplasm. The capsid can then either be directed to the nucleus, providing more genomes for transcription, or bud through the endoplasmic reticulum to provide new virions. Homodimerizes, then multimerizes. Interacts with cytosol exposed regions of viral L glycoprotein present in the reticulum-to-Golgi compartment. Interacts with human FLNB. Phosphorylated form interacts with host importin alpha; this interaction depends on the exposure of the NLS, which itself depends upon genome maturation and/or phosphorylation of the capsid protein. Interacts with host NUP153. Phosphorylated by host SRPK1, SRPK2, and maybe protein kinase C or GAPDH. Phosphorylation is critical for pregenomic RNA packaging. Protein kinase C phosphorylation is stimulated by HBx protein and may play a role in transport of the viral genome to the nucleus at the late step during the viral replication cycle. Belongs to the orthohepadnavirus core antigen family. +General regulator of phagocytosis. Required to uptake Gram negative bacterium by macrophages. N-terminal region is required for phagocytosis of Gram negative bacterium. +May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine. H2O + S-adenosyl-L-homocysteine = adenosine + L-homocysteine Binds 1 NAD(+) per subunit. Amino-acid biosynthesis; L-homocysteine biosynthesis; L-homocysteine from S-adenosyl-L-homocysteine: step 1/1. Belongs to the adenosylhomocysteinase family. +Catalytic component of the histone acetylase B (HAT-B) complex. Acetylates 'Lys-12' of histone H4 which is required for telomeric silencing. Has intrinsic substrate specificity that modifies lysine in recognition sequence GXGKXG. Involved in DNA double-strand break repair. acetyl-CoA + L-lysyl-[protein] = CoA + H(+) + N(6)-acetyl-L-lysyl-[protein] Component of the HAT-B complex composed of at least hat1 and hat2. The HAT-B complex binds to histone H4 tail. Belongs to the HAT1 family. +Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reduction of methionine sulfoxide in proteins to methionine (PubMed:12145281, PubMed:30529269). Does not catalyze the reverse reaction involving the oxidation of methionine residues (PubMed:30529269). [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(S)-S-oxide-[protein] [thioredoxin]-disulfide + H2O + L-methionine = [thioredoxin]-dithiol + L-methionine (S)-S-oxide By ecdysone. Conjugated to URM1, a ubiquitin-like protein. Belongs to the MsrA Met sulfoxide reductase family. Unlike mammalian MSRA, lacks methionine oxidase activity because Cys-232 cannot function as a resolving cysteine to perform the disulfide exchange and instead remains as a free thiol (PubMed:30529269). As a result, the active site cysteine is trapped in disulfide linkage with Cys-246 and is therefore unable to react with a second molecule of methionine sulfoxide to complete methionine oxidation (PubMed:30529269). +Essential for recycling GMP and indirectly, cGMP. ATP + GMP = ADP + GDP Belongs to the guanylate kinase family. +Belongs to the mimivirus BTB/WD family. +This b-type cytochrome is tightly associated with the reaction center of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. With its partner (PsbF) binds heme. PSII binds additional chlorophylls, carotenoids and specific lipids. Heterodimer of an alpha subunit and a beta subunit. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbE/PsbF family. +Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate. AH2 + GTP + S-adenosyl-L-methionine = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + A + H(+) + L-methionine Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate. Cofactor biosynthesis; molybdopterin biosynthesis. Belongs to the radical SAM superfamily. MoaA family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Can be acetylated to form H2BK6ac and H2BK33ac. Monoubiquitinated by BRE1 to form H2BK143ub1 and deubiquitinated by UBP26. Required for heterochromatic histone H3 di- and trimethylation at H3K4me. May give a specific tag for epigenetic transcriptional activation (By similarity). Belongs to the histone H2B family. To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-37; H2BK143ub1 = monoubiquitinated Lys-151. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF2. The gene for this protein contains a UGA in-frame termination codon after Leu-27; a naturally occurring frameshift enables complete translation of RF-2. This provides a mechanism for the protein to regulate its own production (By similarity). Belongs to the prokaryotic/mitochondrial release factor family. +Belongs to the UPF0294 family. +Ligand for members of the frizzled family of seven transmembrane receptors that functions in the canonical Wnt/beta-catenin signaling pathway (By similarity). Plays an important role in embryonic development, including dorsal versus ventral patterning during limb development, skeleton development and urogenital tract development. Required for central nervous system (CNS) angiogenesis and blood-brain barrier regulation (By similarity). Required for normal, sexually dimorphic development of the Mullerian ducts, and for normal fertility in both sexes. Required for normal neural stem cell proliferation in the hippocampus dentate gyrus. Required for normal progress through the cell cycle in neural progenitor cells, for self-renewal of neural stem cells, and for normal neuronal differentiation and maturation. Promotes formation of synapses via its interaction with FZD5 (By similarity). Forms a soluble 1:1 complex with AFM; this prevents oligomerization and is required for prolonged biological activity. The complex with AFM may represent the physiological form in body fluids (By similarity). Interacts with FZD5. Interacts with PORCN (By similarity). Interacts (via intrinsically disordered linker region) with RECK; interaction with RECK confers ligand selectivity for Wnt7 in brain endothelial cells and allows these cells to selectively respond to Wnt7 (By similarity). The intrinsically disordered linker region is required for recognition by RECK in brain endothelial cells. Palmitoleoylation is required for efficient binding to frizzled receptors. Depalmitoleoylation leads to Wnt signaling pathway inhibition. Belongs to the Wnt family. +Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell. Belongs to the MinE family. +Probable assembly factor of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complexes that promotes the exchange of the substrate-recognition F-box subunit in SCF complexes, thereby playing a key role in the cellular repertoire of SCF complexes. Binds TBP, CNOT3 and UBE3C. Expressed in epididymis (at protein level). Ubiquitinated and targeted for proteasomal degradation. Belongs to the CAND family. +Hydrolyzes the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom. Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. H2O + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine = 2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl 1-phosphate + 2 H(+) + UMP Binds 2 Mn(2+) ions per subunit in a binuclear metal center. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 4/6. Belongs to the LpxH family. +Protamines substitute for histones in the chromatin of sperm during the haploid phase of spermatogenesis. They compact sperm DNA into a highly condensed, stable and inactive complex. Interacts with TDRP. Testis. Proteolytic processing into mature chains is required for histone eviction during spermatogenesis. Transition proteins (TNP1 and TNP2) are required for processing. Belongs to the protamine P2 family. +(S)-malate + a quinone = a quinol + oxaloacetate Carbohydrate metabolism; tricarboxylic acid cycle; oxaloacetate from (S)-malate (quinone route): step 1/1. Belongs to the MQO family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +Transcriptional regulator that controls a genetic switch in male development. It is necessary and sufficient for initiating male sex determination by directing the development of supporting cell precursors (pre-Sertoli cells) as Sertoli rather than granulosa cells. Involved in different aspects of gene regulation including promoter activation or repression. Binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SRY HMG box recognizes DNA by partial intercalation in the minor groove and promotes DNA bending. Also involved in pre-mRNA splicing (By similarity). In male adult brain involved in the maintenance of motor functions of dopaminergic neurons (By similarity). Interacts with CALM, EP300, HDAC3, KPNB1, ZNF208 isoform KRAB-O, PARP1, SLC9A3R2 and WT1. The interaction with EP300 modulates its DNA-binding activity. The interaction with KPNB1 is sensitive to dissociation by Ran in the GTP-bound form. Interaction with PARP1 impaired its DNA-binding activity. Acetylation of Lys-136 contributes to its nuclear localization and enhances its interaction with KPNB1. Deacetylated by HDAC3. Belongs to the SRY family. The tenuous nature of sex - Issue 80 of March 2007 +Involved in the degradation of chitin. ChbG is essential for growth on the acetylated chitooligosaccharides chitobiose and chitotriose but is dispensable for growth on cellobiose and chitosan dimer, the deacetylated form of chitobiose. Deacetylation of chitobiose-6-P and chitotriose-6-P is necessary for both the activation of the chb promoter by the regulatory protein ChbR and the hydrolysis of phosphorylated beta-glucosides by the phospho-beta-glucosidase ChbF. Catalyzes the removal of only one acetyl group from chitobiose-6-P to yield monoacetylchitobiose-6-P, the inducer of ChbR and the substrate of ChbF. H2O + N,N'-diacetylchitobiose = acetate + N-acetyl-beta-D-glucosaminyl-(1->4)-D-glucosamine diacetylchitobiose-6'-phosphate + H2O = acetate + N'-monoacetylchitobiose-6'-phosphate Glycan degradation; chitin degradation. Homodimer. Belongs to the YdjC deacetylase family. ChbG subfamily. Extended N-terminus. +Transports viral genome to neighboring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier (By similarity). Belongs to the tombusvirus/aureusvirus movement protein p22 family. +Forms oligomers. Belongs to the MraZ family. +Scaffold protein for the de novo synthesis of iron-sulfur (Fe-S) clusters within mitochondria, which is required for maturation of both mitochondrial and cytoplasmic [2Fe-2S] and [4Fe-4S] proteins. First, a [2Fe-2S] cluster is transiently assembled on the scaffold proteins ISU1 and ISU2. In a second step, the cluster is released from ISU1/ISU2, transferred to glutaredoxin GRX5, followed by the formation of mitochondrial [2Fe-2S] proteins, the synthesis of [4Fe-4S] clusters and their target-specific insertion into the recipient apoproteins. Cluster assembly on ISU1/ISU2 depends on the function of the cysteine desulfurase complex NFS1-ISD11, which serves as the sulfur donor for cluster synthesis, the iron-binding protein frataxin (YFH1) as the putative iron donor, and the electron transfer chain comprised of ferredoxin reductase ARH1 and ferredoxin YAH1, which receive their electrons from NADH. Fe-S cluster release from ISU1/ISU2 is achieved by interaction with the Hsp70 chaperone SSQ1, assisted by the DnaJ-like co-chaperone JAC1 and the nucleotide exchange factor MGE1. ISU1 is the major isoform in yeast, while ISU2 is not detectable in cells grown to stationary phase (PubMed:10588895, PubMed:12970193, PubMed:14741370, PubMed:15123690, PubMed:16341089, PubMed:16431909, PubMed:23615440, PubMed:25358379). Also involved in production of a sulfur precursor required for thiolation of cytoplasmic tRNAs (PubMed:31040179). Binds 1 [2Fe-2S] cluster per subunit. Cofactor biosynthesis; iron-sulfur cluster biosynthesis. Component of the core Fe-S cluster (ISC) assembly machinery. Interacts with frataxin (PubMed:14741370, PubMed:12947415, PubMed:20815377, PubMed:25228696). Interacts with the mitochondrial co-chaperones JAC1 and SSQ1 (PubMed:12756240, PubMed:15123690, PubMed:22306468, PubMed:23946486, PubMed:23615440). Interacts with NFS1 (PubMed:23946486, PubMed:25228696). Interacts with ferredoxin YAH1; interacts with the reduced form (PubMed:25358379). Cells deleted for both ISU1 and ISU2 have decreased activity of several respiratory enzymes that contain Fe-S clusters. As a result, cells grow poorly on carbon sources requiring respiration and also accumulate abnormally high levels of iron in their mitochondria. Knockdown of ISU1 in ISU2 knockout cells decreases cytosolic tRNA thiolation, and increases association between SSQ1 and GRX5 (PubMed:31040179, PubMed:23615440). Present with 10800 molecules/cell in log phase SD medium. Belongs to the NifU family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Belongs to the transglycosylase Slt family. Extend the C-terminal part and restore the similarity to slt. +Sterol 14-alpha demethylase; part of the third module of ergosterol biosynthesis pathway that includes the late steps of the pathway (PubMed:15215142, PubMed:18191972, PubMed:26459890, PubMed:29439966, PubMed:9184358). Demethylates eburicol to yield 4,4,24-trimethyl ergosta-8,14,24(28)-trienol (PubMed:15215142, PubMed:18191972, PubMed:26459890, PubMed:29439966, PubMed:9184358). The third module or late pathway involves the ergosterol synthesis itself through consecutive reactions that mainly occur in the endoplasmic reticulum (ER) membrane. Firstly, the squalene synthase erg9 catalyzes the condensation of 2 farnesyl pyrophosphate moieties to form squalene, which is the precursor of all steroids. Squalene synthase is crucial for balancing the incorporation of farnesyl diphosphate (FPP) into sterol and nonsterol isoprene synthesis. Secondly, squalene is converted into lanosterol by the consecutive action of the squalene epoxidase erg1 and the lanosterol synthase erg7. Then, the delta(24)-sterol C-methyltransferase erg6 methylates lanosterol at C-24 to produce eburicol. Eburicol is the substrate of the sterol 14-alpha demethylase encoded by cyp51A and cyp51B, to yield 4,4,24-trimethyl ergosta-8,14,24(28)-trienol. The C-14 reductase erg24 then reduces the C14=C15 double bond which leads to 4,4-dimethylfecosterol. A sequence of further demethylations at C-4, involving the C-4 demethylation complex containing the C-4 methylsterol oxidases erg25A or erg25B, the sterol-4-alpha-carboxylate 3-dehydrogenase erg26 and the 3-keto-steroid reductase erg27, leads to the production of fecosterol via 4-methylfecosterol. The C-8 sterol isomerase erg2 then catalyzes the reaction which results in unsaturation at C-7 in the B ring of sterols and thus converts fecosterol to episterol. The sterol-C5-desaturase erg3B then catalyzes the introduction of a C-5 double bond in the B ring to produce 5-dehydroepisterol. The 2 other sterol-C5-desaturases, erg3A and erg3C, seem to be less important in ergosterol biosynthesis. The C-22 sterol desaturase erg5 further converts 5-dehydroepisterol into ergosta-5,7,22,24(28)-tetraen-3beta-ol by forming the C-22(23) double bond in the sterol side chain. Finally, ergosta-5,7,22,24(28)-tetraen-3beta-ol is substrate of the C-24(28) sterol reductases erg4A and erg4B to produce ergosterol. Possible alternative sterol biosynthetic pathways might exist from fecosterol to ergosterol, depending on the activities of the erg3 isoforms (PubMed:16110826, PubMed:18191972) (Probable). As a target of azole drugs, plays a crucial role in azole susceptibility. a 14alpha-methyl steroid + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = a Delta(14) steroid + formate + 4 H(+) + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase] The sterol 14-alpha demethylase activity is inhibited by azole compounds (PubMed:15142553, PubMed:15855543, PubMed:9184358, PubMed:26459890). Activity is inhibited by the novel and long-acting fungicidal azole, PC1244 (PubMed:29439966). Steroid metabolism; ergosterol biosynthesis. Expression is decreased upon exposure to voriconazole (PubMed:16622700). Expression is regulated by the GATA transcription factor sreA during hypoxia (PubMed:18721228, PubMed:22144905, PubMed:22006005). Leads to the accumulation of eburicol (PubMed:18191972). Leads to decreased susceptibility to azoles, especially fluconazole and ketoconazole, as well as to itraconazole in an itraconazole-resistant strain. Mutations of Gly-54 or Met-220 lead to the resistance to azoles, clinical drugs used to inhibit the activity and kill Aspergillus fumigatus cells during infections (PubMed:12543662, PubMed:12604551, PubMed:12709346, PubMed:15215142, PubMed:15563516, PubMed:15634974, PubMed:15695702). Duplication in tandem of a 34 bp sequence in the cyp51A promoter located at positions -288 and -322 from the start codon leads also to azole resistance, when associated with a mutation of Leu-98 (PubMed:17371828, PubMed:21907818). In Aspergillus, the biosynthesis pathway of the sterol precursors leading to the prevalent sterol ergosterol differs from yeast. The ring system of lanosterol in S.cerevisiae is firstly demethylised in three enzymatic steps leading to the intermediate zymosterol and secondly a methyl group is added to zymosterol by the sterol 24-C-methyltransferase to form fecosterol. In Aspergillus, lanosterol is firstly transmethylated by the sterol 24-C-methyltransferase leading to the intermediate eburicol and secondly demethylated in three steps to form fecosterol. Belongs to the cytochrome P450 family. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG. Belongs to the NqrDE/RnfAE family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the proton channel; it may play a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Component of an ATP synthase complex composed of ATP5PB, ATP5MC1, ATP5F1E, ATP5PD, ATP5ME, ATP5PF, ATP5MF, MT-ATP6, MT-ATP8, ATP5F1A, ATP5F1B, ATP5F1D, ATP5F1C, ATP5PO, ATP5MG, ATP5MK and ATP5MJ (By similarity). Interacts with DNAJC30; interaction is direct (By similarity). Belongs to the ATPase A chain family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Hydrolyzes the N-acetamido groups of N-acetyl-D-glucosamine residues in chitin to form chitosan and acetate (By similarity). Chitosan is required to anchor melanin to the cell wall, for maintenance of cell wall integrity, and for proper cytokinesis (By similarity). Chitosan offers an advantage during infection as it is less readily detected than chitin by host immunosurveillance mechanisms (By similarity). [(1->4)-N-acetyl-beta-D-glucosaminyl](n) + n H2O = n acetate + chitosan Belongs to the polysaccharide deacetylase family. +Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)). 7-carboxy-7-deazaguanine + ATP + NH4(+) = 7-cyano-7-deazaguanine + ADP + H(+) + H2O + phosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. Homodimer. Belongs to the QueC family. +Involved in the degradation of the plant hormone indole-3-acetic acid (IAA) (PubMed:18205812, PubMed:23881445). Catalyzes the first step of the pathway, the conversion of IAA to 2-hydroxy-IAA (2-OH-IAA) (PubMed:23881445). Can also convert indole to indoxyl, which spontaneously dimerizes in the presence of oxygen to form the blue pigment indigo (PubMed:23881445). (indol-3-yl)acetate + H(+) + NADH + O2 = 2-hydroxy-(1H-indol-3-yl)acetate + H2O + NAD(+) H(+) + indole + NADH + O2 = H2O + indoxyl + NAD(+) Induced in the presence of IAA. Expression is probably repressed by IacR and exposure to IAA relieves this repression. Transformation of P.putida KT2440, which cannot degrade IAA, with the iac gene cluster confers the ability to grow on IAA as a sole source of carbon and energy, but not the ability to chemotaxis towards IAA. Belongs to the HpaH/HsaA monooxygenase family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex (By similarity). Belongs to the universal ribosomal protein uL10 family. +Methylates ribosomal protein L11. L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. PrmA family. +Bifunctional enzyme which can phosphorylate or dephosphorylate isocitrate dehydrogenase (IDH) on a specific serine residue. This is a regulatory mechanism which enables bacteria to bypass the Krebs cycle via the glyoxylate shunt in response to the source of carbon. When bacteria are grown on glucose, IDH is fully active and unphosphorylated, but when grown on acetate or ethanol, the activity of IDH declines drastically concomitant with its phosphorylation. ATP + L-seryl-[isocitrate dehydrogenase] = ADP + H(+) + O-phospho-L-seryl-[isocitrate dehydrogenase] Belongs to the AceK family. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. Binds 2 [4Fe-4S] clusters per subunit. The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG. Belongs to the 4Fe4S bacterial-type ferredoxin family. RnfC subfamily. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Binds 1 zinc ion per subunit. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. Zinc-binding uS14 subfamily. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase gamma chain family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity (By similarity). Belongs to the universal ribosomal protein uS4 family. +Probably plays a role in anchoring the complex to other cellular components. EF-1 is composed of four subunits: alpha, beta, delta, and gamma. Highly expressed in pancreatic tumor tissue and to a lesser extent in normal kidney, intestine, pancreas, stomach, lung, brain, spleen and liver. Down-regulated in response to enterovirus 71 (EV71) infection. +Activates expression of the rhaSR operon in response to L-rhamnose. Binds DNA as a dimer. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the EF-Ts family. +Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family. +Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit. S-adenosyl-L-methionine + uridine(2552) in 23S rRNA = 2'-O-methyluridine(2552) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase RlmE family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Specifically hydrolyzes both 8-oxo-deoxyguanosine triphosphate (8-oxo-dGTP) and 8-oxo-guanosine triphosphate (8-oxo-GTP) to the related monophosphates, thereby cleaning up the nucleotide pools and preventing misincorporation of 8-oxoGua into DNA and RNA. It prevents replicational errors by removing an oxidatively damaged form of guanine (8-oxo-dGTP) from DNA and the nucleotide pool. 8-oxo-dGTP can be inserted opposite dA and dC residues of template DNA with almost equal efficiency thus leading to A.T to G.C transversions. 8-oxo-dGTP + H2O = 8-oxo-dGMP + diphosphate + H(+) 8-oxo-GTP + H2O = 8-oxo-GMP + diphosphate + H(+) Belongs to the Nudix hydrolase family. +SNARE that acts to regulate protein transport between late endosomes and the trans-Golgi network. The SNARE complex containing STX6, STX12, VAMP4 and VTI1A mediates vesicle fusion (in vitro) (By similarity). Through complex formation with GRIP1, GRIA2 and NSG1 controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting (By similarity). Associates with the BLOC-1 complex. Interacts with BLOC1S6. Interacts with NAPA and SNAP23. Identified in a complex containing STX6, STX12, VAMP4 and VTI1A (By similarity). Interacts with GRIPAP1 (PubMed:20098723). Forms a complex with GRIP1, GRIA2 and NSG1; controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting (By similarity). Interacts with NSG1 (PubMed:12070131). Interacts with TPC1 (PubMed:28855648). Belongs to the syntaxin family. +5-dehydro-4-deoxy-D-glucarate + H(+) = 2,5-dioxopentanoate + CO2 + H2O Carbohydrate acid metabolism; D-glucarate degradation; 2,5-dioxopentanoate from D-glucarate: step 2/2. Belongs to the DapA family. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Mediates the voltage-dependent sodium ion permeability of excitable membranes. Plays a role in processing of olfactory information during the olfactory avoidance response. In embryonic and larval stages, expression is limited to very few non-neuronal cells in either the CNS or PNS. In pupal and adult stages, expressed in cell bodies of the fly central nervous system, including optic lobes, central brain, subesophageal ganglion, thoracico-abdominal ganglion, major olfactory organs, the third antennal segment and the maxillary palps. The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1, S2, S3, S5, S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position. Partially edited. Target of Adar. Belongs to the sodium channel (TC 1.A.1.10) family. NaCP60E subfamily. Intron retention. +Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC). Part of the signal recognition particle protein translocation system, which is composed of SRP and FtsY. Belongs to the GTP-binding SRP family. FtsY subfamily. +(S)-malate + a quinone = a quinol + oxaloacetate Carbohydrate metabolism; tricarboxylic acid cycle; oxaloacetate from (S)-malate (quinone route): step 1/1. Belongs to the MQO family. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation (Potential). Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The eIF-3 complex interacts with pix. Belongs to the eIF-3 subunit M family. +Catalyzes the O-methylation, and thereby the inactivation, of catecholamine neurotransmitters and catechol hormones. Also shortens the biological half-lives of certain neuroactive drugs, like L-DOPA, alpha-methyl DOPA and isoproterenol. a catechol + S-adenosyl-L-methionine = a guaiacol + H(+) + S-adenosyl-L-homocysteine 2-hydroxyestrone + S-adenosyl-L-methionine = 2-hydroxy-3-methoxy-estrone + H(+) + S-adenosyl-L-homocysteine 4-hydroxyestrone + S-adenosyl-L-methionine = 4-methoxyestrone + H(+) + S-adenosyl-L-homocysteine 2-hydroxyestrone + S-adenosyl-L-methionine = 2-methoxyestrone + H(+) + S-adenosyl-L-homocysteine 4-hydroxy-17beta-estradiol + S-adenosyl-L-methionine = 4-methoxy-17beta-estradiol + H(+) + S-adenosyl-L-homocysteine 2-hydroxy-17beta-estradiol + S-adenosyl-L-methionine = 2-hydroxy-3-methoxy-17beta-estradiol + H(+) + S-adenosyl-L-homocysteine 2-hydroxy-17beta-estradiol + S-adenosyl-L-methionine = 2-methoxy-17beta-estradiol + H(+) + S-adenosyl-L-homocysteine Binds 1 Mg(2+) ion per subunit. Belongs to the class I-like SAM-binding methyltransferase superfamily. Cation-dependent O-methyltransferase family. +Member of the two-component regulatory system DcuR/DcuS. Involved in the C4-dicarboxylate-stimulated regulation of the genes encoding the anaerobic fumarate respiratory system (frdABCD; nuoAN; dcuB; dcuC; sdhCDAB; etc.). Weakly regulates the aerobic C4-dicarboxylate transporter dctA. Activates DcuR by phosphorylation (By similarity). ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. Homodimer. The periplasmic domain is involved in C4-dicarboxylate binding and sensing. The structural disorder in the cytoplasmic PAS domain has an important role in signal transduction to the kinase domain and may be the decisive structural feature that characterizes the activated kinase (By similarity). Autophosphorylated. The phosphoryl group is rapidly transferred to DcuR (By similarity). +Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). H2O + O2 + pyridoxamine 5'-phosphate = H2O2 + NH4(+) + pyridoxal 5'-phosphate O2 + pyridoxine 5'-phosphate = H2O2 + pyridoxal 5'-phosphate Binds 1 FMN per subunit. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1. Homodimer. Belongs to the pyridoxamine 5'-phosphate oxidase family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Tetramer of two alpha and two beta subunits. Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 2 subfamily. +Alpha-glucuronidase involved in the hydrolysis of xylan, a major structural heterogeneous polysaccharide found in plant biomass representing the second most abundant polysaccharide in the biosphere, after cellulose. Releases 4-O-methylglucuronic acid from xylan (By similarity). an alpha-D-glucuronoside + H2O = an alcohol + D-glucuronate Belongs to the glycosyl hydrolase 67 family. +ATP-dependent chaperone which uses the energy provided by ATP hydrolysis to generate mechanical force to disassemble protein complexes. Plays an essential role in the cytoplasmic maturation steps of pre-60S ribosomal particles by promoting the release of shuttling protein rlp24 from the pre-ribosomal particles. This step facilitates the subsequent release of other shuttling proteins such as nog1 and allows the transition of the pre-ribosomal particles to later maturation forms that bind SPCC550.15c/REI1. ATP + H2O = ADP + H(+) + phosphate Homohexamer; ATP binding induces oligomerization. Forms a ring-shaped particle of about 12 nm diameter, that displays 6-fold radial symmetry. Associates with cytoplasmic pre-60S ribosomal particles. The first ATP-binding region binds ATP with low affinity whereas the second ATP-binding region binds ATP with high affinity. Belongs to the AAA ATPase family. AFG2 subfamily. +Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression (By similarity). Binds 1 zinc ion per subunit. Binds DNA as a homotetramer. Belongs to the p53 family. +Cyclin-dependent kinase that acts as a master regulator of the mitotic and meiotic cell cycles (PubMed:8087848, PubMed:9042863, PubMed:1896017, PubMed:2274045, PubMed:6581157, PubMed:7498766, Ref.6). Required to drive the G1-S and G2-M transitions, and initiation of premeiotic DNA replication and meiosis II (PubMed:8087848, PubMed:9042863, PubMed:1896017, PubMed:2274045, PubMed:6581157, PubMed:7498766, Ref.6). More than 200 substrates have been identified (PubMed:27984725). Substrate specificity is in part regulated by the bound cyclin protein (PubMed:27984725). When complexed with cyclin cig2, it drives the G1-S phase transition (PubMed:8087848). When complexed with cyclin cdc13, it drives the G2-M transition and initiation of meiosis II (PubMed:8087848, PubMed:7498766). Its activity rises throughout the cell cycle and substrate specificity is further influenced by activity thresholds with more sensitive substrates phosphorylated earlier in the cell cycle than less sensitive substrates (PubMed:27984725). Phosphorylates dis1 during metaphase to ensure proper microtubule dynamics and accurate chromosome segregation (PubMed:16920624). Phosphorylates the repetitive C-terminus of the large subunit of RNA polymerase II rpb1 (Probable). Inactivated by checkpoint signaling following detection of cellular damage, leading to cell cycle arrest to allow damage repair (PubMed:9042863, PubMed:16049013). Inactivated during G2 DNA damage checkpoint signaling (PubMed:9042863). Inactivated in response to defective RNA splicing (PubMed:16049013). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Phosphorylation at Thr-14 or Tyr-15 inactivates the enzyme, while phosphorylation at Thr-167 activates it. Forms a stable but non-covalent complex with regulatory subunit suc1 and with a cyclin (PubMed:3322810). Interacts with cyclin cdc13 (PubMed:16390871). Interacts with cyclin cig2 (PubMed:8455610, PubMed:11163211). Interacts with cdc37 (PubMed:8455610, PubMed:11163211, PubMed:16390871). Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily. +Expressed in leaves and flowers. The protein kinase domain is predicted to be catalytically inactive. No visible phenotype. Cannot functionally replace STRUBBELIG. Over-expression of SRF5 led to male-sterility in cv. Columbia but not in cv. Landsberg. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +Accepts the ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine. Protein modification; protein ubiquitination. Expressed in roots, petals, sepals and silique walls. By senescence, but not by heat shock. Belongs to the ubiquitin-conjugating enzyme family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Represents 97% of the global cellulase activity. Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. Belongs to the glycosyl hydrolase 5 (cellulase A) family. +Belongs to the thermonuclease family. +Belongs to the HflD family. +Esterase with broad substrate specificity. Contributes to the inactivation of the neurotransmitter acetylcholine. Can degrade neurotoxic organophosphate esters (By similarity). an acylcholine + H2O = a carboxylate + choline + H(+) Homotetramer; disulfide-linked. Dimer of dimers (By similarity). Belongs to the type-B carboxylesterase/lipase family. +Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. AH2 + H2O2 = A + 2 H2O 2 H2O2 = 2 H2O + O2 Binds 1 heme b (iron(II)-protoporphyrin IX) group per dimer. Homodimer or homotetramer. Formation of the three residue Trp-Tyr-Met cross-link is important for the catalase, but not the peroxidase activity of the enzyme. Belongs to the peroxidase family. Peroxidase/catalase subfamily. +Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+) Binds 1 dipyrromethane group covalently. Inhibited by NH(3), heavy-metal ions, hydroxylamine and 2-bromoporphobilinogen. Not inhibited by N-ethylmaleimide. Optimum pH is 7.7-8.5. Heat stable and fully active up to 70 degrees Celsius. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. Porphyrin-containing compound metabolism; chlorophyll biosynthesis. Monomer. The porphobilinogen subunits are added sequentially to the dipyrromethane cofactor that is covalently attached to the enzyme. The last step of the reaction involves the hydrolysis of the bound polypyrrole chain and the release of hydroxymethylbilane. Belongs to the HMBS family. +Binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit to form the 80S initiation complex in the cytoplasm (PubMed:10085284, PubMed:14654845, PubMed:21536732, PubMed:32669547). Behaves as a stimulatory translation initiation factor downstream insulin/growth factors. Is also involved in ribosome biogenesis. Associates with pre-60S subunits in the nucleus and is involved in its nuclear export. Cytoplasmic release of TIF6 from 60S subunits and nuclear relocalization is promoted by a RACK1 (RACK1)-dependent protein kinase C activity (PubMed:10085284, PubMed:14654845, PubMed:21536732). In tissues responsive to insulin, controls fatty acid synthesis and glycolysis by exerting translational control of adipogenic transcription factors such as CEBPB, CEBPD and ATF4 that have G/C rich or uORF in their 5'UTR. Required for ROS-dependent megakaryocyte maturation and platelets formation, controls the expression of mitochondrial respiratory chain genes involved in reactive oxygen species (ROS) synthesis (By similarity). Involved in miRNA-mediated gene silencing by the RNA-induced silencing complex (RISC). Required for both miRNA-mediated translational repression and miRNA-mediated cleavage of complementary mRNAs by RISC (PubMed:17507929). Modulates cell cycle progression and global translation of pre-B cells, its activation seems to be rate-limiting in tumorigenesis and tumor growth (By similarity). Monomer. Associates with the 60S ribosomal subunit. Interacts with RACK1. Interacts with DICER1, AGO2, TARBP2, MOV10 and RPL7A; they form a large RNA-induced silencing complex (RISC) (PubMed:17507929). Shuttles between cytoplasm and nucleus/nucleolus. Expressed at very high levels in colon carcinoma with lower levels in normal colon and ileum and lowest levels in kidney and muscle (at protein level). Phosphorylation at Ser-174 and Ser-175 by CSNK1D/CK1 promotes nuclear export. Ufmylated by UFL1. Belongs to the eIF-6 family. +Methylates (mono- and asymmetric dimethylation) the guanidino nitrogens of arginyl residues in proteins. May methylate histone H3 at 'Arg-17' and activate transcription via chromatin remodeling. L-arginyl-[protein] + 2 S-adenosyl-L-methionine = 2 H(+) + N(omega),N(omega)-dimethyl-L-arginyl-[protein] + 2 S-adenosyl-L-homocysteine Homodimer. The dimethylated protein is the major form. Belongs to the class I-like SAM-binding methyltransferase superfamily. Protein arginine N-methyltransferase family. +NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. a ubiquinone + H(+) + n Na(+)(in) + NADH = a ubiquinol + n Na(+)(out) + NAD(+) Composed of six subunits; NqrA, NqrB, NqrC, NqrD, NqrE and NqrF. Belongs to the NqrB/RnfD family. +One of the two proteins required for the splicing of precursor tRNA molecules containing introns. The ligation activity requires three enzymatic activities: phosphorylation of the 5' terminus of the 3' half-tRNA in the presence of ATP, opening of the 2'3'-cyclic phosphodiester bond of the 5' half-tRNA leaving a 2'-phosphomonoester and ligation of the two tRNA halves in an ATP-dependent reaction. ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate. Has three domains each corresponding to an enzymatic activity, namely in N- to C-terminal order: ligase, kinase and cyclic phosphodiesterase (CPDase). tRNA ligase is a relatively rare protein with about 400 copies per yeast cell. Present with 3110 molecules/cell in log phase SD medium. Belongs to the TRL1 family. +Variant histone specifically required to direct the transformation of dissociating nucleosomes to protamine in male germ cells. Entirely replaces classical histone H2B prior nucleosome to protamine transition and probably acts as a nucleosome dissociating factor that creates a more dynamic chromatin, facilitating the large-scale exchange of histones. Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. Testis. Expressed in pachytene spermatocytes during meiotic prophase I in the absence of any significant DNA synthesis. Monoubiquitination at Lys-36 by the MSL1/MSL2 dimer is required for histone H3 'Lys-4' (H3K4me) and 'Lys-79' (H3K79me) methylation and transcription activation at specific gene loci, such as HOXA9 and MEIS1 loci. Similarly, monoubiquitination of Lys-122 (H2BK120Ub) by the RNF20/40 complex gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation. It also functions cooperatively with the FACT dimer to stimulate elongation by RNA polymerase II. H2BK120Ub also acts as a regulator of mRNA splicing: deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons (By similarity). Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes (By similarity). Acetylated during spermatogenesis. Acetylated form is most abundant in spermatogonia compared to spermatocytes and round spermatids. Phosphorylated at Thr-117 in spermatogonia, spermatocytes and round spermatids. Methylated at Lys-118 in spermatogonia, spermatocytes and round spermatids. Lactylated in macrophages by EP300/P300 by using lactoyl-CoA directly derived from endogenous or exogenous lactate, leading to stimulates gene transcription. Belongs to the histone H2B family. +ATPase subunit of a proteasome-like degradation complex; this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the ClpX chaperone family. HslU subfamily. +Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate. D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+). Binds 1 thiamine pyrophosphate per subunit. Carbohydrate biosynthesis; Calvin cycle. Carbohydrate degradation; pentose phosphate pathway. Homodimer. Belongs to the transketolase family. +May be involved in thiaminediphosphate transport across the mitochondrial membrane. Repressed by thiamine. +Secreted effector that does not suppress pattern-triggered immunity (PTI) in plant host. Expression is up-regulated in spores. The RxLR-dEER motif acts to carry the protein into the host cell cytoplasm through binding to cell surface phosphatidylinositol-3-phosphate. Belongs to the RxLR effector family. +Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. [sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Monomer. Belongs to the methylthiotransferase family. MiaB subfamily. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +Type I collagen is a member of group I collagen (fibrillar forming collagen). Trimers of one alpha 2(I) and two alpha 1(I) chains. Forms the fibrils of tendon, ligaments and bones. In bones, the fibrils are mineralized with calcium hydroxyapatite. Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains. Belongs to the fibrillar collagen family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Zn(2+) ion per subunit. In cyanobacteria the RNAP catalytic core is composed of 2 alpha, 1 beta, 1 beta', 1 gamma and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. RpoC2 subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Required for the induction of a regulon of hydrogen peroxide inducible genes such as catalase and glutathione-reductase. Belongs to the LysR transcriptional regulatory family. +Catalyzes the trimethylation of eukaryotic elongation factor 2 (EEF2) on 'Lys-525'. L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Interacts with FAM86B2 and FAM86C1P. Belongs to the class I-like SAM-binding methyltransferase superfamily. EEF2KMT family. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I 49 kDa subunit family. +Belongs to the UPF0102 family. +Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell. Homopentamer. Belongs to the MscL family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The NB-protein (ChlN-ChlB) is the catalytic component of the complex. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per heterodimer. The cluster is bound at the heterodimer interface by residues from both subunits. Porphyrin-containing compound metabolism; chlorophyll biosynthesis (light-independent). Protochlorophyllide reductase is composed of three subunits; ChlL, ChlN and ChlB. Forms a heterotetramer of two ChlB and two ChlN subunits. Belongs to the BchN/ChlN family. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP = 7,8-dihydrofolate + dTMP Pyrimidine metabolism; dTTP biosynthesis. Homodimer. Belongs to the thymidylate synthase family. Bacterial-type ThyA subfamily. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site. Although the small subunit is not catalytic it is essential for maximal activity. Heterohexadecamer of 8 large and 8 small subunits. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO small chain family. +The AROM polypeptide catalyzes 5 consecutive enzymatic reactions in prechorismate polyaromatic amino acid biosynthesis. 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate 3-dehydroquinate = 3-dehydroshikimate + H2O NADP(+) + shikimate = 3-dehydroshikimate + H(+) + NADPH ATP + shikimate = 3-phosphoshikimate + ADP + H(+) 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate Binds 2 Zn(2+) ions per subunit. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 3/7. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 4/7. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 5/7. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 6/7. Homodimer. In the N-terminal section; belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. In the 2nd section; belongs to the EPSP synthase family. In the 3rd section; belongs to the shikimate kinase family. In the 4th section; belongs to the type-I 3-dehydroquinase family. In the C-terminal section; belongs to the shikimate dehydrogenase family. +acetyl-CoA + L-glutamate = CoA + H(+) + N-acetyl-L-glutamate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 1/4. Belongs to the acetyltransferase family. ArgA subfamily. +Involved in the regulation of glutamine synthetase GlnA, a key enzyme in the process to assimilate ammonia. When cellular nitrogen levels are high, the C-terminal adenylyl transferase (AT) inactivates GlnA by covalent transfer of an adenylyl group from ATP to specific tyrosine residue of GlnA, thus reducing its activity. Conversely, when nitrogen levels are low, the N-terminal adenylyl removase (AR) activates GlnA by removing the adenylyl group by phosphorolysis, increasing its activity. The regulatory region of GlnE binds the signal transduction protein PII (GlnB) which indicates the nitrogen status of the cell. [glutamine synthetase]-O(4)-(5'-adenylyl)-L-tyrosine + phosphate = [glutamine synthetase]-L-tyrosine + ADP [glutamine synthetase]-L-tyrosine + ATP = [glutamine synthetase]-O(4)-(5'-adenylyl)-L-tyrosine + diphosphate Belongs to the GlnE family. +Paramyosin is a major structural component of many thick filaments isolated from invertebrate muscles. Homodimer. Thick filaments of the myofibrils. Belongs to the paramyosin family. +Catalyzes the conversion of L-arabinose to L-ribulose. beta-L-arabinopyranose = L-ribulose Binds 1 Mn(2+) ion per subunit. Carbohydrate degradation; L-arabinose degradation via L-ribulose; D-xylulose 5-phosphate from L-arabinose (bacterial route): step 1/3. Homohexamer. Belongs to the arabinose isomerase family. +Transports arginine, lysine, homoarginine, methylarginine and, to a much lesser extent, ornithine and histidine. Can restore ornithine transport in cells lacking the primary mitochondrial ornithine transporter SLC25A15. Does not transport carnitine nor acylcarnitines. Functions by both counter-exchange and uniport mechanisms. Belongs to the mitochondrial carrier (TC 2.A.29) family. +Catalyzes the stereospecific oxidation of D-lactate to pyruvate. (R)-lactate + 2 Fe(III)-[cytochrome c] = 2 Fe(II)-[cytochrome c] + 2 H(+) + pyruvate Binds 2 FAD. By D-lactate. Induced during respiratory adaptation. Present with 10800 molecules/cell in log phase SD medium. Belongs to the FAD-binding oxidoreductase/transferase type 4 family. +Sce70 may play a role in the transport of polypeptides across the envelope membrane and into the chloroplast. SCE70 expression is neither significantly influenced by light nor heat shock. There exists a 70 kDa heat-inducible gene (HSE70) in spinach leaves with sequence homology to SCE70. Belongs to the heat shock protein 70 family. +Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn-glycerol 3-phosphate. ATP + glycerol = ADP + H(+) + sn-glycerol 3-phosphate Inhibited by fructose 1,6-bisphosphate (FBP). Polyol metabolism; glycerol degradation via glycerol kinase pathway; sn-glycerol 3-phosphate from glycerol: step 1/1. Belongs to the FGGY kinase family. +Catalyzes the conjugation of long-chain fatty acyl-CoA thioester and glycine to produce long-chain N-(fatty acyl)glycine, an intermediate in the primary fatty acid amide biosynthetic pathway. an acyl-CoA + glycine = an N-acylglycine + CoA + H(+) (9Z)-octadecenoyl-CoA + glycine = CoA + H(+) + N-(9Z-octadecenoyl)glycine glycine + hexadecanoyl-CoA = CoA + H(+) + N-hexadecanoylglycine Lipid metabolism. +Interacts with CbpA and inhibits both the DnaJ-like co-chaperone activity and the DNA binding activity of CbpA. Together with CbpA, modulates the activity of the DnaK chaperone system. Does not inhibit the co-chaperone activity of DnaJ. Belongs to the CbpM family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +Belongs to the nitroreductase family. HadB/RutE subfamily. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Involved in ribosome biogenesis. Belongs to the RRS1 family. +Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 1 subfamily. +Cell wall formation. ATP + L-alanine + UDP-N-acetyl-alpha-D-muramate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Transfers 2-(5''-triphosphoribosyl)-3'-dephosphocoenzyme-A on a serine residue to the apo-acyl carrier protein (gamma chain) of the citrate lyase to yield holo-acyl carrier protein. 2'-(5''-triphospho-alpha-D-ribosyl)-3'-dephospho-CoA + apo-[citrate lyase ACP] = diphosphate + holo-[citrate lyase ACP] Belongs to the CitX family. +acetyl-CoA + phosphate = acetyl phosphate + CoA Metabolic intermediate biosynthesis; acetyl-CoA biosynthesis; acetyl-CoA from acetate: step 2/2. Belongs to the phosphate acetyltransferase and butyryltransferase family. +Multifunctional enzyme involved in mRNA capping. Catalyzes the formation of the 5' cap structure on the viral plus-strand transcripts. Specifically binds to GTP and displays guanylyltransferase and methyltransferase activities. Has affinity for ssRNA but not for dsRNA. Capping activity is non-specific and caps RNAs that initiate with either a G or an A residue. Together with VP1 polymerase, forms a VP1-VP3 complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are capped by VP3 and extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. DLPs probably have an RNA triphosphatase activity as well, whereas open cores do not. Counteracts the host innate immune response thanks to its phosphodiesterase that degrades the 5'-triphosphorylated, 2'-5' linked adenylate oligomers produced by the host cell IFN-inducible 2',5'-oligoadenylate synthetase (OAS). The host RNaseL is therefore not activated. a 5'-end diphospho-ribonucleoside in mRNA + GTP + H(+) = a 5'-end (5'-triphosphoguanosine)-(ribonucleoside) in mRNA + diphosphate a 5'-end (5'-triphosphoguanosine)-(ribonucleoside) in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine 5'-triphosphoadenylyl-(2'->5')-adenylyl-(2'->5')-adenosine + 2 H2O = 2 AMP + ATP + 2 H(+) Interacts with VP1 (By similarity). Interacts with VP2 (PubMed:9420216). Attached inside the inner capsid as a minor component. There are about 11 to 12 copies per virion. Contains a bipartite N7-methyltransferase domain, a 2'-O-methyltransferase domain and a GTase/RTPase domain. The C-terminus contains a phosphodiesterase domain that degrades the 5'-triphosphorylated, 2'-5' linked adenylate oligomers produced by the host cell in response to IFN stimulation. Belongs to the rotavirus VP3 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate. L-leucyl-tRNA(Leu) + N-terminal L-glutamyl-[protein] = H(+) + N-terminal L-leucyl-L-glutamyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-aspartyl-[protein] = H(+) + N-terminal L-leucyl-L-aspartyl-[protein] + tRNA(Leu) Belongs to the R-transferase family. Bpt subfamily. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +Endoplasmic reticulum membrane sensor that translocates into the nucleus in response to various stresses to act as a transcription factor (PubMed:20932482, PubMed:24448410). Constitutes a precursor of the transcription factor NRF1 (By similarity). Able to detect various cellular stresses, such as cholesterol excess, oxidative stress or proteasome inhibition (PubMed:20932482). In response to stress, it is released from the endoplasmic reticulum membrane following cleavage by the protease DDI2 and translocates into the nucleus to form the transcription factor NRF1 (By similarity). Acts as a key sensor of cholesterol excess: in excess cholesterol conditions, the endoplasmic reticulum membrane form of the protein directly binds cholesterol via its CRAC motif, preventing cleavage and release of the transcription factor NRF1, thereby allowing expression of genes promoting cholesterol removal, such as CD36 (By similarity). Involved in proteasome homeostasis: in response to proteasome inhibition, it is released from the endoplasmic reticulum membrane, translocates to the nucleus and activates expression of genes encoding proteasome subunits (PubMed:20932482). CNC-type bZIP family transcription factor that translocates to the nucleus and regulates expression of target genes in response to various stresses (PubMed:8932385, PubMed:9421508). Heterodimerizes with small-Maf proteins (MAFF, MAFG or MAFK) and binds DNA motifs including the antioxidant response elements (AREs), which regulate expression of genes involved in oxidative stress response (PubMed:8932385, PubMed:9421508). Activates or represses expression of target genes, depending on the context (PubMed:8932385, PubMed:9421508). Plays a key role in cholesterol homeostasis by acting as a sensor of cholesterol excess: in low cholesterol conditions, translocates into the nucleus and represses expression of genes involved in defense against cholesterol excess, such as CD36 (By similarity). In excess cholesterol conditions, the endoplasmic reticulum membrane form of the protein directly binds cholesterol via its CRAC motif, preventing cleavage and release of the transcription factor NRF1, thereby allowing expression of genes promoting cholesterol removal (By similarity). Critical for redox balance in response to oxidative stress: acts by binding the AREs motifs on promoters and mediating activation of oxidative stress response genes, such as GCLC, GCLM, GSS, MT1 and MT2 (By similarity). Plays an essential role during fetal liver hematopoiesis: probably has a protective function against oxidative stress and is involved in lipid homeostasis in the liver (By similarity). Involved in proteasome homeostasis: in response to proteasome inhibition, mediates the 'bounce-back' of proteasome subunits by translocating into the nucleus and activating expression of genes encoding proteasome subunits (PubMed:20932482). Also involved in regulating glucose flux (By similarity). Together with CEBPB; represses expression of DSPP during odontoblast differentiation (PubMed:15308669). In response to ascorbic acid induction, activates expression of SP7/Osterix in osteoblasts. Interacts with KEAP1. Interacts (via CPD region) with FBXW7; leading to its ubiquitination and degradation (By similarity). Interacts with SYVN1/HRD1; leading to its ubiquitination and degradation (By similarity). Interacts (when ubiquitinated) with DDI2; leading to its cleavage (PubMed:27528193). Interacts (via the bZIP domain) with small MAF protein (MAFF, MAFG or MAFK); required for binding to antioxidant response elements (AREs) on DNA (PubMed:8932385, PubMed:9421508). Interacts (via Destruction motif) with BTRC; leading to its ubiquitination and degradation (By similarity). Interacts with CEBPB; the heterodimer represses expression of DSPP during odontoblast differentiation (PubMed:15308669). Interacts with MOTS-c, a peptide produced by the mitochondrially encoded 12S rRNA MT-RNR1 (PubMed:29983246). In normal conditions, probably has a single-pass type II membrane protein topology, with the DNA-binding domain facing the endoplasmic reticulum lumen (PubMed:24448410). Following cellular stress, it is rapidly and efficiently retrotranslocated to the cytosolic side of the membrane, a process dependent on p97/VCP, to have a single-pass type III membrane protein topology with the major part of the protein facing the cytosol (PubMed:24448410). Retrotranslocated proteins are normally rapidly degraded by the proteasome and active species do not accumulate (PubMed:24448410). However, retrotranslocated protein NFE2L1 escapes degradation and is cleaved at Leu-104 by DDI2, releasing the protein from the endoplasmic reticulum membrane and forming the transcription factor NRF1 that translocates into the nucleus (PubMed:24448410). Translocates into the nucleus following cleavage of Endoplasmic reticulum membrane sensor NFE2L1 by aspartyl protease DDI2. The cholesterol recognition/amino acid consensus (CRAC) region directly binds cholesterol, as well as campesterol and 27-hydroxycholesterol. Has much lower affinity for epicholesterol. Cleaved at Leu-104 by the aspartyl protease DDI2 following retrotranslocation, releasing the protein from the endoplasmic reticulum membrane and forming the transcription factor NRF1 that translocates into the nucleus (PubMed:24448410, PubMed:27676297, PubMed:27676298, PubMed:27528193). Ubiquitination is prerequisite for cleavage by aspartyl protease DDI2 (PubMed:27676298). N-glycosylated in normal conditions, when it has a single-pass type II membrane protein topology, with the DNA-binding domain facing the endoplasmic reticulum lumen (PubMed:20932482, PubMed:24998528, PubMed:24448410, PubMed:27528193). Deglycosylated during retrotranslocation to the cytosolic side of the membrane, to have a single-pass type III membrane protein topology with the major part of the protein facing the cytosol (PubMed:20932482, PubMed:24998528, PubMed:24448410). Ubiquitinated by the SCF(FBXW7) complex and SYVN1/HRD1, leading to its degradation by the proteasome (PubMed:20932482). Ubiquitinated during retrotranslocation to the cytosolic side of the membrane: ubiquitination does not lead to degradation and is required for processing by the aspartyl protease DDI2 and subsequent release from the endoplasmic reticulum membrane (PubMed:24998528, PubMed:27676298). Phosphorylation by CK2 at Ser-528 inhibits transcription factor activity, possibly by affecting DNA-binding activity (By similarity). Phosphorylation at Ser-599 is required for interaction with CEBPB (PubMed:15308669). Ubiquitinated by the SCF(BTRC) complex in the nucleus, leading to its degradation by the proteasome. Belongs to the bZIP family. CNC subfamily. According to a report, processing following retrotranslocation is dependent on the proteasome (PubMed:24998528). However, it was later shown that processing takes place in a proteasome-independent manner (PubMed:27676297, PubMed:27676298). Its topology is subject to discussion. According to some groups, it has a single-pass type II membrane protein in normal conditions and is retrotranslocated into a single-pass type III membrane protein in response to stress (PubMed:24448410). According to other reports, it is integrated into the endoplasmic reticulum membrane via multiple membrane-spanning alpha-helices. Was initially thought to activate erythroid-specific, globin gene expression (PubMed:8036168). Knockout experiments in mouse however demonstrated that it is not the case. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiC family. +By inhibiting Nav1.7/SCN9A sodium channel, may prevent signal transmission caused by tick penetration and the blood taken, allowing the tick to avoid discovery (PubMed:27407029). Weakly and specifically inhibits Nav1.7/SCN9A (IC(50)=1.6 uM) (PubMed:27407029). Significantly shifts the steady-state inactivation curve of the Nav1.7/SCN9A in the hyperpolarized direction (PubMed:27407029). Does not induce changes to I-V curve and conductance-voltage relationship (PubMed:27407029). Expressed by the salivary glands. Adopts a novel structural fold that may be an intermediate scaffold between disulfide-directed hairpin (DDH) and the inhibitor cystine knot motif (ICK). Shows very weak or no effect on human Nav1.1/SCN1A, Nav1.2/SCN2A, Nav1.3/SCN3A, Nav1.4/SCN4A, hNav1.5/SCN5A, and Nav1.6/SCN8A sodium channels (PubMed:27407029). Does not show obvious effects on potassium and calcium channels (PubMed:27407029). +Plays a role in the recycling mechanism in neurons of multiple receptors, including AMPAR, APP and L1CAM and acts at the level of early endosomes to promote sorting of receptors toward a recycling pathway (PubMed:15187090, PubMed:12070131, PubMed:21084623, PubMed:16037816). Regulates sorting and recycling of GRIA2 through interaction with GRIP1 and then contributes to the regulation of synaptic transmission and plasticity by affecting the recycling and targeting of AMPA receptors to the synapse (PubMed:16037816). Is required for faithful sorting of L1CAM to axons by facilitating trafficking from somatodendritic early endosome or the recycling endosome (By similarity). In an other hand, induces apoptosis via the activation of CASP3 in response to DNA damage (By similarity). Forms a complex with GRIP1, GRIA2 and STX12 through direct interaction with GRIP1; controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting. Interacts with STX12 (PubMed:12070131). Interacts with APP; could regulate APP processing (PubMed:21084623). Interacts with FAM171A1 (By similarity). Endocytosed from the cell surface, thus enters into early endosomes, trafficks to late endosomes and degradates in lysosomes (By similarity). Endoplasmic reticulum targeting is essential for apoptosis (By similarity). Found in both stationary and motile endosomes (PubMed:28874679). A previous study supports a type I membrane protein topology (PubMed:12070131). Pituitary and less in adrenal gland and testis. Expressed in the hippocampus throughout development. At P0, highly and broadly expressed throughout the cortical plate, but is down-regulated overall at P8 and P14, but remains relatively enriched in layer V. At P0 is expressed ubiquitously in the developing cerebellum namely Purkinje neurons as well as granule neurons. However, it becomes restricted to Purkinje cells by P8. This exclusive expression in Purkinje cells is maintained throughout adulthood. At 17.5 dpc, highly expressed in the cortical plate and in the subplate (SP). Belongs to the NSG family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +RNA-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the eIF-3 subunit B family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Catalyzes the conversion of N-formimidoyl-L-glutamate to L-glutamate and formamide. H2O + N-formimidoyl-L-glutamate = formamide + L-glutamate Binds 2 manganese ions per subunit. Amino-acid degradation; L-histidine degradation into L-glutamate; L-glutamate from N-formimidoyl-L-glutamate (hydrolase route): step 1/1. Belongs to the arginase family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Belongs to the histone H3 family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate. ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterodimer of GatD and GatE. Belongs to the GatB/GatE family. GatE subfamily. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline. carbamoyl phosphate + L-ornithine = H(+) + L-citrulline + phosphate Amino-acid degradation; L-arginine degradation via ADI pathway; carbamoyl phosphate from L-arginine: step 2/2. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. OTCase family. +Involved in the toluene-4-sulfonate degradation pathway. Does not discriminate between the sulfonate and the carboxyl substituents and can also be involved in the p-toluenecarboxylate degradation pathway (By similarity). H(+) + NADH + O2 + toluene-4-sulfonate = 4-(hydroxymethyl)benzenesulfonate + H2O + NAD(+) Binds 1 [2Fe-2S] cluster per subunit. Homotetramer. Part of the p-toluenesulfonate methyl-monooxygenase complex TsaBM, comprising the reductase TsaB and the oxygenase TsaM. Could be the product of a pseudogene. Probably not expressed, due to the absence of promoter-like sequences upstream of the operon tsaMBCD2 (PubMed:11282598). +The pili are polar flexible filaments of about 5.4 nanometers diameter and 2.5 micrometers average length; they consist of only a single polypeptide chain arranged in a helical configuration of five subunits per turn in the assembled pilus. O-glycosylated; glycan consists of 5NbetaOHC47NFmPse(alpha2-4)Xyl(beta1-3)FucNAc in beta1-O linkage to Ser. Belongs to the N-Me-Phe pilin family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits. The heterotrimers can form oligomers, although 1 heterotrimer is thought to be able to translocate proteins. Interacts with the ribosome. Interacts with SecDF, and other proteins may be involved. Interacts with SecA. Belongs to the SecE/SEC61-gamma family. +Catalyzes the ATP- as well as the pyrophosphate-dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK/P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P-Ser-HPr). The two antagonistic activities of HprK/P are regulated by several intracellular metabolites, which change their concentration in response to the absence or presence of rapidly metabolisable carbon sources (glucose, fructose, etc.) in the growth medium. Therefore, by controlling the phosphorylation state of HPr, HPrK/P is a sensor enzyme that plays a major role in the regulation of carbon metabolism and sugar transport: it mediates carbon catabolite repression (CCR), and regulates PTS-catalyzed carbohydrate uptake and inducer exclusion. [HPr protein]-L-serine + ATP = [HPr protein]-O-phospho-L-serine + ADP + H(+) [HPr protein]-O-phospho-L-serine + H(+) + phosphate = [HPr protein]-L-serine + diphosphate Homohexamer. The Walker A ATP-binding motif also binds Pi and PPi. Both phosphorylation and phosphorolysis are carried out by the same active site and suggest a common mechanism for both reactions. Belongs to the HPrK/P family. +Cell wall formation. NADP(+) + UDP-N-acetyl-alpha-D-muramate = H(+) + NADPH + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurB family. +Ion channel inhibitor. Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 13 (insecticidal toxin ABC) family. ICK-21 subfamily. +Catalytic subunit of the periplasmic nitrate reductase complex NapAB. Receives electrons from NapB and catalyzes the reduction of nitrate to nitrite. 2 Fe(II)-[cytochrome] + 2 H(+) + nitrate = 2 Fe(III)-[cytochrome] + H2O + nitrite Binds 1 [4Fe-4S] cluster. Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit. Component of the periplasmic nitrate reductase NapAB complex composed of NapA and NapB. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/NapA/NarB subfamily. +Splits dipeptides with a prolyl residue in the C-terminal position. Hydrolysis of Xaa-|-Pro dipeptides. Also acts on aminoacyl-hydroxyproline analogs. No action on Pro-|-Pro. Binds 2 manganese ions per subunit. Belongs to the peptidase M24B family. Bacterial-type prolidase subfamily. +Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Involved in the translocation of the substrate across the membrane. The complex is composed of two ATP-binding proteins (BtuD), two transmembrane proteins (BtuC) and a solute-binding protein (BtuF). Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Belongs to the ATP-dependent AMP-binding enzyme family. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. Required to maintain the reduced state of SoxR. The complex is composed of six subunits: RsxA, RsxB, RsxC, RsxD, RsxE and RsxG. Belongs to the NqrDE/RnfAE family. +Has 11 beta-hydroxylation, 18-hydroxylation activities and aldosterone synthetic activity. Catalyzes the final steps of glucocorticoid and mineralocorticoid biosynthesis. a steroid + 2 H(+) + O2 + 2 reduced [adrenodoxin] = an 11beta-hydroxysteroid + H2O + 2 oxidized [adrenodoxin] Belongs to the cytochrome P450 family. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner. ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) Binds 2 Zn(2+) ions per subunit. Monomer. ValRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated threonine is translocated from the active site to the editing site. The C-terminal coiled-coil domain is crucial for aminoacylation activity. Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily. +Required for proper maturation of seed storage proteins. Forms a complex with MAG2, ZW10/MIP1 and MIP2 on the endoplasmic reticulum that may be responsible for efficient transport of seed storage proteins. Forms a complex with MAG2, ZW10/MIP1 and MIP2 on the endoplasmic reticulum. A number of isoforms are produced. According to EST sequences. Accumulation of the precursors of the two major storage proteins albumin 2S and globulin 12S in dry seeds. Belongs to the STXBP/unc-18/SEC1 family. +Transcriptional activator that binds to DNA sequences containing the consensus pentanucleotide 5'-CGGA[AT]-3' (By similarity). Required for olfactory dopaminergic neuron differentiation; may directly activate expression of tyrosine hydroxylase (TH) (By similarity). Sumoylated. Phosphorylated at Ser-191 and Ser-216 by RPS6KA1 and RPS6KA5; phosphorylation activates transcriptional activity. Belongs to the ETS family. +With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS5 family. +Component of the 40S small ribosomal subunit. Detected on cytosolic polysomes (By similarity). Detected in ribosomes that are associated with the rough endoplasmic reticulum (By similarity). Belongs to the universal ribosomal protein uS12 family. +Guanine nucleotide-binding proteins (G proteins) are involved as a modulator or transducer in various transmembrane signaling systems. The beta and gamma chains are required for the GTPase activity, for replacement of GDP by GTP, and for G protein-effector interaction. G proteins are composed of 3 units, alpha, beta and gamma. Belongs to the WD repeat G protein beta family. +Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules (By similarity). The COPII coat is composed of at least 5 proteins: the sec23/24 complex, the sec13/31 complex, and the protein sar1. sec13 and sec31 make a 2:2 tetramer that forms the edge element of the COPII outer coat. The tetramer self-assembles in multiple copies to form the complete polyhedral cage. Interacts (via WD 8) with sec13 (By similarity). Belongs to the WD repeat SEC31 family. +Functions by promoting the formation of the first peptide bond. Belongs to the eIF-5A family. +Involved in the tethering and targeting of pkc-3 to modulate the intracellular distribution of the kinase. The complex formed with pkc-3 complexes are likely to be involved in assembly, maintenance, and/or regulation of protein complexes that execute asymmetric and/or polarized cell functions. Interacts with pkc-3. Expressed at the inner surface of the plasma membrane at the cell periphery (which includes a region corresponding to plasma membrane and/or actin cortical cytoskeleton) in early embryos. Tightly associated with organelles and/or cytoskeletal structures with some diffuse expression in the cytoplasm. Differentially routed to lateral junctions between polarized cells. Expressed in cells comprising the intestine, pharyngeal cells, the anal sphincter and depressor muscles. Expressed at each stage of development with predominance of isoform c in early larvae and isoform a in adults. The PID domain (phosphotyrosine interaction domain) of isoform a and isoform c is capable of binding residues 212-224 of pkc-3. Produced by alternative splicing. Produced by alternative initiation at Met-45 of isoform a. +Belongs to the AIM11 family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Also displays broad nucleoside diphosphate kinase activity. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. AK1 subfamily. +Probably participates in a plant defense mechanism. Expressed in midvein, lamina and periphery of leaves (at protein level). The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Contains 3 disulfide bonds. Belongs to the cyclotide family. Bracelet subfamily. This peptide is linear but closely related to cyclotides. Since in UniProtKB the primary structure is preferred to classify proteins, the sequence is assigned to the cyclotide family. +DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. Belongs to the NAD-dependent DNA ligase family. LigA subfamily. +Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser) ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec) Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. Homodimer. The tRNA molecule binds across the dimer. Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +Oxidizes mannitol to mannose. Provides the initial step by which translocated mannitol is committed to central metabolism and, by regulating mannitol pool size, is important in regulating salt tolerance at the cellular level (By similarity). D-mannitol + NAD(+) = D-mannose + H(+) + NADH Binds 2 Zn(2+) ions per subunit. Belongs to the zinc-containing alcohol dehydrogenase family. Was originally thought to be a cinnamyl-alcohol dehydrogenase. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]. Belongs to the radical SAM superfamily. Lipoyl synthase family. +Kinase involved in a signal transduction pathway that is activated by changes in the osmolarity of the extracellular environment. Activates the PBS2 MAP kinase kinase by phosphorylation. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts with by SSK1. Present with 56 molecules/cell in log phase SD medium. Belongs to the protein kinase superfamily. STE Ser/Thr protein kinase family. MAP kinase kinase kinase subfamily. +May be involved in the regulation of the proteolytic processing of the amyloid precursor protein (APP) possibly also implicating APOE. May form homodimers and heterodimers with TMCC2 or TMCC3 via the coiled-coil domains. Interacts with ribosomal proteins RPL4 and RPS6. Interacts with APOE and proteolytic processed C-terminal fragment C99 of the amyloid precursor protein (APP C99). Concentrates in discrete patches along peripheral endoplasmic reticulum tubules. Belongs to the TEX28 family. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +Methylates ribosomal protein L11. L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. PrmA family. +Belongs to the UPF0284 family. Extended N-terminus. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 2 [4Fe-4S] clusters per subunit. NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I 23 kDa subunit family. +Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). H(+) + orotidine 5'-phosphate = CO2 + UMP Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. Homodimer. Belongs to the OMP decarboxylase family. Type 1 subfamily. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Belongs to the V-ATPase F subunit family. +Forms an efflux pump with AaeB. Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Catalyzes the formation of CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol (CDP-archaeol) from 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate (DGGGP) and CTP. This reaction is the third ether-bond-formation step in the biosynthesis of archaeal membrane lipids. 2,3-bis-O-(geranylgeranyl)-sn-glycerol 1-phosphate + CTP + H(+) = CDP-2,3-bis-O-(geranylgeranyl)-sn-glycerol + diphosphate Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the CDP-archaeol synthase family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of a catalytic core of 3 subunits and several supernumerary subunits. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII). Belongs to the cytochrome c oxidase subunit 5A family. +May be involved in ribosome biogenesis. Has also been proposed to play a role in calcium homeostasis (PubMed:23569283). Expression is GCR1-dependent. Promoter is also bound by the RAP1 transcription factor. Present with 2170 molecules/cell in log phase SD medium. Belongs to the GDT1 family. +A cytochrome P450 monooxygenase involved in the metabolism of endocannabinoids and steroids (PubMed:21289075, PubMed:12865317). Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (NADPH--hemoprotein reductase). Catalyzes the epoxidation of double bonds of arachidonoylethanolamide (anandamide) to 8,9-, 11,12-, and 14,15-epoxyeicosatrienoic acid ethanolamides (EpETrE-EAs), potentially modulating endocannabinoid system signaling (PubMed:21289075). Hydroxylates steroid hormones, including testosterone at C-16 and estrogens at C-2 (PubMed:21289075, PubMed:12865317). Plays a role in the oxidative metabolism of xenobiotics, including plant lipids and drugs (PubMed:11695850, PubMed:22909231). Acts as a 1,4-cineole 2-exo-monooxygenase (PubMed:11695850). Allele 2B6*9: Has low affinity for anandamide and can only produce 11,12 EpETrE-EAs. N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H(+) + H2O + N-(14,15-epoxy-5Z,8Z,11Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase] N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H(+) + H2O + N-(11,12-epoxy-5Z,8Z,14Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase] N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H(+) + H2O + N-(8,9-epoxy-5Z,11Z,14Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase] O2 + reduced [NADPH--hemoprotein reductase] + testosterone = 16alpha,17beta-dihydroxyandrost-4-en-3-one + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] O2 + reduced [NADPH--hemoprotein reductase] + testosterone = 16beta,17beta-dihydroxyandrost-4-en-3-one + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] 17beta-estradiol + O2 + reduced [NADPH--hemoprotein reductase] = 2-hydroxy-17beta-estradiol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] estrone + O2 + reduced [NADPH--hemoprotein reductase] = 2-hydroxyestrone + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] 1,4-cineole + O2 + reduced [NADPH--hemoprotein reductase] = 2-exo-hydroxy-1,4-cineole + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Expressed in liver, lung and heart right ventricle. By phenobarbital. Phosphorylation is accompanied by a decrease in enzyme activity. Variability among CYP2B6 alleles may account for differential metabolism of endogenous steroids and endocannabinoids among individuals. For 16-alpha hydroxylation of testosterone, Vmax/Km values between alleles decrease in the following order: 2B6*1 > 2B6*6 > 2B6*9 > 2B7*4. For 16-beta hydroxylation of testosterone, 2B6*6 has the highest catalytic efficiency. For anandamide metabolism, 2B6*6 and 2B6*9 alleles show significantly lower rates of epoxidation (PubMed:21289075). Genetic variations in CYP2B6 are responsible for poor metabolism of efavirenz and, therefore, susceptibility to efavirenz toxicity in the central nervous system [MIM:614546]. Efavirenz is a non-nucleoside reverse transcriptase inhibitor frequently prescribed with 2 nucleoside reverse transcriptase inhibitors as initial therapy for human immunodeficiency virus (HIV) infection. Up to half of patients treated with efavirenz, experience side effects in the central nervous system, including dizziness, insomnia, impaired concentration, somnolence, and abnormal dreams. Severe depression, aggressive behavior, and paranoid or manic reactions may also occur, depending on efavirenz concentration in the plasma. Patients homozygous for 2B6*6 have significantly higher plasma efavirenz levels when compared to 2B6*6 heterozygous ones (PubMed:15622315, PubMed:15194512, PubMed:20639527). Belongs to the cytochrome P450 family. CYP2B6 alleles +Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain. acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine Binds 1 Mg(2+) ion per subunit. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; N-acetyl-alpha-D-glucosamine 1-phosphate from alpha-D-glucosamine 6-phosphate (route II): step 2/2. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; UDP-N-acetyl-alpha-D-glucosamine from N-acetyl-alpha-D-glucosamine 1-phosphate: step 1/1. Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. In the N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family. In the C-terminal section; belongs to the transferase hexapeptide repeat family. +Probable transcriptional activator. Belongs to the krueppel C2H2-type zinc-finger protein family. ZFX/ZFY subfamily. +Member of the two-component regulatory system CreC/CreB involved in catabolic regulation. CreC may function as a membrane-associated protein kinase that phosphorylates CreB in response to environmental signals. CreC can also phosphorylate PhoB. ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. Autophosphorylated. +Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of mRNAs, a modification that plays a role in the efficiency of mRNA splicing and is required for sex determination (PubMed:27919077). Required for sex determination and dosage compensation via Sxl alternative splicing: m6A methylation acts as a key regulator of Sxl pre-mRNA and promotes female-specific alternative splicing of Sxl, which determines female physiognomy (PubMed:11156988, PubMed:27919077). M6A methylation is also required for neuronal functions (PubMed:27919077). Required for proper inclusion of regulated exons in Ubx transcripts, leading to isoforms Ia/b and IIa/b (PubMed:10101174). Component of the WMM complex, a N6-methyltransferase complex composed of a catalytic subcomplex, named MAC, and of an associated subcomplex, named MACOM (PubMed:27919077, PubMed:29535189, PubMed:29555755). The MAC subcomplex is composed of Ime4/Mettl3 and Mettl14 (PubMed:29535189, PubMed:29555755). The MACOM subcomplex is composed of fl(2)d, Flacc/Xio, Hakai, vir, and, in some cases of nito (PubMed:27919077,PubMed:29535189, PubMed:29555755). Part of a complex containing fl(2)d, Sxl and vir (PubMed:12444081). Ubiquitously expressed in males and females throughout embryogenesis (PubMed:11156988, PubMed:27919077). Expression levels decrease from gastrulation toward late embryogenesis (PubMed:11156988). Enriched in the neuroectoderm at later stages (PubMed:27919077). Belongs to the vir family. +Catalyzes the NADPH-dependent reduction of N-acetyl-5-glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde. N-acetyl-L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + N-acetyl-L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 3/4. Belongs to the NAGSA dehydrogenase family. Type 1 subfamily. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +Involved in transport. +Gastrin stimulates the stomach mucosa to produce and secrete hydrochloric acid and the pancreas to secrete its digestive enzymes. It also stimulates smooth muscle contraction and increases blood circulation and water secretion in the stomach and intestine. Sulfation enhances proteolytic processing, and blocks peptide degradation. Levels of sulfation differ between proteolytically-cleaved gastrins and between tissues (By similarity). Belongs to the gastrin/cholecystokinin family. +Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (By similarity). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (By similarity). Subunit H is essential for V-ATPase activity, but not for the assembly of the complex (By similarity). V-ATPase is a heteromultimeric enzyme made up of two complexes: the ATP-hydrolytic V1 complex and the proton translocation V0 complex (By similarity). The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H (By similarity). The proton translocation complex V0 consists of the proton transport subunit a, a ring of proteolipid subunits c9c'', rotary subunit d, subunits e and f, and the accessory subunits vah-19/Ac45 and vah-20/PRR (By similarity). Belongs to the V-ATPase H subunit family. +Has antibacterial activity. Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Brevinin subfamily. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Regulates the gating properties of AMPA-selective glutamate receptors (AMPARs). Modulates their gating properties by accelerating their rates of activation, deactivation and desensitization. Displays subunit-specific AMPA receptor regulation. Shows specificity for GRIA1, GRIA4 and the long isoform of GRIA2. Thought to stabilize the calcium channel in an inactivated (closed) state (By similarity). The L-type calcium channel is composed of five subunits: alpha-1, alpha-2/delta, beta and gamma. Acts as an auxiliary subunit for AMPA-selective glutamate receptors (AMPARs). Found in a complex with GRIA1, GRIA2, GRIA3, GRIA4, CNIH2, CNIH3, CACNG2, CACNG3, CACNG4, CACNG7 and CACNG8. Interacts with GRIA1, GRIA2, GRIA3 and GRIA4 (By similarity). Brain. Enriched in Bergman glia, as well as a variety of neuronal populations including locus coeruleus, olfactory bulb, lateral septal nucleus, interpeduncular nucleus, and the CA2 and rostral/medial CA1 regions of hippocampus. Belongs to the PMP-22/EMP/MP20 family. CACNG subfamily. +This venom insulin, from a fish-hunting cone snail, facilitates prey capture by rapidly inducing hypoglycemic shock. It is one of the smallest known insulin found in nature and lacks the C-terminal segment of the B chain that, in human insulin, mediates engagement of the insulin receptor and assembly of the hormone's hexameric storage form. Despite lacking this segment, it both binds and activates human insulin receptor (long isoform (HIR-B)) with only a 10-fold lower potency. In vivo, intraperitoneal injection of this peptide into zebrafish lowers blood glucose with the same potency than human insulin. In addition, when applied to water, this peptide reduces overall locomotor activity of zebrafish larvae, observed as a significant decrease in the percentage of time spent swimming and movement frequency. Heterodimer of A and B chains; disulfide-linked. Expressed by the venom gland. Is different from Con-Ins G1a (AC A0A0B5AC95) due to absence of amidation at Cys-114. Venom insulins constitute about 1/25 of the total venom of C.geographus. Belongs to the insulin family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Belongs to the UbiD family. +Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction. acetate + ATP = acetyl phosphate + ADP Mg(2+). Can also accept Mn(2+). Metabolic intermediate biosynthesis; acetyl-CoA biosynthesis; acetyl-CoA from acetate: step 1/2. Homodimer. Belongs to the acetokinase family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine (PubMed:20392080, PubMed:22378791). Target for the antibiotic fosfomycin. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine In vitro inhibited by covalent binding of fosfomycin and the fungal product terreic acid in the presence of substrate UDP-N-acetylglucosamine, with an inactivation rate constant of 130 M(-1)sec(-1) for terreic acid. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Catalyzes the ATP-dependent phosphorylation of L-homoserine to L-homoserine phosphate. ATP + L-homoserine = ADP + H(+) + O-phospho-L-homoserine Amino-acid biosynthesis; L-threonine biosynthesis; L-threonine from L-aspartate: step 4/5. Belongs to the GHMP kinase family. Homoserine kinase subfamily. +Attaches the virion to the host cell membrane by interacting with glycosaminoglycans, initiating the infection. Unlike other paramyxovirus attachment proteins, lacks both neuraminidase and hemagglutinating activities. In addition to its role in attachment, glycoprotein G interacts with host DDX58 and inhibits DDX58-mediated signaling pathway in order to prevent the establishment of the antiviral state. Homooligomer. Interacts (via N-terminus) with protein M. Interacts with protein F; this interaction occurs on the surface of infected cells. Interacts with protein SH (By similarity). Interacts with host DDX58; this interaction inhibits host immune response. Belongs to the metapneumoviruses glycoprotein G family. +Belongs to the UPF0307 family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate. adenosylcob(III)inamide-GDP + alpha-ribazole = adenosylcob(III)alamin + GMP + H(+) adenosylcob(III)inamide-GDP + alpha-ribazole 5'-phosphate = adenosylcob(III)alamin 5'-phosphate + GMP + H(+) Cofactor biosynthesis; adenosylcobalamin biosynthesis; adenosylcobalamin from cob(II)yrinate a,c-diamide: step 7/7. Belongs to the CobS family. +Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (PubMed:32165585). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (PubMed:32165585). V-ATPase is a heteromultimeric enzyme made up of two complexes: the ATP-hydrolytic V1 complex and the proton translocation V0 complex (PubMed:32165585). The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H (PubMed:32165585). The proton translocation complex V0 consists of the proton transport subunit a, a ring of proteolipid subunits c9c'', rotary subunit d, subunits e and f, and the accessory subunits ATP6AP1/Ac45 and ATP6AP2/PRR (PubMed:32165585). Interacts with RABL2/RABL2A; binds preferentially to GTP-bound RABL2 (By similarity). Interacts with ALDOC (By similarity). Interacts with RAB11B (By similarity). Expressed in brain (at protein level). Belongs to the V-ATPase E subunit family. +Cell wall formation. ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) + phosphate Binds 2 magnesium or manganese ions per subunit. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the D-alanine--D-alanine ligase family. +Membrane-associated form that antagonizes canonical Wnt signaling by triggering lysosome-dependent degradation of Wnt-activated LRP6. Regulates thymocyte proliferation. During intrathymic development, resides in punctate cytoplasmic structures in DN1 and DN2 cells. In DN3 cells, found in large crescent-shaped membrane structures, which preferentially localize in cell-to-cell contact zones. Transmembrane localization is essential for Wnt signaling inhibition. Scattered throughout the cytoplasm in small-sized punctate structures. Expressed in thymocytes. During intrathymic development, transcript levels strongly increase from pro-DN1 thymocytes to DN3a cells, in which they peak, and drop immediately after beta-selection in their DN3b successors. The subcellular location of the protein also varies, from punctate cytoplasmic structures in DN1 and DN2 cells to large crescent-shaped membrane structures in DN3 cells, which preferentially localize in cell-to-cell contact zones. Belongs to the TMEM131 family. +Protein S12 is involved in the translation initiation step. Belongs to the universal ribosomal protein uS12 family. +Can hydrolyze phosphorylated Ser-, Thr- or Tyr-substrates in vitro. The natural substrate is unknown. H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Inhibited by cadmium, copper, zinc when added cobalt when added concomitantly with manganese. Optimum pH is 6-7. Optimum temperature is 45-55 degrees Celsius. Thermostable. Neither magnesium nor calcium stimulates activity. Belongs to the PPP phosphatase family. PP-1 subfamily. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel. Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL. Belongs to the GroES chaperonin family. +Up-regulated upon milbemycins A3 oxim derivative (A3Ox) treatment. +Belongs to the cyclin family. Cyclin U/P subfamily. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Regulatory subunit of the slx1-slx4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Forms a heterodimer with slx1. Phosphorylated in response to DNA damage. Belongs to the SLX4 family. +Blocks contraction of smooth muscle elicited by high potassium-induced depolarization, but does not block caffeine-stimulated contraction. May target voltage-gated calcium channels on smooth muscle (By similarity). Expressed by the venom gland. Belongs to the CRISP family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +May play a role in axonal development. Belongs to the FAX family. +Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel. Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL. Belongs to the GroES chaperonin family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Can dephosphorylate single and diphosphorylated synthetic MAPK peptides, with preference for the phosphotyrosine and diphosphorylated forms over phosphothreonine. In vitro, dephosphorylates p-nitrophenyl phosphate (pNPP). H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Translocates to cytoplasm in response to apoptotic stimuli such as staurosporine treatment. Belongs to the protein-tyrosine phosphatase family. Non-receptor class dual specificity subfamily. +Extracellular signaling peptide that may regulate primary root growth rate and systemic nitrogen (N)-demand signaling. Interacts with CEP receptors (e.g. CEPR1 and CEPR2). Accumulates in xylem sap. The mature small signaling peptide is generated by proteolytic processing of the longer precursor. Belongs to the C-terminally encoded plant signaling peptide (CEP) family. +Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Contributes to the structuring of the Rrp41 active site. Component of the archaeal exosome complex. Forms a hexameric ring-like arrangement composed of 3 Rrp41-Rrp42 heterodimers. The hexameric ring associates with a trimer of Rrp4 and/or Csl4 subunits. Belongs to the RNase PH family. Rrp42 subfamily. +A beta subtype methylase that recognizes the double-stranded sequence 5'-GAAGA-3', methylates A-5 on the top strand, and protects the DNA from cleavage by the MboII endonuclease. It is not known if the cytosine of the complementary sequence TCTTC is also methylated by this enzyme. a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an N(6)-methyl-2'-deoxyadenosine in DNA + H(+) + S-adenosyl-L-homocysteine At low concentration exists as a monomer and homodimer (PubMed:12954781). Probably binds to DNA as a monomer (Probable). Belongs to the N(4)/N(6)-methyltransferase family. +Involved in the hydrocarbon hydroxylating system, which transfers electrons from NADH to rubredoxin reductase and then through rubredoxin to alkane 1 monooxygenase. Binds 2 Fe(3+) ions per subunit. Hydrocarbon metabolism; alkane degradation. Induced by AlkS and n-alkanes. Unlike other rubredoxins, this rubredoxin is unique in that it contains two binding sites for iron. It is most probably the product of a gene duplication event. The 2Fe form of the rubredoxin is a physiological form but it is less stable than the readily isolated 1Fe form. Both domains can form productive electron transfer complexes with rubredoxin reductase and accept electrons from the enzyme bound FAD. Belongs to the rubredoxin family. +Required for pre-mRNA splicing as component of the spliceosome (By similarity). Binds double-stranded RNA (By similarity). Component of the pre-catalytic and post-catalytic spliceosome complexes. Belongs to the PRKRIP1 family. +A + choline = AH2 + betaine aldehyde Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway; betaine aldehyde from choline (cytochrome c reductase route): step 1/1. Belongs to the GMC oxidoreductase family. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. Belongs to the radical SAM superfamily. Lipoyl synthase family. +Methylates ribosomal protein L11. L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. PrmA family. +Cleaves both 3' and 5' ssDNA extremities of branched DNA structures. Belongs to the NucS endonuclease family. +Belongs to the elongation factor P family. +Involved in nucleolar processing of pre-18S ribosomal RNA. Belongs to the UTP6 family. +Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis. ATP + beta-D-fructose 6-phosphate = ADP + beta-D-fructose 1,6-bisphosphate + H(+) Allosterically activated by ADP and other diphosphonucleosides, and allosterically inhibited by phosphoenolpyruvate. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 3/4. Homotetramer. Belongs to the phosphofructokinase type A (PFKA) family. ATP-dependent PFK group I subfamily. Prokaryotic clade 'B1' sub-subfamily. +Mediates electroneutral sodium- and carbonate-dependent chloride-HCO3(-) exchange with a Na(+):HCO3(-) stoichiometry of 2:1. Plays a major role in pH regulation in neurons. May be involved in cell pH regulation by transporting HCO3(-) from blood to cell. Enhanced expression in severe acid stress could be important for cell survival by mediating the influx of HCO3(-) into the cells. Also mediates lithium-dependent HCO3(-) cotransport. May be regulated by osmolarity. Activity is inhibited by 4,4'-Di-isothiocyanatostilbene-2,2'-disulfonic acid (DIDS - an inhibitor of several anion channels and transporters). Expressed in the pyramidal cells of the hippocampus (at protein level). Highly expressed in all major regions of the brain, spinal column and in testis, and moderate levels in trachea, thyroid and medulla region of kidney. Low expression levels observed in pancreas and kidney cortex. May be due to an intron retention. May be due to an intron retention. Belongs to the anion exchanger (TC 2.A.31) family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL2 family. +N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 3/5. Belongs to the TrpF family. +Activator of cell division through the inhibition of FtsZ GTPase activity, therefore promoting FtsZ assembly into bundles of protofilaments necessary for the formation of the division Z ring. It is recruited early at mid-cell but it is not essential for cell division. Homodimer. Interacts with FtsZ. Localizes at mid-cell. Belongs to the ZapA family. Type 1 subfamily. +NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. a ubiquinone + H(+) + n Na(+)(in) + NADH = a ubiquinol + n Na(+)(out) + NAD(+) Composed of six subunits; NqrA, NqrB, NqrC, NqrD, NqrE and NqrF. Belongs to the NqrDE/RnfAE family. +H2O + L-glutamine = L-glutamate + NH4(+) Homotetramer. Belongs to the glutaminase family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Belongs to the UPF0102 family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +2-oxoglutarate + L-aspartate = L-glutamate + oxaloacetate Homodimer. Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor, and NADPH and FADH(2) as the reductant. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP + H(+) + NADPH = (6S)-5,6,7,8-tetrahydrofolate + dTMP + NADP(+) Binds 4 FAD per tetramer. Each FAD binding site is formed by three monomers. Pyrimidine metabolism; dTTP biosynthesis. Homotetramer. Belongs to the thymidylate synthase ThyX family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiC family. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Involved in the biosynthesis of phenolic monoterpenes natural products thymol and carvacrol which have a broad range of biological activities acting as antimicrobial compounds, insecticides, antioxidants and pharmaceutical agents (PubMed:23624978). Monoterpene synthase which catalyzes the conversion of geranyl diphosphate (GPP) to gamma-terpinene and minor amounts of other monoterpenes (e.g. alpha-thujene, alpha-terpinene, myrcene, sabinene, (+)-R-limonene, alpha-pinene and alpha-phellandrene) (PubMed:23624978). (2E)-geranyl diphosphate = diphosphate + gamma-terpinene Binds 3 Mg(2+) or Mn(2+) ions per subunit. Secondary metabolite biosynthesis; terpenoid biosynthesis. Homodimer. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg(2+). The monoterpenic phenol thymol is widely used as a fragrance and a flavoring ingredient in food and cosmetic industries (PubMed:29785774). Its derivatives have also several biological and pharmacological properties such as antimicrobial, antioxidant, anticarcinogenesis, anti-inflammatory and antispasmodic activities (PubMed:29785774, PubMed:29874939). Medical applications include the treatment of disorders affecting the respiratory, nervous, and cardiovascular systems (PubMed:29785774). It may also act as a growth enhancer and immunomodulator (PubMed:29785774). Thymol may also have antiviral activity toward COVID-19 by binding to the S1 receptor binding domain of the SARS-CoV-2 spike (S) glycoprotein (PubMed:32834111, PubMed:33855010). The monoterpenic phenol carvacrol is commonly used as a fragrance and a food flavoring ingredient and preservative (PubMed:24915411). Its derivatives exhibit also various biological and pharmacological properties including antioxidant, antibacterial, antifungal, insecticid, nematicid, anticancer, anti-inflammatory, hepatoprotective, spasmolytic, and vasorelaxant (PubMed:24915411, PubMed:29874939, PubMed:30836858, PubMed:33664752). Phytochemical inhibitor targeting the main SARS-CoV-2 viral protease (Mpro) and ACE2 in human host cells, carvacrol is a possible candidate for treating COVID-19 (PubMed:33664752, PubMed:32448034). Carvacrol may also have antiviral activity toward COVID-19 by binding to the S1 receptor binding domain of the SARS-CoV-2 spike (S) glycoprotein (PubMed:32834111, PubMed:33855010). Belongs to the terpene synthase family. +Catalyzes the sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine. H2O + L-histidinol + 2 NAD(+) = 3 H(+) + L-histidine + 2 NADH Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 9/9. Belongs to the histidinol dehydrogenase family. +Regulates the organization of the actin cytoskeleton. With OSPBL3, modulates integrin beta-1 (ITGB1) activity. GTP + H2O = GDP + H(+) + phosphate Interacts with PLCE1 (By similarity). Interacts (active GTP-bound form preferentially) with RGS14 (By similarity). Interacts with OSBPL3 (By similarity). Interacts with ZDHHC19 (By similarity). Inner surface of plasma membrane possibly with attachment requiring acylation of the C-terminal cysteine (By similarity with RAS). S-palmitoylated by ZDHHC19, leading to increased association with membranes and with rafts/caveolae as well as enhanced cell viability. Belongs to the small GTPase superfamily. Ras family. +Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane. Homotrimer. Consists of 16-stranded beta-barrel sheets, with large surface-exposed loops, that form a transmembrane pore at the center of each barrel. The pore is partially ocluded by a peptide loop that folds into the pore lumen. The pore formed by Omp2a is larger than the one formed by Omp2b. Omp2b pores have optimal permeability to allow growth and protection against harmful compounds. The larger pore formed by Omp2a may be advantageous for intracellular growth, when the bacterium is competing with the host cell for nutrients whose concentration is particularly low within the phagosome. Belongs to the alphaproteobacteria porin family. +Belongs to the universal ribosomal protein uS9 family. +Belongs to the universal ribosomal protein uS2 family. +Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit binds the periplasmic potassium ions and delivers the ions to the membrane domain of KdpB through an intramembrane tunnel. The system is composed of three essential subunits: KdpA, KdpB and KdpC. Belongs to the KdpA family. +Plays a role in female and male fertility. Involved in distal reproductive tract development (PubMed:26964900). Expressed in the epithelium of the vas deferens (at protein level). Widely expressed (PubMed:26964900). Strongly expressed in heart, spleen, liver, kidney, thymus, testis, brain, lung, intestine, vagina, ovary and uterus (PubMed:26964900). Expressed in follicle cells of the ovary, epithelial cells of the oviduct, both luminal and glandular epithelial cells of the uterus, and epithelial cells of the vagina (PubMed:26964900). Belongs to the LHFP family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Component of the SRB8-11 complex. The SRB8-11 complex is a regulatory module of the Mediator complex which is itself involved in regulation of basal and activated RNA polymerase II-dependent transcription. The SRB8-11 complex may be involved in the transcriptional repression of a subset of genes regulated by Mediator. It may inhibit the association of the Mediator complex with RNA polymerase II to form the holoenzyme complex. The SRB8-11 complex phosphorylates the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (By similarity). Component of the SRB8-11 complex, a regulatory module of the Mediator complex. Belongs to the cyclin family. Cyclin C subfamily. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Cadherins are calcium-dependent cell adhesion proteins (PubMed:11976333). They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. CDH1 is involved in mechanisms regulating cell-cell adhesions, mobility and proliferation of epithelial cells (PubMed:11976333). Has a potent invasive suppressor role. It is a ligand for integrin alpha-E/beta-7 (By similarity). E-Cad/CTF2 promotes non-amyloidogenic degradation of Abeta precursors. Has a strong inhibitory effect on APP C99 and C83 production (By similarity). (Microbial infection) Does not function as a receptor for L.monocytogenes internalin A (InlA); mutating a single surface-exposed residue confers receptor activity to this protein and promotes uptake of the bacteria. Homodimer; disulfide-linked (By similarity). Component of an E-cadherin/ catenin adhesion complex composed of at least E-cadherin/CDH1, beta-catenin/CTNNB1 or gamma-catenin/JUP, and potentially alpha-catenin/CTNNA1; the complex is located to adherens junctions (PubMed:7982500, PubMed:19759396). Interacts with the TRPV4 and CTNNB1 complex (PubMed:20413591, PubMed:11348595). Interacts with CTNND1 (By similarity). The stable association of CTNNA1 is controversial as CTNNA1 was shown not to bind to F-actin when assembled in the complex (PubMed:16325582). Alternatively, the CTNNA1-containing complex may be linked to F-actin by other proteins such as LIMA1 (PubMed:18093941). Interaction with PSEN1, cleaves CDH1 resulting in the disassociation of cadherin-based adherens junctions (CAJs) (By similarity). Interacts with AJAP1 and DLGAP5 (By similarity). Interacts with TBC1D2 (By similarity). Interacts with LIMA1 (By similarity). Interacts with CAV1 (By similarity). Interacts with PIP5K1C (By similarity). Interacts with RAB8B (By similarity). Interacts with DDR1; this stabilizes CDH1 at the cell surface and inhibits its internalization (By similarity). Interacts with RAPGEF2 (By similarity). Interacts with KLRG1 (By similarity). Forms a ternary complex composed of ADAM10, CADH1 and EPHA4; within the complex, CADH1 is cleaved by ADAM10 which disrupts adherens junctions (PubMed:30639848). Interacts with SPEF1 (By similarity). Colocalizes with DLGAP5 at sites of cell-cell contact in intestinal epithelial cells. Anchored to actin microfilaments through association with alpha-, beta- and gamma-catenin. Sequential proteolysis induced by apoptosis or calcium influx, results in translocation from sites of cell-cell contact to the cytoplasm. Colocalizes with RAB11A endosomes during its transport from the Golgi apparatus to the plasma membrane (By similarity). Expressed in inner and outer pillar cells of the organ of Corti (at protein level) (PubMed:30639848). Non-neural epithelial tissues. In the testis, expression is highest in fetal gonad, then decreases 5-fold in newborn. Detectable in 7-day-old but not in 21-day-old or adult. Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain. During apoptosis or with calcium influx, cleaved by a membrane-bound metalloproteinase (ADAM10), PS1/gamma-secretase and caspase-3 (By similarity). Processing by the metalloproteinase, induced by calcium influx, causes disruption of cell-cell adhesion and the subsequent release of beta-catenin into the cytoplasm (By similarity). The residual membrane-tethered cleavage product is rapidly degraded via an intracellular proteolytic pathway (By similarity). Cleavage by caspase-3 releases the cytoplasmic tail resulting in disintegration of the actin microfilament system (By similarity). The gamma-secretase-mediated cleavage promotes disassembly of adherens junctions (By similarity). During development of the cochlear organ of Corti, cleavage by ADAM10 at adherens junctions promotes pillar cell separation (PubMed:30639848). O-glycosylated. O-manosylated by TMTC1, TMTC2, TMTC3 or TMTC4. Ser-287 and Thr-511 are O-manosylated by TMTC2 or TMTC4 but not TMTC1 or TMTC3. N-glycosylation at Asn-639 is essential for expression, folding and trafficking. Addition of bisecting N-acetylglucosamine by MGAT3 modulates its cell membrane location (By similarity). Ubiquitinated by a SCF complex containing SKP2, which requires prior phosphorylation by CK1/CSNK1A1. Ubiquitinated by CBLL1/HAKAI, requires prior phosphorylation at Tyr-756 (By similarity). +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase gamma chain family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the LeuD family. LeuD type 1 subfamily. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine. H(+) + S-adenosyl-L-methionine = CO2 + S-adenosyl 3-(methylsulfanyl)propylamine Binds 1 pyruvoyl group covalently per subunit. Amine and polyamine biosynthesis; S-adenosylmethioninamine biosynthesis; S-adenosylmethioninamine from S-adenosyl-L-methionine: step 1/1. Heterooctamer of four alpha and four beta chains arranged as a tetramer of alpha/beta heterodimers. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl group blocking the N-terminus of the alpha chain. Belongs to the prokaryotic AdoMetDC family. Type 2 subfamily. +Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate. 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 6/7. Monomer. Belongs to the EPSP synthase family. +Regulates voltage-gated potassium channels assembled from KCNA1, KCNA4 and KCNAB1. It slows down channel inactivation by precluding channel closure mediated by the KCNAB1 subunit. Ligand for ADAM22 that positively regulates synaptic transmission mediated by AMPA-type glutamate receptors (By similarity). Plays a role in suppressing the production of MMP1/3 through the phosphatidylinositol 3-kinase/ERK pathway. May play a role in the control of neuroblastoma cell survival. Oligomer. Interacts with KCNA1 within a complex containing KCNA1, KCNA4 and KCNAB1. Part of a complex containing ADAM22, DLG4/PSD95 and CACNG2/Stargazin (PubMed:27066583). Can bind to ADAM11 and ADAM23. Isoform 1 but not isoform 2 is secreted. Isoform 1 is enriched in the Golgi apparatus while isoform 2 accumulates in the endoplasmic reticulum. Predominantly expressed in neural tissues, especially in brain. Expression is reduced in low-grade brain tumors and significantly reduced or absent in malignant gliomas. Isoform 1 is absent in the cerebellum and is detectable in the occipital cortex and hippocampus; higher amounts are observed in the parietal and frontal cortices, putamen, and, particularly, in the temporal neocortex, where it is 3.5 times more abundant than in the hippocampus (at protein level). Isoform 3 shows the highest expression in the occipital cortex and the lowest in the hippocampus (at protein level). Down-regulated in neuroblastoma cells. Glycosylated. The disease is caused by variants affecting the gene represented in this entry. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate + tRNA(n) Homohexameric ring arranged as a trimer of dimers. Belongs to the RNase PH family. +Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP). diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 1/2. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrE subfamily. +Alpha-L-fucosidase is responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Active only against 2'-fucosyl-lactitol when heterologously expressed. an alpha-L-fucoside + H2O = an alcohol + L-fucose Belongs to the glycosyl hydrolase 29 family. +A number of isoforms are produced. According to EST sequences. Belongs to the BPI/LBP/Plunc superfamily. BPI/LBP (TC 1.C.40) family. +Repressed by acid stress. +Scaffold protein that may play a role in cell adhesion, cell spreading and in the reorganization of the actin cytoskeleton. Plays a role in the regulation of cell proliferation. May act as a tumor suppressor (By similarity). Interacts via LIM domain 1 with ZYX. Interacts (via LIM domain 3) with ENAH and VASP. Interacts with ALKBH4, talin, actin, alpha-actinin, GRIP1 and PXN (By similarity). Interacts (via LIM domain 2) with ACTL7A (via N-terminus). Heterodimer with ACTL7A; the heterodimer interacts with ENAH to form a heterotrimer (By similarity). Detected along actin stress fibers. The N-terminal and the C-terminal halves of the protein can associate with each other, thereby hindering interactions with ZYX. Belongs to the prickle / espinas / testin family. +Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The formation of the proteasomal ATPase ARC-20S proteasome complex, likely via the docking of the C-termini of ARC into the intersubunit pockets in the alpha-rings, may trigger opening of the gate for substrate entry. Interconversion between the open-gate and close-gate conformations leads to a dynamic regulation of the 20S proteasome proteolysis activity. Protein degradation; proteasomal Pup-dependent pathway. The 20S proteasome core is composed of 14 alpha and 14 beta subunits that assemble into four stacked heptameric rings, resulting in a barrel-shaped structure. The two inner rings, each composed of seven catalytic beta subunits, are sandwiched by two outer rings, each composed of seven alpha subunits. The catalytic chamber with the active sites is on the inside of the barrel. Has a gated structure, the ends of the cylinder being occluded by the N-termini of the alpha-subunits. Is capped by the proteasome-associated ATPase, ARC. Belongs to the peptidase T1A family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the synthesis of IGP and AICAR. The resulting ammonia molecule is channeled to the active site of HisF. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate H2O + L-glutamine = L-glutamate + NH4(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. +Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria. 3-deoxy-alpha-D-manno-oct-2-ulosonate + CTP = CMP-3-deoxy-beta-D-manno-octulosonate + diphosphate Nucleotide-sugar biosynthesis; CMP-3-deoxy-D-manno-octulosonate biosynthesis; CMP-3-deoxy-D-manno-octulosonate from 3-deoxy-D-manno-octulosonate and CTP: step 1/1. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsB family. +Participates in both the initiation and recycling phases of transcription. In the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling. RNAP is composed of a core of 2 alpha, a beta and a beta' subunits. The core is associated with a delta subunit and one of several sigma factors. Belongs to the RpoE family. +Catalyzes the deacylation of acyl-homoserine lactone (AHL or acyl-HSL), releasing homoserine lactone (HSL) and the corresponding fatty acid. Possesses a specificity for the degradation of long-chain acyl-HSLs (side chains of 11 to 14 carbons in length) (By similarity). an N-acyl-L-homoserine lactone + H2O = a carboxylate + L-homoserine lactone Heterodimer of an alpha subunit and a beta subunit processed from the same precursor. AHL-mediated signaling mediates quorum sensing in many species of Proteobacteria, regulating hundreds of genes, including many that code for extracellular virulence factors. Belongs to the peptidase S45 family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Inner capsid protein that self-assembles to form an icosahedral capsid with a T=2 symmetry, which consists of 120 copies of VP2, with channels at each of its five-fold vertices. This capsid constitutes the innermost concentric layer of the viral mature particle. It encapsidates the polymerase VP1, the capping enzyme VP3 and the genomic dsRNA, thereby defining the core. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels formed by VP2 N-termini. VP2 is required for the replicase activity of VP1 polymerase. Probably recruits a copy of a VP1-VP3 complex, potentially along with a segment of plus-strand RNA, as a decamer of VP2 assembles. May activate the autoinhibited VP1/RNA complex to coordinate packaging and genome replication. Homodecamer; each decamer is made up of two conformers of VP2, called VP2A and VP2B. Interacts with a VP1-VP3 complex. Interacts with the intermediate capsid protein VP6. Interacts with NSP5. Interacts (via N-terminus) with NSP2. Inner capsid protein. Also found in spherical cytoplasmic structures, called virus factories, that appear early after infection and are the site of viral replication and packaging. Belongs to the rotavirus VP2 family. +Subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation. N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity. Component of the oligosaccharyltransferase (OST) complex. Belongs to the OST4 family. +Involved in the biosynthesis of isoprenoids. Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP). isopentenyl diphosphate = dimethylallyl diphosphate Homooctamer. Dimer of tetramers. Belongs to the IPP isomerase type 2 family. +Catalyzes the coenzyme F420-dependent oxidation of glucose 6-phosphate (G6P) to 6-phosphogluconolactone. D-glucose 6-phosphate + H(+) + oxidized coenzyme F420-(gamma-L-Glu)(n) = 6-phospho-D-glucono-1,5-lactone + reduced coenzyme F420-(gamma-L-Glu)(n) Homodimer. Belongs to the F420-dependent glucose-6-phosphate dehydrogenase family. +Belongs to the AaeX family. +NAD-dependent oxidoreductase with broad substrate specificity that shows both oxidative and reductive activity (in vitro). Has 17-beta-hydroxysteroid dehydrogenase activity towards various steroids (in vitro). Converts 5-alpha-androstan-3-alpha,17-beta-diol to androsterone and estradiol to estrone (in vitro). Has 3-alpha-hydroxysteroid dehydrogenase activity towards androsterone (in vitro). Has retinol dehydrogenase activity towards all-trans-retinol (in vitro). Can convert androsterone to epi-androsterone. Androsterone is first oxidized to 5-alpha-androstane-3,17-dione and then reduced to epi-andosterone. Can act on both C-19 and C-21 3-alpha-hydroxysteroids. all-trans-retinol--[retinol-binding protein] + NAD(+) = all-trans-retinal--[retinol-binding protein] + H(+) + NADH all-trans-retinol + NAD(+) = all-trans-retinal + H(+) + NADH 3alpha-hydroxy-5alpha-androstan-17-one + NAD(+) = 5alpha-androstan-3,17-dione + H(+) + NADH NAD(+) + testosterone = androst-4-ene-3,17-dione + H(+) + NADH 5alpha-androstane-3alpha,17beta-diol + NAD(+) = 17beta-hydroxy-5alpha-androstan-3-one + H(+) + NADH 17beta-estradiol + NAD(+) = estrone + H(+) + NADH 17beta-estradiol + NADP(+) = estrone + H(+) + NADPH 3alpha-hydroxy-5alpha-pregnan-20-one + NAD(+) = 5alpha-pregnane-3,20-dione + H(+) + NADH 5alpha-androstane-3beta,17beta-diol + NAD(+) = 17beta-hydroxy-5alpha-androstan-3-one + H(+) + NADH 3beta-hydroxy-5alpha-androstan-17-one + NAD(+) = 5alpha-androstan-3,17-dione + H(+) + NADH The kinetic parameters were determined using microsomes from transfected cells. Detected in liver and prostate (at protein level). Detected in adult liver, lung, brain, placenta, prostate, adrenal gland, testis, mammary gland, spleen, spinal cord and uterus. Detected in caudate nucleus, and at lower levels in amygdala, corpus callosum, hippocampus, substantia nigra and thalamus. Detected in fetal lung, liver and brain. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). 2-oxoglutarate + H(+) + isochorismate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2 Binds 1 thiamine pyrophosphate per subunit. Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 2/7. Quinol/quinone metabolism; menaquinone biosynthesis. Homodimer. Belongs to the TPP enzyme family. MenD subfamily. +Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in the wobble position of the QUC anticodon. Binds 1 zinc ion per subunit. Belongs to the class-I aminoacyl-tRNA synthetase family. GluQ subfamily. +Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +A cytochrome P450 monooxygenase that plays a major role in adrenal steroidogenesis. Catalyzes the hydroxylation at C-21 of progesterone and 17alpha-hydroxyprogesterone to respectively form 11-deoxycorticosterone and 11-deoxycortisol, intermediate metabolites in the biosynthetic pathway of mineralocorticoids and glucocorticoids (PubMed:25855791, PubMed:10602386, PubMed:16984992, PubMed:22014889, PubMed:27721825). Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (CPR; NADPH-ferrihemoprotein reductase) (PubMed:25855791). O2 + progesterone + reduced [NADPH--hemoprotein reductase] = 21-hydroxyprogesterone + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] 17alpha-hydroxyprogesterone + O2 + reduced [NADPH--hemoprotein reductase] = 11-deoxycortisol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] The leucine-rich hydrophobic amino acid N-terminal region probably helps to anchor the protein to the microsomal membrane. Seven non deleterious alleles are known: CYP21A2*1A, CYP21A2*1B, CYP21A2*2, CYP21A2*3, CYP21A2*4, CYP21A2*5 and CYP21A2*6. The sequence shown corresponds to allele CYP21A2*1B. Deleterious alleles are mostly generated by recombinations between CYP21A2 and the pseudogene CYP21A1P through gene conversion. This process consists of recombination events that either delete CYP21A2 or transfer deleterious mutations from CYP21A1P to CYP21A2. The disease is caused by variants affecting the gene represented in this entry. Belongs to the cytochrome P450 family. CYP21A2 alleles +Transcription repressor that specifically binds the 5'-GGAG[GA]A[GA]A-3' consensus sequence. Represses transcription by recruiting the chromatin multiprotein complex NuRD to target promoters. Negatively regulates expression of EGFR, a gene involved in cell proliferation, survival and migration. Its ability to repress genes of the EGFR pathway suggest it may act as a tumor suppressor (By similarity). Interacts with CHD4/Mi-2; the interaction is direct. +Part of the ABC transporter complex ThiBPQ involved in thiamine import. Responsible for energy coupling to the transport system. ATP + H2O + thiamine(out) = ADP + H(+) + phosphate + thiamine(in) The complex is composed of two ATP-binding proteins (ThiQ), two transmembrane proteins (ThiP) and a solute-binding protein (ThiB). Belongs to the ABC transporter superfamily. Thiamine importer (TC 3.A.1.19.1) family. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Catalyzes the first step of the methylation pathway of phosphatidylcholine biosynthesis, the SAM-dependent methylation of phosphatidylethanolamine (PE) to phosphatidylmonomethylethanolamine (PMME). Preferentially converts di-C16:1 substrates. a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + S-adenosyl-L-methionine = 1,2-diacyl-sn-glycero-3-phospho-N-methylethanolamine + H(+) + S-adenosyl-L-homocysteine Optimum pH is 9.9. Phospholipid metabolism; phosphatidylcholine biosynthesis. Repressed by myo-inositol and choline. Present with 1810 molecules/cell in log phase SD medium. Belongs to the class VI-like SAM-binding methyltransferase superfamily. CHO2 family. +Belongs to the SUI1 family. +Catalyzes the cross-linking of a glutamate residue and a tyrosine residue in the PqqA protein as part of the biosynthesis of pyrroloquinoline quinone (PQQ). [PQQ precursor protein] + S-adenosyl-L-methionine = 5'-deoxyadenosine + E-Y cross-linked-[PQQ precursor protein] + H(+) + L-methionine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. Interacts with PqqD. The interaction is necessary for activity of PqqE. Belongs to the radical SAM superfamily. PqqE family. +Sodium permeable non-voltage-sensitive ion channel inhibited by the diuretic amiloride. Mediates the electrodiffusion of the luminal sodium (and water, which follows osmotically) through the apical membrane of epithelial cells. Plays an essential role in electrolyte and blood pressure homeostasis, but also in airway surface liquid homeostasis, which is important for proper clearance of mucus. Heterotrimer containing an alpha/SCNN1A, a beta/SCNN1B and a gamma/SCNN1G subunit. An additional delta/SCNN1D subunit exists only in some organisms and can replace the alpha/SCNN1A subunit to form an alternative channel with specific properties. Apical membrane of epithelial cells. Belongs to the amiloride-sensitive sodium channel (TC 1.A.6) family. SCNN1B subfamily. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity). Belongs to the bacterial ribosomal protein bL20 family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Essential for normal spermatogenesis and male fertility (By similarity). Required for the completion of meiosis in male germ cells (By similarity). Predominantly localized to the cytoplasm. Translocates from the cytoplasm to the nucleus in the G2/M transition upon treatment with cadmium, cobalt or zinc. Expressed specifically in testis. Belongs to the lin-54 family. +Might be involved in Fe(2+) ion uptake (By similarity). Belongs to the FeoA family. +Part of the ABC transporter complex CcmAB involved in the biogenesis of c-type cytochromes; once thought to export heme, this seems not to be the case, but its exact role is uncertain. Responsible for energy coupling to the transport system. ATP + H2O + heme b(in) = ADP + H(+) + heme b(out) + phosphate The complex is composed of two ATP-binding proteins (CcmA) and two transmembrane proteins (CcmB). Belongs to the ABC transporter superfamily. CcmA exporter (TC 3.A.1.107) family. +Belongs to the TolB family. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseB family. +Catalyzes the phosphorylation of the dietary vitamin B6 vitamers pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM) to form pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), respectively (By similarity). PLP is the active form of vitamin B6, and acts as a cofactor for over 140 different enzymatic reactions (By similarity). ATP + pyridoxal = ADP + H(+) + pyridoxal 5'-phosphate ATP + pyridoxamine = ADP + H(+) + pyridoxamine 5'-phosphate ATP + pyridoxine = ADP + H(+) + pyridoxine 5'-phosphate Activity is increased in the presence of K(+)or Na(+). Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxal: step 1/1. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxine 5'-phosphate from pyridoxine: step 1/1. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxamine 5'-phosphate from pyridoxamine: step 1/1. Homodimer. Belongs to the pyridoxine kinase family. +Belongs to the eukaryotic ribosomal protein eL39 family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Probable downstream regulator of strigolactones signaling. Tetramer (PubMed:26601214). Interacts with D53 (PubMed:24336200). Interacts with WOX1 (PubMed:25697101, PubMed:24336200, PubMed:26601214). Interacts with MOF1 (PubMed:32680975). Expressed in panicles, stems, leaves, spikelets and seed endosperm. Highest expression in endosperm at 7 days after pollination and in flag leaf at 14 days after heading. The N-terminal TOPLESS domain (TPD)(1-209) binds directly to a 12-amino acid LxLxL EAR motif peptide, but no binding if the leucin residues are replaced. +Fatty acid synthase beta subunit; part of the pki gene cluster that mediates the biosynthesis of 2,4-dihydroxy-3-methyl-6-(2-oxoundecyl)benzaldehyde (PubMed:22510154). The first step in the pathway is the generation of the decanoyl starter unit by the FAS composed of subunits pkiB and pkiC, which is then transferred directly from the FAS to the SAT domain of the non-reducing polyketide synthase pkiA (PubMed:22510154). PkiA condenses the decanoyyl starter unit with 4 malonyl-CoA units and performs one methylation step to yield 2,4-dihydroxy-3-methyl-6-(2-oxoundecyl)benzaldehyde (PubMed:22510154). acetyl-CoA + 2n H(+) + n malonyl-CoA + 2n NADPH = a long-chain fatty acyl-CoA + n CO2 + n CoA + H2O + 2n NADP(+) acetyl-CoA + holo-[ACP] = acetyl-[ACP] + CoA holo-[ACP] + malonyl-CoA = CoA + malonyl-[ACP] a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O a 2,3-saturated acyl-[ACP] + NAD(+) = a (2E)-enoyl-[ACP] + H(+) + NADH (9Z)-octadecenoyl-[ACP] + H2O = (9Z)-octadecenoate + H(+) + holo-[ACP] Secondary metabolite biosynthesis. [Alpha(6)beta(6)] hexamers of two multifunctional subunits (alpha and beta). Belongs to the fungal fatty acid synthetase subunit beta family. +Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA. S-adenosyl-L-methionine + uridine(1939) in 23S rRNA = 5-methyluridine(1939) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Alpha-glucuronidase involved in the hydrolysis of xylan, a major structural heterogeneous polysaccharide found in plant biomass representing the second most abundant polysaccharide in the biosphere, after cellulose. Releases 4-O-methylglucuronic acid from xylan (By similarity). an alpha-D-glucuronoside + H2O = an alcohol + D-glucuronate Belongs to the glycosyl hydrolase 67 family. +Forms oligomers. Belongs to the MraZ family. +Belongs to the RemA family. +Heme-dependent dioxygenase that catalyzes the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring and converts L-tryptophan to N-formyl-L-kynurenine. Catalyzes the oxidative cleavage of the indole moiety. L-tryptophan + O2 = N-formyl-L-kynurenine Binds 1 heme group per subunit. Amino-acid degradation; L-tryptophan degradation via kynurenine pathway; L-kynurenine from L-tryptophan: step 1/2. Pigment biosynthesis; ommochrome biosynthesis. Homotetramer. Dimer of dimers. Belongs to the tryptophan 2,3-dioxygenase family. +Catalyzes the dehydration of D-mannonate. D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O Carbohydrate metabolism; pentose and glucuronate interconversion. Belongs to the mannonate dehydratase family. +Pore-forming toxin (PFT) that consists of a crown-shaped octamer or nonamer that forms cation-selective hydrophilic pores of about 1.5 nm (inside) and 13 nm (outside) (PubMed:21300287, PubMed:25716479). It causes cardiac stimulation and hemolysis (HC(50)=1.6 nM) (PubMed:19563820, PubMed:31295915, PubMed:25759390). Interestingly, the Phe-16 is crucial for hemolysis (PubMed:25759390). Pore formation is a multi-step process that involves specific recognition of membrane sphingomyelin (but neither cholesterol nor phosphatidylcholine) using aromatic rich region and adjacent phosphocholine (POC) binding site, firm binding to the membrane (mainly driven by hydrophobic interactions) accompanied by the transfer of the N-terminal region to the lipid-water interface and finally pore formation after oligomerization of monomers (PubMed:19563820, PubMed:25716479). It is probable that a dimeric form is an assembly intermediate before the complete oligomerization (PubMed:25716479). The formation of stable pores occurs only in vesicles composed of DOPC/SM (there is no oligomerization when the PFT is treated with vesicles of DOPC or SM alone) (PubMed:25716479). The transmembrane pore displays 8 lateral perforations, one at each subunit-subunit interface, partially occupied by the acyl-chain region of a bridging lipid (PubMed:25716479). Each pore contains 24 lipid molecules, firmly bound to each subunit, that is, 3 lipids (L1, L2, L3, L4 and/or L5) are associated to each subunit (PubMed:25716479). Lipid L1 bridges 2 subunits, whereas lipids L2 and L3 bind to sites at single subunit (PubMed:25716479). Stable up to about 53 degrees Celsius. Octamer or nonamer in membranes (PubMed:21300287, PubMed:22728830, PubMed:25716479). Monomer in the soluble state (PubMed:21300287, PubMed:22728830, PubMed:25716479). Forms an alpha-helical membrane channel in the prey (PubMed:19563820,PubMed:21300287,PubMed:25716479). The N-terminal region, before the pore is formed, is bound to the lipid membrane. It partitions into the lipid-water interface and stabilizes the monomeric molecule on the membrane. Finally, it traverses the bilayer, thus forming the transmembrane pore. Has been engineered for DNA analysis in nanopore technology. This protein has been found to bind carbohydrates, since it shows a substantial delay in elution profile in size-exclusion chromatography. The carbohydrate pocket ovelaps with the lipid-binding module of actinoporins. Belongs to the actinoporin family. Sea anemone subfamily. +Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA). NADP(+) + shikimate = 3-dehydroshikimate + H(+) + NADPH Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 4/7. Homodimer. Belongs to the shikimate dehydrogenase family. +Catalyzes the ferrous insertion into protoporphyrin IX. 2 H(+) + heme b = Fe(2+) + protoporphyrin IX Porphyrin-containing compound metabolism; protoheme biosynthesis; protoheme from protoporphyrin-IX: step 1/1. Belongs to the ferrochelatase family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be a menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 49 kDa subunit family. +Esterase that hydrolyzes short to medium chain fatty acid esters with the highest specific activity for p-nitrophenyl caproate (pNPC6). Has lower activity with p-nitrophenyl caprylate (pNPC8) and p-nitrophenyl butyrate (pNPC4). Has weak activity with p-nitrophenyl caprate (pNPC10) and p-nitrophenyl laurate (pNPC12). Does not possess lipolytic activity and cutinase activity. a hexanoate ester + H2O = an aliphatic alcohol + H(+) + hexanoate an octanoate ester + H2O = an aliphatic alcohol + H(+) + octanoate a butanoate ester + H2O = an aliphatic alcohol + butanoate + H(+) Esterase activity is significantly inhibited by the serine modifier phenylmethylsulfonyl fluoride (PMSF). kcat is 341 sec(-1) with pNPC4 as substrate. kcat is 534 sec(-1) with pNPC6 as substrate. kcat is 305 sec(-1) with pNPC8 as substrate. Optimum pH is 7.0-8.0. Optimum temperature is 37-38 degrees Celsius. Belongs to the mycobacterial PE family. +(R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Belongs to the prokaryotic pantothenate kinase family. +Participates in cysteine desulfuration mediated by SufS. Cysteine desulfuration mobilizes sulfur from L-cysteine to yield L-alanine and constitutes an essential step in sulfur metabolism for biosynthesis of a variety of sulfur-containing biomolecules. Functions as a sulfur acceptor for SufS, by mediating the direct transfer of the sulfur atom from the S-sulfanylcysteine of SufS, an intermediate product of cysteine desulfuration process. Cofactor biosynthesis; iron-sulfur cluster biosynthesis. Homodimer. Interacts with SufS. Belongs to the SufE family. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. A number of isoforms are produced. According to EST sequences. There are four genes for EF-1-alpha in Arabidopsis thaliana. The sequence of genes 1, 2, and 3 are identical. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Catalyzes the hydrolysis of 4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate (HMP-PP) to 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate (HMP-P). Can also hydrolyze other substrates such as MeO-HMP-PP and 4-amino-2-trifluoromethyl 5-hydroxymethylpyrimidine pyrophosphate (CF3-HMP-PP) to give MeO-HMP-P and 4-amino-2-trifluoromethyl-5-hydroxymethylpyrimidine phosphate. This hydrolysis generates resistance to the antibiotics (bacimethrin, CF3-HMP) by reducing the formation of their toxic forms, 2'-methoxythiamin pyrophosphate (MeO-TPP) and CF3-HMP-PP. Also hydrolyzes pyridoxal-phosphate (PLP) and flavin mononucleotide (FMN), and purines (GMP and IMP) as secondary substrates. 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + H2O = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + H(+) + phosphate Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc. Optimum pH is between 6 and 7.5. Belongs to the HAD-like hydrolase superfamily. Cof family. Extended N-terminus. Extended N-terminus. +ATP + oxaloacetate = ADP + CO2 + phosphoenolpyruvate Carbohydrate biosynthesis; gluconeogenesis. Belongs to the phosphoenolpyruvate carboxykinase (ATP) family. +This gamma chain was obtained from antibody to type III pneumococci and was isolated from the serum of a single rabbit. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be a menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Shows particularly broad specificity; although bonds involving phenylalanine and leucine are preferred, many others are also cleaved to some extent. Preferential cleavage: hydrophobic, preferably aromatic, residues in P1 and P1' positions. Cleaves 1-Phe-|-Val-2, 4-Gln-|-His-5, 13-Glu-|-Ala-14, 14-Ala-|-Leu-15, 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17, 23-Gly-|-Phe-24, 24-Phe-|-Phe-25 and 25-Phe-|-Tyr-26 bonds in the B chain of insulin. Belongs to the peptidase A1 family. +May act as a neuromodulator or neurotransmitter. Expressed by the skin dorsal glands. Belongs to the frog skin active peptide (FSAP) family. Tryptophillin subfamily. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Part of the RNA polymerase complex. Belongs to the archaeal Rpo11/eukaryotic RPB11/RPC19 RNA polymerase subunit family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Feedback inhibited by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Belongs to the ATP phosphoribosyltransferase family. Long subfamily. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +Involved in the regulation of melanogenesis. The binding of ASP to MC1R precludes alpha-MSH initiated signaling and thus blocks production of cAMP, leading to a down-regulation of eumelanogenesis (brown/black pigment) and thus increasing synthesis of pheomelanin (yellow/red pigment) (By similarity). The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. +Mitochondrial enzyme that catalyzes reactions of the mitochondrial beta-oxidation pathway. acetyl-CoA + an acyl-CoA = a 3-oxoacyl-CoA + CoA Lipid metabolism; fatty acid beta-oxidation. Belongs to the thiolase-like superfamily. Thiolase family. +Giardins are involved in parasite attachment to the intestinal mucosa and in the cytoskeletal disassembly and reassembly that marks the transition from infectious trophozoite to transmissible cyst. They may interact with other cytoskeletal proteins such as microtubules in the microribbons or crossbridges, to maintain the integrity of the ventral disk (By similarity). Belongs to the annexin family. Giardin subunit alpha subfamily. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs (By similarity). It interacts with LexA causing its activation and leading to its autocatalytic cleavage (By similarity). Required for DNA transformation; protects transforming DNA from degradation, possibly in combination with DprA (PubMed:14617176, PubMed:17803906). Present at 15,000-30,000 monomers per competent cell (PubMed:14617176). Interacts with DprA; probably forms mixed DprA-RecA-ssDNA filaments (PubMed:17803906). By competence and DNA damage (PubMed:7798154). Loss of DNA transformation; incoming DNA is very rapidly degraded (PubMed:14617176). Belongs to the RecA family. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +Might form homotrimers; these trimers are only formed in retina. Widely expressed, including in retina and brain (at protein level), as well as in kidney, testis and ovary. Expressed in all layers of the retina, including inner segments of photoreceptor cells and ganglion cells (at protein level). In the developing eye, already detected at 10.5 dpc. Expression increases from 12.5 though 18.5 dpc in all retinal cells (at protein level). At P1, expressed in a small number of cells at the level of the ganglion cell layer and in the inner edge of the ventricular zone of the retina. The number of expressing cells increases and, by P8 to P11, entirely occupies the ganglion cell layer and inner nuclear layer. At that stage, not detected in the photoreceptor cell bodies of the outer nuclear layer. At P21, expressed in all nuclear layers of the retina, including cones (at protein level). Belongs to the peptidase S54 family. Although strongly related to the peptidase S54 family, it lacks the conserved active sites, suggesting that it has no peptidase activity. +Virulence effector that plays a role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). Acts as a phosphocholine hydrolase by mediating the hydrolysis of phosphocholine to Ser residues of host RAB1 (RAB1A, RAB1B or RAB1C). Dephosphocholination of target proteins restores accessibility to GTPase effector LepB. Can act on both GDP-bound and GTP-bound Rab proteins. [Rab1 protein]-O-phosphocholine-L-serine + H2O = [Rab1 protein]-L-serine + H(+) + phosphocholine Translocated into the host cell via the type IV secretion system (T4SS). +Represses thailandamide production. No production of thailandamide antibiotic. When the promoter region is disrupted (121 bases before the start codon) thailandamide production increases (PubMed:20853892). In 2 other promoter disruption mutants (617 and 624 bases before the start codon) this bacterium no longer inhibits growth of Salmonella in an overlay assay, suggesting no thailandamide is produced (PubMed:29914944). Thailandamide is a polyketide that is toxic to human cell lines but also has antibacterial activity on E.coli, S.typhimurium and S.aureus. It probably acts on acetyl-CoA carboxylase in the fatty acid synthesis pathway, which is rarely found to be an antibiotic target. These data suggest it might be a good starting point for engineering of novel antibiotics. Belongs to the autoinducer-regulated transcriptional regulatory protein family. +H2O + L-histidinol phosphate = L-histidinol + phosphate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 8/9. Belongs to the PHP hydrolase family. HisK subfamily. +ATP + uridine = ADP + H(+) + UMP ATP + cytidine = ADP + CMP + H(+) Pyrimidine metabolism; CTP biosynthesis via salvage pathway; CTP from cytidine: step 1/3. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uridine: step 1/1. Belongs to the uridine kinase family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)). Belongs to the cytochrome c oxidase VIII family. +Involved in the synthesis of meso-diaminopimelate (m-DAP or DL-DAP), required for both lysine and peptidoglycan biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate. (2S,6S)-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O + L-glutamate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route): step 1/1. Homodimer. Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. LL-diaminopimelate aminotransferase subfamily. +Belongs to the FAM234 family. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'-nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Magnesium is required for nucleotidyltransferase activity. Nickel for phosphatase activity. Monomer. Can also form homodimers and oligomers. Comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain associated with both phosphodiesterase and phosphatase activities. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 1 subfamily. +Has potent hemolytic activity. Is lethal to crayfish. Causes cutaneous inflammation in humans. May act as a pore-forming toxin, disrupting normal transmembrane ion concentration gradients in susceptible cells. Forms a membrane channel in the prey. Nematocytes. Contains disulfide bonds. Belongs to the jellyfish toxin family. +VSG forms a coat on the surface of the parasite. The trypanosome evades the immune response of the host by expressing a series of antigenically distinct VSGs from an estimated 1000 VSG genes. A soluble form is released from ruptured cells by the action of a PI-PLC. +Toxic component of a type I toxin-antitoxin (TA) system (By similarity). When overexpressed kills cells within minutes; causes collapse of the transmembrane potential and arrest of respiration (By similarity). Its toxic effect is probably neutralized by an antisense antitoxin Sok RNA (By similarity). Belongs to the Hok/Gef family. Extended N-terminus. +Involved in parasite invasion of erythrocytes. Belongs to the apicomplexan parasites AMA1 family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Involved in DNA repair and RecF pathway recombination. Belongs to the RecO family. +Part of the TCR-CD3 complex present on T-lymphocyte cell surface that plays an essential role in adaptive immune response. When antigen presenting cells (APCs) activate T-cell receptor (TCR), TCR-mediated signals are transmitted across the cell membrane by the CD3 chains CD3D, CD3E, CD3G and CD3Z. All CD3 chains contain immunoreceptor tyrosine-based activation motifs (ITAMs) in their cytoplasmic domain. Upon TCR engagement, these motifs become phosphorylated by Src family protein tyrosine kinases LCK and FYN, resulting in the activation of downstream signaling pathways. In addition of this role of signal transduction in T-cell activation, CD3E plays an essential role in correct T-cell development. Initiates the TCR-CD3 complex assembly by forming the two heterodimers CD3D/CD3E and CD3G/CD3E. Participates also in internalization and cell surface down-regulation of TCR-CD3 complexes via endocytosis sequences present in CD3E cytosolic region. The TCR-CD3 complex is composed of a CD3D/CD3E and a CD3G/CD3E heterodimers that preferentially associate with TCRalpha and TCRbeta, respectively, to form TCRalpha/CD3E/CD3G and TCRbeta/CD3G/CD3E trimers. In turn, the hexamer interacts with CD3Z homodimer to form the TCR-CD3 complex. Alternatively, TCRalpha and TCRbeta can be replaced by TCRgamma and TCRdelta. Interacts with CD6. Interacts with NCK1. Interacts with NUMB; this interaction is important for TCR-CD3 internalization and subsequent degradation. Phosphorylated on Tyr residues after T-cell receptor triggering by LCK in association with CD4/CD8. +Involved in rRNA-processing at A0, A1 and A2 sites and regulates negatively telomerase. Belongs to the PINX1 family. +ER (microsomal) omega-6 fatty acid desaturase introduces the second double bond in the biosynthesis of 18:3 fatty acids, important constituents of plant membranes. It is thought to use cytochrome b5 as an electron donor and to act on fatty acids esterified to phosphatidylcholine and, possibly, other phospholipids (By similarity). Lipid metabolism; polyunsaturated fatty acid biosynthesis. The histidine box domains may contain the active site and/or be involved in metal ion binding. Belongs to the fatty acid desaturase type 1 family. +Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B). 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds a copper A center. Belongs to the cytochrome c oxidase subunit 2 family. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Important for the epidermal barrier integrity. Found in corneodesmosomes, the intercellular structures that are involved in desquamation. Exclusively expressed in skin. Genetic variation in CDSN may be associated with susceptibility to psoriasis [MIM:177900] (PubMed:10599883, PubMed:12472658,PubMed:10844560). Various CDSN alleles are known including alleles 1.11, 1.21, 1.31, 1.32, 1.41, 1.42, 1.43, 1.51, 1.52, 2.11, 2.21, 2.22 and 2.23 (PubMed:11169256). The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. CDNS mutations are responsible for generalized, inflammatory peeling skin syndrome type B (PubMed:20691404). Truncated N-terminus. Truncated N-terminus. +Brain-specific. In some cancer patients, specifically expressed by testicular tumor cells. Antibodies against PNMA2 are present in sera from patients suffering of paraneoplastic neurological disorders. Belongs to the PNMA family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. (2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 4/5. Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface. Belongs to the enolase family. +Receptor-like cytoplasmic kinase (RLCK) that triggers abscisic acid (ABA) signaling by phosphorylating and activating ABA receptors (e.g. PYL8/RCAR3 and PYR1/RCAR11), which in turn repress ABI1, a negative regulator of ABA responses (PubMed:29928509). Promotes drought tolerance (PubMed:29970817). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts with PYL8/RCAR3 and PYR1/RCAR11 in the cytosol. Autophosphorylated at threonine residues and to a lesser extent at serine residues. Impaired kinase activity and reduced plant sensitivity to abscisic acid (ABA). Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +Required for checkpoint signaling in response to DNA replication stress; either resulting from normal embryogenesis or induced by the DNA synthesis inhibitor hydroxyurea (HU). It is not required for the G2 arrest resulting from DNA double strand breaks induced by ionizing irradiation (IR). Necessary for the timely phosphorylation of Cdk1 at the mid-blastula transition. May have a minor role in maintaining genomic stability in mitotic cells. Detected in the ovary but not in the testis (at protein level). Expressed during S phase, in a cell-cycle-dependent fashion. Expression levels are highest in embryos (0-4 hours old) and in the ovaries of adult females. Little to no expression in larvae and pupae (at protein level). Phosphorylated in response to DNA damage by IR and HU treatment. Phosphorylation does not require mei-41 or tefu. Hatch rate of embryos is less than one percent. Nuclear morphology of embryos is normal until the 10th nuclear cycle when the shape and size of nuclei becomes abnormal and surface nuclei also begin to exhibit an irregular distribution. The phosphorylation of Cdk1 at the mid-blastula transition (between 2 to 4 hours after egg deposition) is also severely delayed. Increased sensitivity to HU with reduced survival rates. In the eye disks from mutant third stage larvae treated with HU, there is a higher percentage of mitotic cells compared to untreated mutant larvae. Is insensitive to ionizing radiation; the percentage of mitotic cells is unaffected in the eye disks of larvae treated with IR, and IR-induced apoptosis in larvae also appears to be unaffected. Belongs to the claspin family. Truncated N-terminus. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +Causes a rapid but short-lived drop in the level of calcium and phosphate in blood by promoting the incorporation of those ions in the bones. Belongs to the calcitonin family. +May be involved in a process influencing telomere capping. Belongs to the RTC5 family. +Involved in the biosynthesis of galactolipids found in the photosynthetic membranes. Catalyzes the isomerization of monoglucosyldiacylglycerol (GlcDG) to yield monogalactosyldiacylglycerol (MGDG). a 1,2-diacyl-3-O-(beta-D-glucopyranosyl)-sn-glycerol = a 1,2-diacyl-3-O-(beta-D-galactosyl)-sn-glycerol The mutant lacks both monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), and accumulates GlcDG. It possesses intact thylakoid membranes and shows normal maximal photosynthetic activity, albeit with reduced utilization of light energy. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +Constitutes 1-2% of the total bone protein. It binds strongly to apatite and calcium. Bone. Gamma-carboxyglutamate residues are formed by vitamin K dependent carboxylation. These residues are essential for the binding of calcium. Belongs to the osteocalcin/matrix Gla protein family. +Murein-degrading enzyme. May play a role in recycling of muropeptides during cell elongation and/or cell division. Exolytic cleavage of the (1->4)-beta-glycosidic linkage between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues in peptidoglycan, from either the reducing or the non-reducing ends of the peptidoglycan chains, with concomitant formation of a 1,6-anhydrobond in the MurNAc residue. Belongs to the transglycosylase Slt family. +Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly. Belongs to the UreE family. +Has a post-transcriptional repressor function in flagellum biogenesis. Associates with the 5'-UTR of fljK mRNA and promotes its degradation. Belongs to the FlbT family. +Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG (By similarity). Occurs in many kinds of cells as a complex with monomeric actin in a 1:1 ratio. Causes an allergic reaction in human. Belongs to the profilin family. +ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate + H(+) Carbohydrate biosynthesis; Calvin cycle. Belongs to the phosphoribulokinase family. +Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate. (2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate + CO2 + NADH Binds 1 Mg(2+) or Mn(2+) ion per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4. Homodimer. Belongs to the isocitrate and isopropylmalate dehydrogenases family. +SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes. Homodimer (By similarity). Forms long polymer filaments with other SOKs proteins polymers crucial for polar localization and biological activity (PubMed:32004461). The DIX-like oligomerization domain is required for polymerization, edge localization and biological activity. 'Soseki' means cornerstone in Japanese. Belongs to the SOSEKI family. +Phosphorylates 6-deoxy-6-sulfo-D-fructose (SF) to 6-deoxy-6-sulfo-D-fructose 1-phosphate (SFP). 6-deoxy-6-sulfo-D-fructose + ATP = 6-deoxy-6-sulfo-D-fructose 1-phosphate + ADP + H(+) Induced during growth with sulfoquinovose. Mutant fails to grow on sulfoquinovose as a sole carbon source. Belongs to the carbohydrate kinase PfkB family. Extended N-terminus. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +Catalyzes the deamination of dCTP to dUTP. dCTP + H(+) + H2O = dUTP + NH4(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 1/2. Homotrimer. Belongs to the dCTP deaminase family. +Plays several crucial roles in viral infection. Participates in the opening of the viral DNA origin to initiate replication by interacting with the origin-binding protein. May disrupt loops, hairpins and other secondary structures present on ssDNA to reduce and eliminate pausing of viral DNA polymerase at specific sites during elongation. Promotes viral DNA recombination by performing strand-transfer, characterized by the ability to transfer a DNA strand from a linear duplex to a complementary single-stranded DNA circle. Can also catalyze the renaturation of complementary single strands. Additionally, reorganizes the host cell nucleus, leading to the formation of prereplicative sites and replication compartments. This process is driven by the protein which can form double-helical filaments in the absence of DNA. Homooligomers. Forms double-helical filaments necessary for the formation of replication compartments within the host nucleus. Interacts with the origin-binding protein. Interacts with the helicase primase complex; this interaction stimulates primer synthesis activity of the helicase-primase complex. Interacts with the DNA polymerase. Interacts with the alkaline exonuclease; this interaction increases its nuclease processivity. In the absence of DNA replication, found in the nuclear framework-associated structures (prereplicative sites). As viral DNA replication proceeds, it migrates to globular intranuclear structures (replication compartments). Belongs to the herpesviridae major DNA-binding protein family. +Subunit of malonate decarboxylase, it is an acyl carrier protein to which acetyl and malonyl thioester residues are bound via a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group and turn over during the catalytic mechanism. Covalently binds the prosthetic group of malonate decarboxylase. Belongs to the MdcC family. +Cell wall formation. ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) + phosphate Binds 2 magnesium or manganese ions per subunit. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the D-alanine--D-alanine ligase family. +Belongs to the universal ribosomal protein uL29 family. +Belongs to the psbP family. Could be the product of a pseudogene. Created by a base pair loss in a duplication of PSBP1 (At1g06680). Not detected at the protein level in purified chloroplasts. +Specifically catalyzes the 21-hydroxylation of steroids. Required for the adrenal synthesis of mineralocorticoids and glucocorticoids. 17alpha-hydroxyprogesterone + O2 + reduced [NADPH--hemoprotein reductase] = 11-deoxycortisol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] O2 + progesterone + reduced [NADPH--hemoprotein reductase] = 21-hydroxyprogesterone + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] The leucine-rich hydrophobic amino acid N-terminal region probably helps to anchor the protein to the microsomal membrane. Belongs to the cytochrome P450 family. +Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system. ATP + H2O + L-methionine(out) = ADP + H(+) + L-methionine(in) + phosphate ATP + D-methionine(out) + H2O = ADP + D-methionine(in) + H(+) + phosphate The complex is composed of two ATP-binding proteins (MetN), two transmembrane proteins (MetI) and a solute-binding protein (MetQ). Belongs to the ABC transporter superfamily. Methionine importer (TC 3.A.1.24) family. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +H2O + L-tryptophan = indole + NH4(+) + pyruvate Amino-acid degradation; L-tryptophan degradation via pyruvate pathway; indole and pyruvate from L-tryptophan: step 1/1. Homotetramer. Belongs to the beta-eliminating lyase family. +Serine protease inhibitor. Expressed by the venom gland. Belongs to the venom Kunitz-type family. The P1 reactive site residue Lys-41 is replaced by Asn-41. The impact of this replacement on the protease inhibition has not yet been determined. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS8 family. +Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Heterohexamer, formed by a dimer of trimers. The hexameric TusBCD complex contains 2 copies each of TusB, TusC and TusD. The TusBCD complex interacts with TusE. Belongs to the DsrF/TusC family. +Belongs to the CYYR1 family. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homotetramer; dimer of dimers. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 magnesium ions per subunit. Monomer. Belongs to the DNA polymerase type-Y family. +Component of the alkene monooxygenase multicomponent enzyme system which catalyzes the O2- and NADH-dependent epoxidation of short chain (C2 to C6) alkenes to their corresponding epoxides (PubMed:10103255, PubMed:1444418, PubMed:9312093). Also able to catalyze the oxidation of a number of chlorinated alkenes, including trichloroethylene, cis- and trans-1,2-dichloroethylene, vinyl chloride, 1-chloropropylene, 1,3-dichloropropylene and 2,3-dichloropropylene (PubMed:1444418). H(+) + NADH + O2 + propene = 1,2-epoxypropane + H2O + NAD(+) Binds 2 Fe(2+) ions per subunit (PubMed:9312093). The two iron ions could form a binuclear cluster (Probable). Inhibited by propyne. The alkene monooxygenase multicomponent enzyme system is composed of an electron transfer component and a monooxygenase component interacting with the effector protein XamoD. The electron transfer component is composed of a ferredoxin reductase (XamoF) and a ferredoxin (XamoC), and the monooxygenase component is formed by a heterohexamer (dimer of heterotrimers) of two alpha subunits (XamoA), two beta subunits (XamoE) and two gamma subunits (XamoB). Induced during growth on aliphatic alkenes (such as propylene, ethylene and 1-butylene), epoxides (such as propylene oxide and 1,2-epoxybutane) and chlorinated alkenes and epoxides (such as vinyl chloride, cis- and trans-1,2-dichloroethylene, 1-chloropropylene, 1,3-dichloropropylene, epichlorohydrin, and epifluorohydrin). Repressed during growth on other carbon sources. Belongs to the TmoA/XamoA family. +H(+) + NADP(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADPH + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Homodimer. Belongs to the ferredoxin--NADP reductase type 2 family. +Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner. ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) Monomer. ValRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated threonine is translocated from the active site to the editing site. The C-terminal coiled-coil domain is crucial for aminoacylation activity. Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Interacts with TMEM186. Interacts with TMEM242 (By similarity). Belongs to the complex I subunit 3 family. +Catalyzes the transfer of 4-deoxy-4-formamido-L-arabinose from UDP to undecaprenyl phosphate. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. di-trans,octa-cis-undecaprenyl phosphate + UDP-4-deoxy-4-formamido-beta-L-arabinose = 4-deoxy-4-formamido-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + UDP Glycolipid biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate from UDP-4-deoxy-4-formamido-beta-L-arabinose and undecaprenyl phosphate: step 1/2. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the glycosyltransferase 2 family. +Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA. acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate Acetylated. Deacetylation by the SIR2-homolog deacetylase activates the enzyme. Belongs to the ATP-dependent AMP-binding enzyme family. +Catalyzes the strictly specific dephosphorylation of 2'-deoxyribonucleoside 5'-monophosphates. a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-deoxyribonucleoside + phosphate Homodimer. Belongs to the 5DNU family. +Hydrolysis of 6-phosphogluconolactone to 6-phosphogluconate. 6-phospho-D-glucono-1,5-lactone + H2O = 6-phospho-D-gluconate + H(+) Carbohydrate degradation; pentose phosphate pathway; D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 2/3. Belongs to the glucosamine/galactosamine-6-phosphate isomerase family. 6-phosphogluconolactonase subfamily. +Belongs to the bacterial ribosomal protein bL36 family. +Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. Alpha-5 may be the major laminin alpha chain of adult epithelial and/or endothelial basal laminae. Laminin is a complex glycoprotein, consisting of three different polypeptide chains (alpha, beta, gamma), which are bound to each other by disulfide bonds into a cross-shaped molecule comprising one long and three short arms with globules at each end. Alpha-5 is a subunit of laminin-10 (laminin-511), laminin-11 (laminin-521) and laminin-15 (laminin-523). Major component. In adult, high levels in heart, lung, and kidney; lower in brain, muscle and testis; very low in liver, gut and skin. Expressed in many tissues in embryonic day 11. The alpha-helical domains I and II are thought to interact with other laminin chains to form a coiled coil structure. Domains VI, IV and G are globular. +Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins. Interacts with the Sec translocase complex via SecD. Specifically interacts with transmembrane segments of nascent integral membrane proteins during membrane integration. Belongs to the OXA1/ALB3/YidC family. Type 1 subfamily. +Low-affinity glucose transporter. HXT1 is as well involved in the transport of mannose. Expression is maximal during lag and early exponential phases of growth, decreasing upon further entry into exponential growth. Repressed at high glucose concentrations. Glucose transport is thought to be mediated by two kinetically distinct systems, a glucose-repressible high-affinity system and a constitutive low-affinity system. Present with 23300 molecules/cell in log phase SD medium. Belongs to the major facilitator superfamily. Sugar transporter (TC 2.A.1.1) family. +Major component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Requires SYCP1 in order to be incorporated into the central element. May have a role in the synaptonemal complex assembly, stabilization and recombination (By similarity). Homodimer. Found in a complex with SYCP1 and SYCE1. Interacts with SYCP1, SYCE1 and SYCE3 (By similarity). Interacts with TEX12 (By similarity). Associates with chromatin. In prophase I stage of meiosis, localizes in the transverse central elements of the central region between lateral elements of the synaptonemal complexes. Found only where the chromosome cores are synapsed. Colocalizes with SYCE1 in the central elements (By similarity). Belongs to the SYCE family. +Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS. [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + a uridine in tRNA + ATP + H(+) + 2 reduced [2Fe-2S]-[ferredoxin] = [ThiI sulfur-carrier protein]-L-cysteine + a 4-thiouridine in tRNA + AMP + diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] [sulfur-carrier protein ThiS]-C-terminal Gly-Gly-AMP + AH2 + S-sulfanyl-L-cysteinyl-[cysteine desulfurase] = [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH + A + AMP + H(+) + L-cysteinyl-[cysteine desulfurase] Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiI family. +Catalyzes the hydrolysis of N-formyl-L-kynurenine to L-kynurenine, the second step in the kynurenine pathway of tryptophan degradation. H2O + N-formyl-L-kynurenine = formate + H(+) + L-kynurenine Binds 2 zinc ions per subunit. kcat is 50.56 sec(-1) for N-formyl-L-kynurenine as substrate. Amino-acid degradation; L-tryptophan degradation via kynurenine pathway; L-kynurenine from L-tryptophan: step 2/2. Homodimer. Belongs to the Cyclase 1 superfamily. KynB family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Catalyzes the covalent attachment of ubiquitin to other proteins. Plays a role in transcription regulation by catalyzing the monoubiquitination of histone H2B to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation and is also a prerequisite for H3K4me and H3K79me formation. Also involved in postreplication repair of UV-damaged DNA, in N-end rule-dependent protein degradation and in sporulation. S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine. Protein modification; protein ubiquitination. Belongs to the ubiquitin-conjugating enzyme family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the synthesis of IGP and AICAR. The resulting ammonia molecule is channeled to the active site of HisF. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate H2O + L-glutamine = L-glutamate + NH4(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP). (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate Cofactor biosynthesis; molybdopterin biosynthesis. Homohexamer; trimer of dimers. Belongs to the MoaC family. +Binds directly to 23S rRNA. Probably involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of its operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be a menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine. L-leucyl-tRNA(Leu) + N-terminal L-lysyl-[protein] = H(+) + N-terminal L-leucyl-L-lysyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-arginyl-[protein] = H(+) + N-terminal L-leucyl-L-arginyl-[protein] + tRNA(Leu) an N-terminal L-alpha-aminoacyl-[protein] + L-phenylalanyl-tRNA(Phe) = an N-terminal L-phenylalanyl-L-alpha-aminoacyl-[protein] + tRNA(Phe) Belongs to the L/F-transferase family. +Belongs to the slowmo family. +Belongs to the G-protein coupled receptor 1 family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA. Forms a complex with SecD. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved. Belongs to the SecD/SecF family. SecF subfamily. +Member of the two-component regulatory system FleS/FleR that regulates the expression of multiple genes involved in flagellar synthesis, adhesion, swarming, motility and antibiotic resistance (PubMed:7591148, PubMed:30877999, PubMed:8876537). May function as a transcriptional activator by direct binding to a cis-acting sequence upstream of the target genes (Probable). Deletion leads to loss of motility due to the absence of flagella as well as swimming defect (PubMed:7591148, PubMed:30877999). In addition, mutant possessing pili adheres poorly to mucins (PubMed:8876537). +Belongs to the phospholipase D family. In contrast to other members of the family, it lacks the conserved active sites, suggesting that it has no phospholipase activity. +Required for exine pattern formation during pollen development, especially for primexine deposition. Mostly expressed in buds, and, to a lower extent, in leaves, roots and seedlings. Male sterile. Defective pollen wall pattern formation at early tetrad stage; delayed and reduced primexine deposition, as well as abnormal rippling of the plasma membrane and no production of spacers. Random sporopollenin deposition on the plasma membrane along the microspore wall. +Expressed by the venom duct. The cysteine framework is VI/VII (C-C-CC-C-C). Has the PXY motif between the first and the second Cys residues. Contains 3 disulfide bonds. +Involved in lipopolysaccharide (LPS) biosynthesis. Catalyzes the transfer of two 3-deoxy-D-manno-octulosonate (Kdo) residues from CMP-Kdo to lipid IV(A), the tetraacyldisaccharide-1,4'-bisphosphate precursor of lipid A. CMP-3-deoxy-beta-D-manno-octulosonate + lipid IVA (E. coli) = alpha-Kdo-(2->6)-lipid IVA + CMP + H(+) alpha-Kdo-(2->6)-lipid IVA + CMP-3-deoxy-beta-D-manno-octulosonate = alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-lipid IVA + CMP + H(+) Catalytic activity is inhibited by the antibiotic polymixin B and by Re endotoxin. Optimum pH is 7. Glycolipid biosynthesis; KDO(2)-lipid A biosynthesis; KDO(2)-lipid A from CMP-3-deoxy-D-manno-octulosonate and lipid IV(A): step 1/4. Glycolipid biosynthesis; KDO(2)-lipid A biosynthesis; KDO(2)-lipid A from CMP-3-deoxy-D-manno-octulosonate and lipid IV(A): step 2/4. Bacterial outer membrane biogenesis; LPS core biosynthesis. The N-terminal half of KdtA is responsible for determining the number of Kdo residues that are transferred to lipid IVA. Degraded by the protease FtsH; therefore FtsH regulates the addition of the sugar moiety to the LPS and thus the maturation of the LPS precursor. Cells lacking this gene display growth defects, absence of Kdo transferase activity, and accumulate massive amounts of lipid IV(A). Belongs to the glycosyltransferase group 1 family. Glycosyltransferase 30 subfamily. +May play some role in mitochondrial processes. Belongs to the OPA3 family. +Its target is unknown, but this toxin may modulate voltage-activated calcium channels (Cav) or calcium-dependent potassium channels (KCa). Expressed by the venom duct. The cysteine framework is C-C. Exists in two forms, due to cis-trans isomerization at 4-Cys-hydroxyPro-5. The cis conformation is the major form. Belongs to the O2 superfamily. Contryphan family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Specifically inactivates macrolides via 2'-O-glycosylation using UDP-glucose. Belongs to the UDP-glycosyltransferase family. +Self assembles to form an icosahedral capsid. Most capsids appear to be large particles with an icosahedral symmetry of T=4 and consist of 240 copies of capsid protein, though a fraction forms smaller T=3 particles consisting of 180 capsid proteins. Entering capsids are transported along microtubules to the nucleus. Phosphorylation of the capsid is thought to induce exposure of nuclear localization signal in the C-terminal portion of the capsid protein that allows binding to the nuclear pore complex via the importin (karyopherin-) alpha and beta. Capsids are imported in intact form through the nuclear pore into the nuclear basket, where it probably binds NUP153. Only capsids that contain the mature viral genome can release the viral DNA and capsid protein into the nucleoplasm. Immature capsids get stuck in the basket. Capsids encapsulate the pre-genomic RNA and the P protein. Pre-genomic RNA is reverse-transcribed into DNA while the capsid is still in the cytoplasm. The capsid can then either be directed to the nucleus, providing more genomes for transcription, or bud through the endoplasmic reticulum to provide new virions. Homodimerizes, then multimerizes. Interacts with cytosol exposed regions of viral L glycoprotein present in the reticulum-to-Golgi compartment. Interacts with human FLNB. Phosphorylated form interacts with host importin alpha; this interaction depends on the exposure of the NLS, which itself depends upon genome maturation and/or phosphorylation of the capsid protein. Interacts with host NUP153. Phosphorylated by host SRPK1, SRPK2, and maybe protein kinase C or GAPDH. Phosphorylation is critical for pregenomic RNA packaging. Protein kinase C phosphorylation is stimulated by HBx protein and may play a role in transport of the viral genome to the nucleus at the late step during the viral replication cycle. Belongs to the orthohepadnavirus core antigen family. +Part of an energy-coupled inorganic carbon pump. Forms a complex with DabA. Belongs to the inorganic carbon transporter (TC 9.A.2) DabB family. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]CCGAC-3'. Binding to the C-repeat/DRE element mediates high salinity- and dehydration-inducible transcription (By similarity). Belongs to the AP2/ERF transcription factor family. ERF subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. Binds 1 lipoyl cofactor covalently. The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvH family. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +Component of the autophagy machinery that is recruited to phosphatidylinositols on preautophagosomal structures, which are early autophagic structures, to promote autophagosome formation, and the subsequent degradation and clearance of engulfed apoptotic cells and P-granules in somatic cells (PubMed:12958363, PubMed:19167332, PubMed:21183797, PubMed:21802374, PubMed:22451698, PubMed:25124690, PubMed:28557996). In particular, binds with high affinity to phosphatidylinositols including phosphatidylinositol 3-phosphate (PtdIns(3)P), phosphatidylinositol 4-phosphate (PtdIns(4)P), and phosphatidylinositol 5-phosphate (PtdIns(5)P), and more weakly to phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) (PubMed:21802374, PubMed:22451698). Plays a role in mitophagy, which is the autophagic consumption of mitochondria, in response to dietary restriction (PubMed:30133321). Involved in xenophagy, the autophagy-mediated degradation of pathogens and pathogen products, such as toxins (PubMed:27875098). Also plays a role in membrane-pore repair (PubMed:27875098). In a daf-18/PTEN- and daf-16/FOXO-dependent manner, required for the proliferation of germ stem cell progenitors in the gonad during the late phases of larval development (PubMed:28285998). By regulating the release of neurotransmitters and neuropeptides, involved in the control of lifespan in response to dietary restriction and daf-2 signaling (PubMed:28557996). Probably through its involvement in autophagy, required for dauer formation (PubMed:12958363). Partially localizes to the phagosome membrane of engulfed apoptotic cells. Expressed in neurons and intestinal cells. The L/FRRG motif is required for recruitment to phosphatidylinositols including phosphatidylinositol 3-phosphate (PtdIns(3)P), phosphatidylinositol 4-phosphate (PtdIns(4)P), phosphatidylinositol 5-phosphate (PtdIns(5)P), and phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). RNAi-mediated knockdown results in defective clearance of engulfed apoptotic cells (PubMed:21183797). RNAi-mediated knockdown reduces autophagic degradation of membrane pore-forming toxin Cry5B (PubMed:27875098). RNAi-mediated knockdown results in reduced germ stem cell proliferation during larval development (PubMed:28285998). RNAi-mediated knockdown causes abnormalities in constitutive dauer formation in daf-2 e1370 mutant including a lack of autophagosome formation (PubMed:12958363). Belongs to the WD repeat PROPPIN family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity (By similarity). Belongs to the universal ribosomal protein uS4 family. +Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. Interacts with H3K4me3 and to a lesser extent with H3K4me2. The PHD-type zinc finger mediates the binding to H3K4me3. Belongs to the Alfin family. Truncated N-terminus. Truncated N-terminus. +H(+) + NADP(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADPH + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Homodimer. Belongs to the ferredoxin--NADP reductase type 2 family. +Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with mlh1 to form MutL alpha. DNA repair is initiated by MutS alpha (msh2-msh6) or MutS beta (msh2-msh3) binding to a dsDNA mismatch, then MutL alpha is recruited to the heteroduplex. Assembly of the MutL-MutS-heteroduplex ternary complex in presence of rfc and pcna is sufficient to activate endonuclease activity of pms1. It introduces single-strand breaks near the mismatch and thus generates new entry points for the exonuclease exo1 to degrade the strand containing the mismatch (By similarity). Heterodimer of pms1 and mlh1 (MutL alpha). Forms a ternary complex with MutS alpha (msh2-msh6) or MutS beta (msh2-msh3) (By similarity). Belongs to the DNA mismatch repair MutL/HexB family. +Putative transcription factor involved in pancreas development and function. Expressed in lymphoid and pancreatic tissues. The disease is caused by variants affecting the gene represented in this entry. +Catalyzes oxidation of L-threonate to 2-oxo-tetronate. Can use either NAD(+) or NADP(+) as cosubstrate, with a preference for NAD(+). L-threonate + NAD(+) = 2-dehydro-L-erythronate + H(+) + NADH kcat is 28 sec(-1) with NAD(+) as cosubstrate. kcat is 3.5 sec(-1) with NADP(+) as cosubstrate. Belongs to the HIBADH-related family. L-threonate dehydrogenase subfamily. +Probably part of the PhnSTUV complex (TC 3.A.1.11.5) involved in 2-aminoethylphosphonate import. Probably responsible for the translocation of the substrate across the membrane. Induced when inorganic phosphate is limiting; this is controlled by PhoB. Maps to a phosphate-starvation-inducible locus previously known as psiC. Belongs to the binding-protein-dependent transport system permease family. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +Removes 5-oxoproline from various penultimate amino acid residues except L-proline. Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro. Homotetramer. Belongs to the peptidase C15 family. +Calsequestrin is a high-capacity, moderate affinity, calcium-binding protein and thus acts as an internal calcium store in muscle (PubMed:28895244). Calcium ions are bound by clusters of acidic residues at the protein surface, often at the interface between subunits. Can bind around 80 Ca(2+) ions (PubMed:28895244). Regulates the release of lumenal Ca(2+) via the calcium release channel RYR1; this plays an important role in triggering muscle contraction. Negatively regulates store-operated Ca(2+) entry (SOCE) activity (PubMed:27185316). Monomer; increases in response to a depletion of intracellular calcium (PubMed:27185316, PubMed:26136523). Homodimer (PubMed:27185316, PubMed:26136523, PubMed:28895244). Homotetramer and homopolymer. Can form linear homooligomers. Ca(2+) ions promote oligomerization. Interacts (via C-terminal end and preferentially with the monomeric form) with STIM1; this interaction increases in response to a depletion of intracellular calcium, decreases both STIM1 aggregation and clustering, interaction of STIM1 with ORAI1 and store-operated Ca(2+) entry (SOCE) activity (PubMed:27185316). Interacts with ASPH and TRDN (By similarity). This isoform of calsequestrin occurs in the sarcoplasmic reticulum's terminal cisternae luminal spaces of fast skeletal muscle cells. Preferentially forms linear and round aggregates in the endoplasmic reticulum (ER) of resting cells (PubMed:28895244). In a minority of cells, homogeneously detected in the ER lumen (PubMed:28895244). Colocalizes with STIM1 at endoplasmic reticulum in response to a depletion of intracellular calcium (PubMed:27185316). Expressed in myoblasts (at protein level). N-glycosylated. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the calsequestrin family. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. Calsequestrin entry +Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids. acetyl-CoA + H(+) + malonyl-[ACP] = 3-oxobutanoyl-[ACP] + CO2 + CoA Lipid metabolism; fatty acid biosynthesis. Homodimer. The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH. Belongs to the thiolase-like superfamily. FabH family. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Belongs to the UPF0227 family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Tetramer of two alpha and two beta subunits. Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 2 subfamily. +Necessary for the introduction of cis unsaturation into fatty acids. Catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to E-(2)-decenoyl-ACP and then its isomerization to Z-(3)-decenoyl-ACP. Can catalyze the dehydratase reaction for beta-hydroxyacyl-ACPs with saturated chain lengths up to 16:0, being most active on intermediate chain length. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O (3R)-hydroxydecanoyl-[ACP] = (2E)-decenoyl-[ACP] + H2O (2E)-decenoyl-[ACP] = (3Z)-decenoyl-[ACP] Lipid metabolism; fatty acid biosynthesis. Homodimer. Belongs to the thioester dehydratase family. FabA subfamily. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 4L family. +Specifically methylates the guanine in position 1835 (m2G1835) of 23S rRNA. guanosine(1835) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(2)-methylguanosine(1835) in 23S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RlmG family. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +Golgi-localized palmitoyltransferase that catalyzes the addition of palmitate onto various protein substrates (PubMed:19001095, PubMed:21926431, PubMed:22240897, PubMed:23034182, PubMed:22314500). Has no stringent fatty acid selectivity and in addition to palmitate can also transfer onto target proteins myristate from tetradecanoyl-CoA and stearate from octadecanoyl-CoA (By similarity). Plays an important role in G protein-coupled receptor signaling pathways involving GNAQ and potentially other heterotrimeric G proteins by regulating their dynamic association with the plasma membrane (PubMed:19001095). Palmitoylates ITGA6 and ITGB4, thereby regulating the alpha-6/beta-4 integrin localization, expression and function in cell adhesion to laminin (PubMed:22314500). Plays a role in the TRAIL-activated apoptotic signaling pathway most probably through the palmitoylation and localization to the plasma membrane of TNFRSF10A (PubMed:22240897). In the brain, by palmitoylating the gamma subunit GABRG2 of GABA(A) receptors and regulating their postsynaptic accumulation, plays a role in synaptic GABAergic inhibitory function and GABAergic innervation. Palmitoylates the neuronal protein GAP43 which is also involved in the formation of GABAergic synapses. Palmitoylates NCDN thereby regulating its association with endosome membranes. Probably palmitoylates PRCD and is involved in its proper localization within the photoreceptor. Could mediate the palmitoylation of NCAM1 and regulate neurite outgrowth. Could palmitoylate DNAJC5 and regulate its localization to Golgi membranes. Also constitutively palmitoylates DLG4. May also palmitoylate SNAP25. Could palmitoylate the glutamate receptors GRIA1 and GRIA2 but this has not been confirmed in vivo (By similarity). Could also palmitoylate the D(2) dopamine receptor DRD2 (PubMed:26535572). May also function as a calcium transporter. hexadecanoyl-CoA + L-cysteinyl-[protein] = CoA + S-hexadecanoyl-L-cysteinyl-[protein] L-cysteinyl-[protein] + tetradecanoyl-CoA = CoA + S-tetradecanoyl-L-cysteinyl-[protein] L-cysteinyl-[protein] + octadecanoyl-CoA = CoA + S-octadecanoyl-L-cysteinyl-[protein] Monomer. Homooligomers. The monomeric form has a higher catalytic activity. Forms heterooligomers with ZDHHC7 (By similarity). Interacts with TNFRSF10A (PubMed:22240897). Localizes to the Golgi cis cisterna. Widely expressed with significant expression in heart, lung, liver, skeletal muscle, kidney, testis, thymus, small intestine and leukocyte. The DHHC domain is required for palmitoyltransferase activity. Autopalmitoylated. Phosphorylation by FGFR1 and SRC probably regulates the palmitoyltransferase activity. Belongs to the DHHC palmitoyltransferase family. +Involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a '216-Asp-|-Gly-217' bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop-helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9. Triggers cell adhesion in sympathetic neurons through RET cleavage (By similarity). Cleaves IL-1 beta between an Asp and an Ala, releasing the mature cytokine which is involved in a variety of inflammatory processes (By similarity). Cleaves and inhibits serine/threonine-protein kinase AKT1 in response to oxidative stress. Acts as an inhibitor of type I interferon production during virus-induced apoptosis by mediating cleavage of antiviral proteins CGAS, IRF3 and MAVS, thereby preventing cytokine overproduction. Cleaves XRCC4 and phospholipid scramblase proteins XKR4, XKR8 and XKR9, leading to promote phosphatidylserine exposure on apoptotic cell surface (By similarity). Strict requirement for an Asp residue at positions P1 and P4. It has a preferred cleavage sequence of Asp-Xaa-Xaa-Asp-|- with a hydrophobic amino-acid residue at P2 and a hydrophilic amino-acid residue at P3, although Val or Ala are also accepted at this position. Heterotetramer that consists of two anti-parallel arranged heterodimers, each one formed by a 17 kDa (p17) and a 12 kDa (p12) subunit. Interacts with BIRC6/bruce. Cleavage by granzyme B, caspase-6, caspase-8 and caspase-10 generates the two active subunits. Additional processing of the propeptides is likely due to the autocatalytic activity of the activated protease. Active heterodimers between the small subunit of caspase-7 protease and the large subunit of caspase-3 also occur and vice versa (By similarity). S-nitrosylated on its catalytic site cysteine in unstimulated human cell lines and denitrosylated upon activation of the Fas apoptotic pathway, associated with an increase in intracellular caspase activity. Fas therefore activates caspase-3 not only by inducing the cleavage of the caspase zymogen to its active subunits, but also by stimulating the denitrosylation of its active site thiol (By similarity). Belongs to the peptidase C14A family. +Shows cytolytic activity on many different cells by forming pore in lipid membranes. In vivo, increases heart rate or kills the animal by cardiac arrest. In addition, it binds to heparin with high affinity, interacts with Kv channel-interacting protein 1 (KCNIP1) in a calcium-independent manner, and binds to integrin alpha-V/beta-3 (ITGAV/ITGB3) with moderate affinity. Monomer in solution; Homodimer and oligomer in the presence of negatively charged lipids forming a pore with a size ranging between 20 and 30 Angstroms. Expressed by the venom gland. LD(50) is 2.61 mg/kg by subcutaneous injection. Is classified as a P-type cytotoxin, since a proline residue stands at position 30 (Pro-31 in standard classification). Belongs to the snake three-finger toxin family. Short-chain subfamily. Type IA cytotoxin sub-subfamily. +Part of the nuclear pore complex (NPC). The NPC has an eight-fold symmetrical structure comprising a central transport channel and two rings, the cytoplasmic and nuclear rings, to which eight filaments are attached. The cytoplasmic filaments have loose ends, while the nuclear filaments are joined in a distal ring, forming a nuclear basket. NPCs are highly dynamic in configuration and composition, and can be devided in 3 subcomplexes, the NUP62 subcomplex, the NUP107-160 subcomplex and the NUP93 subcomplex, containing approximately 30 different nucleoporin proteins. Interacts with DDB1A. The DWD box is required for interaction with DDB1A. Belongs to the WD repeat rae1 family. +Cleaves proteins, imported into the mitochondrion, to their mature size. While most mitochondrial precursor proteins are processed to the mature form in one step by mitochondrial processing peptidase (MPP), the sequential cleavage by MIP of an octapeptide after initial processing by MPP is a required step for a subgroup of nuclear-encoded precursor proteins destined for the matrix or the inner membrane (By similarity). Release of an N-terminal octapeptide as second stage of processing of some proteins imported into the mitochondrion. Binds 1 zinc ion. Belongs to the peptidase M3 family. Truncated N-terminus. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +Catalyzes the transfer of acetyl from acetyl-CoA to desacetylmycothiol (Cys-GlcN-Ins) to form mycothiol. 1D-myo-inositol 2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranoside + acetyl-CoA = CoA + H(+) + mycothiol Monomer. Belongs to the acetyltransferase family. MshD subfamily. +Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. 2 H(+) + 2 superoxide = H2O2 + O2 Binds 1 Mn(2+) ion per subunit. Homotetramer. Belongs to the iron/manganese superoxide dismutase family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The enzyme II complex composed of SrlA, SrlB and SrlE is involved in glucitol/sorbitol transport. D-sorbitol(out) + N(pros)-phospho-L-histidyl-[protein] = D-sorbitol 6-phosphate(in) + L-histidyl-[protein] Activated by sorbitol and repressed by glucose. The EIIB domain is phosphorylated by phospho-EIIA on a cysteinyl or histidyl residue, depending on the transported sugar. Then, it transfers the phosphoryl group to the sugar substrate concomitantly with the sugar uptake processed by the EIIC domain. +Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. [sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Monomer. Belongs to the methylthiotransferase family. MiaB subfamily. +Receptor for extracellular UDP > UTP > ATP. The activity of this receptor is mediated by G proteins which activate a phosphatidylinositol-calcium second messenger system. Belongs to the G-protein coupled receptor 1 family. +Possesses the property of inducing both aggregation of amebocytes and agglutination of erythrocytes. Secreted from amebocyte large secretory granules. Belongs to the dermatopontin family. +May be involved in vacuolar sorting and osmoregulation. Binds 2 Zn(2+) ions per subunit. Belongs to the peptidase M28 family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Involved in cell division and chromosome segregation. Belongs to the WhiA family. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids. acetyl-CoA + H(+) + malonyl-[ACP] = 3-oxobutanoyl-[ACP] + CO2 + CoA Lipid metabolism; fatty acid biosynthesis. Homodimer. The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH. Belongs to the thiolase-like superfamily. FabH family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Belongs to the peptidase S1 family. Granzyme subfamily. +Phosphorelay protein that supplies phosphate to regA or accepts phosphate from regA; depending on the relative concentration of the phosphodonor proteins. In vitro, acts as a substrate for cheA (bacterial kinase). Plays a role in the development. ypd1 (yeast) can complement rdeA defect. Expressed early in development in the form of precocious cell aggregation. Expressed at a significant level during vegetative growth and peaks at 8-16 hours of development. Even at its peak, the level of expression is low. The phosphorelay mechanism involves the sequential transfer of a phosphate group from 'Asp-212' of pde2 to His-65 of rdeA. In vitro, dephosphorylated by dokA. Final morphogenesis aberrant, rapid development (body formation accelerated), premature spore maturation and elevated levels of cAMP. PkaR and rdeA double mutants are rapidly developing and sporogenous. acaA and rdeA double mutant forms only a very small number of spores and no cAMP synthesis. +Plays an important role in the de novo pathway and in the salvage pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP (By similarity). GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Binds 2 divalent ions per subunit. Binds 1 potassium ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Homotetramer; dimer of dimers. Belongs to the AdoMet synthase family. +Antiproliferative and proapoptotic protein involved in cell stress response which acts as a dual regulator of transcription and autophagy. Acts as a positive regulator of autophagy. In response to cellular stress or activation of autophagy, relocates to autophagosomes where it interacts with autophagosome-associated proteins GABARAP, GABARAPL1/L2, MAP1LC3A/B/C and regulates autophagy. Acts as an antioxidant and plays a major role in p53/TP53-driven oxidative stress response. Possesses both a p53/TP53-independent intracellular reactive oxygen species (ROS) regulatory function and a p53/TP53-dependent transcription regulatory function. Positively regulates p53/TP53 and p73/TP73 and stimulates their capacity to induce apoptosis and regulate cell cycle. In response to double-strand DNA breaks, promotes p53/TP53 phosphorylation on 'Ser-46' and subsequent apoptosis. Acts as a tumor suppressor by inducing cell death by an autophagy and caspase-dependent mechanism. Can reduce cell migration by regulating the expression of SPARC. Interacts with p53/TP53 and HIPK2. Interacts with PRKCG, GABARAP, GABARAPL1, GABARAPL2, MAP1LC3A, MAP1LC3B AND MAP1LC3C. Shuttles between the nucleus and the cytoplasm, depending on cellular stress conditions, and re-localizes to autophagosomes on autophagy activation. Ubiquitously expressed. By adriamycin, gamma irradiation and H(2)O(2), in a p53/TP53-dependent way. At lower levels by UV irradiation. By TP73. The LC3 interacting region (LIR) motif mediates interaction with GABARAP, GABARAPL1, GABARAPL2, MAP1LC3A, MAP1LC3B and MAP1LC3C. +Catalyzes the non-heme iron(II)-dependent oxidative cleavage of 2,3-dihydroxyphenylpropionic acid and 2,3-dihydroxicinnamic acid into 2-hydroxy-6-ketononadienedioate and 2-hydroxy-6-ketononatrienedioate, respectively. 3-(2,3-dihydroxyphenyl)propanoate + O2 = (2Z,4E)-2-hydroxy-6-oxonona-2,4-dienedioate + H(+) (2E)-3-(2,3-dihydroxyphenyl)prop-2-enoate + O2 = (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-trienedioate + H(+) Aromatic compound metabolism; 3-phenylpropanoate degradation. Homotetramer. Belongs to the LigB/MhpB extradiol dioxygenase family. +Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach (Probable). Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons (PubMed:12867448, PubMed:14594828, PubMed:19578361, PubMed:21368142). Probably undergoes several conformational states in order to translocate the substrate across the membrane; keeps the substrate accessible to only 1 side of the membrane at a time by opening and closing 3 membrane-internal gates (Probable). agmatine(in) + L-arginine(out) = agmatine(out) + L-arginine(in) Optimum pH is 2.5 for Arg-Agm exchange. Homodimer; each subunit has its own individual transport capacity. By acidic conditions, a monocistronic operon (at protein level). Each subunit has 12 transmembrane (TM) helices; TM1 and TM6 are interrupted by short non-helical Gly-rich loops in the middle of their transmembrane spans. Each subunit has a central cavity which binds substrate. Loss of arginine-dependent acid resistance. No coupled transport of arginine and agmatine (PubMed:12867448, PubMed:14594828). No effect on levels of AdiA (PubMed:12867448). Belongs to the amino acid-polyamine-organocation (APC) superfamily. Basic amino acid/polyamine antiporter (APA) (TC 2.A.3.2) family. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Has no hyaluronidase activity. Expressed by the venom gland. N-glycosylated on at least two Asn residues by identical heptasaccharide units composed of Man, GlcNAc, and Fuc residues in the molar ration of 3:2:2. Causes an allergic reaction in human. Belongs to the glycosyl hydrolase 56 family. Lacks the typical Glu active site in position 111 that is replaced by a His residue, preventing the hyaluronidase activity. +Peptidoglycan hydrolase (autolysin) specifically acting on polyglycine interpeptide bridges of the cell wall peptidoglycan. Hydrolysis of the -Gly-|-Gly- bond in the pentaglycine inter-peptide link joining staphylococcal cell wall peptidoglycans. Binds 1 zinc ion per subunit. Completely inhibited by DEPC, HgCl(2), ammonium sulfate and glucosamine. Inhibited by 1,10-phenanthroline at concentrations as low as 1 mM. Glycine hydroxamate, Zn(2+), Hg(2+) and EDTA inhibit the activity at 10 mM. Sodium chloride (NaCl) and potassium chloride (KCl) inhibit protease activity at 100 mM. Optimum pH is 5-8. Thermostable at 100 degrees Celsius for 15 minutes, but loses activity at the same temperature within 30 minutes. Monomer. Repressed by MgrA. More protein is secreted in a double secG/secY2 mutant (at protein level). Belongs to the peptidase M23B family. Extended N-terminus. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Belongs to the AsmA family. +Required during biogenesis of c-type cytochromes (cytochrome c6 and cytochrome f) at the step of heme attachment. May interact with Ccs1. Belongs to the CcmF/CycK/Ccl1/NrfE/CcsA family. +Cytoplasmic and mitochondrial threonylcarbamoyl-AMP synthase required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine (PubMed:29760464, PubMed:31481669, PubMed:34545459). Catalyzes the conversion of L-threonine, HCO(3)(-)/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate (PubMed:29760464). Participates in t(6)A37 formation in cytoplasmic and mitochondrial tRNAs (PubMed:29760464). May regulate the activity of some transporters (By similarity). ATP + hydrogencarbonate + L-threonine = diphosphate + H2O + L-threonylcarbamoyladenylate Interacts with RSC1A1. A large fraction localizes in the cytoplasm, whereas a smaller fraction is imported to mitochondria. Ubiquitously expressed. The mitochondrial targeting sequence (MTS) is weak and only mediates import of a small fraction of YRDC in mitochondria. The disease is caused by variants affecting the gene represented in this entry. Belongs to the SUA5 family. +Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate. 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 6/7. Monomer. Belongs to the EPSP synthase family. +Catalyzes the formation of succinate and glyoxylate from isocitrate, a key step of the glyoxylate cycle, which operates as an anaplerotic route for replenishing the tricarboxylic acid cycle. Required for growth on ethanol or acetate, but dispensable when fermentable carbon sources are available. Acts also on 2-methylisocitrate. D-threo-isocitrate = glyoxylate + succinate (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate Carbohydrate metabolism; glyoxylate cycle; (S)-malate from isocitrate: step 1/2. Homotetramer. Belongs to the isocitrate lyase/PEP mutase superfamily. Isocitrate lyase family. +Actin-binding protein involved in motile and morphological processes. Inhibits actin polymerization, likely by sequestering G-actin. By capping the barbed ends of filaments, it also regulates motility. Seems to play an important role in clathrin-mediated endocytosis and distribution of endocytic organelles (By similarity). Interacts with G-actin; ADP-actin form and capping protein (CP). May also be able to interact with TWF2 and phosphoinositides, PI(4,5)P2. When bound to PI(4,5)P2, it is down-regulated. Interacts with ACTG1. Diffuse cytoplasmic localization with perinuclear and G-actin-rich cortical actin structures sublocalization. Also found at membrane ruffles and cell-cell contacts (By similarity). Phosphorylated on serine and threonine residues. Belongs to the actin-binding proteins ADF family. Twinfilin subfamily. Molecular embrace - Issue 73 of August 2006 +Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. May function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism. Interacts with TBP and the transcription factor IID (TFIID) complex, NR5A2, NR1H3 and PPARG. Interaction with TBP is regulated by phosphorylation. Binds NR5A1, ATF1, FOS and JUN via their conserved basic region. Binding to calmodulin is regulated by calcium and phosphorylation of the IQ motif. Also nuclear upon binding to NR5A1 and treatment of cells with TPA or forskolin. Expressed in brain, liver, lung, kidney and heart (at protein level). Ubiquitously expressed. More abundant in heart, pancreas, liver, intestine and adipose tissues. Expressed in fetal tissues. More abundant in kidney. Down-regulated by HIV-1 Tat or phorbol ester (TPA) treatment in endothelial cells (at mRNA and protein levels). The IQ motif, which is involved in calmodulin binding, overlaps with the binding domain for nuclear receptors and transcription factors. Its phosphorylation probably allows a switch between the two activities of the protein (By similarity). Phosphorylated (by PKA and PKC). +3-hydroxy-2-methylpropanoate + NAD(+) = 2-methyl-3-oxopropanoate + H(+) + NADH Amino-acid degradation; L-valine degradation. Homodimer. Detected in skin fibroblasts. Belongs to the HIBADH-related family. 3-hydroxyisobutyrate dehydrogenase subfamily. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Belongs to the bacterial ribosomal protein bL33 family. +Acts in the modification of cell walls via demethylesterification of cell wall pectin. [(1->4)-alpha-D-galacturonosyl methyl ester](n) + n H2O = [(1->4)-alpha-D-galacturonosyl](n) + n H(+) + n methanol Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-gluconate from pectin: step 1/5. Expressed in flower buds. The PMEI region may act as an autoinhibitory domain and prevent untimely PME activity during transport. In the N-terminal section; belongs to the PMEI family. In the C-terminal section; belongs to the pectinesterase family. +Involved in the activation cascade of caspases responsible for apoptosis execution. Recruited to both Fas- and TNFR-1 receptors in a FADD dependent manner. May participate in the granzyme B apoptotic pathways. Cleaves and activates caspase-3, -4, -6, -7, -8, and -9. Hydrolyzes the small- molecule substrates, Tyr-Val-Ala-Asp-|-AMC and Asp-Glu-Val-Asp-|-AMC. Isoform 7 can enhance NF-kappaB activity but promotes only slight apoptosis. Isoform C is proteolytically inactive. Strict requirement for Asp at position P1 and has a preferred cleavage sequence of Leu-Gln-Thr-Asp-|-Gly. Heterotetramer that consists of two anti-parallel arranged heterodimers, each one formed by a 23/17 kDa (p23/17) (depending on the splicing events) and a 12 kDa (p12) subunit (By similarity). Self-associates. Interacts with FADD and CASP8. Found in a Fas signaling complex consisting of FAS, FADD, CASP8 and CASP10. Interacts with RFFL and RNF34; negatively regulate CASP10 through proteasomal degradation. Interacts with RIOK3. Detectable in most tissues. Lowest expression is seen in brain, kidney, prostate, testis and colon. Cleavage by granzyme B and autocatalytic activity generate the two active subunits. The disease is caused by variants affecting the gene represented in this entry. The gene represented in this entry is involved in disease pathogenesis. The gene represented in this entry is involved in disease pathogenesis. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the peptidase C14A family. CASP10 mutation db Caspase-10 mutations causing ALPS type II +With CysD forms the ATP sulfurylase (ATPS) that catalyzes the adenylation of sulfate producing adenosine 5'-phosphosulfate (APS) and diphosphate, the first enzymatic step in sulfur assimilation pathway. APS synthesis involves the formation of a high-energy phosphoric-sulfuric acid anhydride bond driven by GTP hydrolysis by CysN coupled to ATP hydrolysis by CysD. ATP + H(+) + sulfate = adenosine 5'-phosphosulfate + diphosphate Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 1/3. Heterodimer composed of CysD, the smaller subunit, and CysN. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. CysN/NodQ subfamily. +Possesses antifungal activity. Seed specific. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the AMP family. +Catalyzes the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH 5,10-methenyltetrahydrofolate + H2O = (6S)-10-formyltetrahydrofolate + H(+) One-carbon metabolism; tetrahydrofolate interconversion. Homodimer. Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +Belongs to the bacterial ribosomal protein bL35 family. +Na(+)/H(+) antiporter that extrudes sodium in exchange for external protons. 2 H(+)(out) + Na(+)(in) = 2 H(+)(in) + Na(+)(out) Belongs to the NhaA Na(+)/H(+) (TC 2.A.33) antiporter family. +Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. The kidney P-450 system is rather specialized for the omega-hydroxylation of fatty acids. Both P450-KA1 and P450-KA2 catalyze the omega- and (omega-1)-hydroxylation of various fatty acids with no drug-metabolizing activity, and hydroxylate prostaglandin A1 and A2 solely at the omega-position. an omega-methyl-long-chain fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy-long-chain fatty acid + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Liver, kidney, small intestine. P450 can be induced to high levels in liver and other tissues by various foreign compounds, including drugs, pesticides, and carcinogens. Belongs to the cytochrome P450 family. +Catalyzes the reversible interconversion of fructoselysine with its C-3 epimer, psicoselysine. Allows E.coli to utilize psicoselysine for growth. Does not act on psicose or fructoselysine 6-phosphate. N(6)-(D-psicosyl)-L-lysine = N(6)-(D-fructosyl)-L-lysine Can use Ni(2+) or Co(2+) in vitro, and, to a lesser extent, Fe(2+) or Mn(2+), but not Ca(2+) or Cu(2+). Inhibited by Zn(2+). Homooctamer. Induced by psicoselysine. Makes part of the frl operon with FrlA, FrlB, FrlD and FrlR. Belongs to the FrlC family. +Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Belongs to the OXA1/ALB3/YidC family. Type 2 subfamily. +Thick filament-associated protein located in the crossbridge region of vertebrate striated muscle a bands. In vitro it binds MHC, F-actin and native thin filaments, and modifies the activity of actin-activated myosin ATPase. It may modulate muscle contraction or may play a more structural role (By similarity). Heart. Expression begins between stage 30 and 35/36 in the heart and at stages 35-41 in skeletal muscles. Level of expression in the juvenile skeletal muscle is significantly lower compared to embryonic skeletal muscle. Belongs to the immunoglobulin superfamily. MyBP family. +Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatE shares overlapping functions with TatA. Belongs to the TatA/E family. TatE subfamily. +Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. 3 H2O + hydrogen sulfide + 3 NADP(+) = 4 H(+) + 3 NADPH + sulfite Binds 1 siroheme per subunit. Binds 1 [4Fe-4S] cluster per subunit. Sulfur metabolism; hydrogen sulfide biosynthesis; hydrogen sulfide from sulfite (NADPH route): step 1/1. Alpha(8)-beta(8). The alpha component is a flavoprotein, the beta component is a hemoprotein. Belongs to the nitrite and sulfite reductase 4Fe-4S domain family. +Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA. a fatty acyl-[ACP] + phosphate = an acyl phosphate + holo-[ACP] Lipid metabolism; phospholipid metabolism. Homodimer. Probably interacts with PlsY. Associated with the membrane possibly through PlsY. Belongs to the PlsX family. +eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. Heterotrimer composed of an alpha, a beta and a gamma chain. Belongs to the eIF-2-beta/eIF-5 family. +Key negative regulator of Shh signaling, which promotes the processing of GLI3 into GLI3R during neural tube development. Recruited by TULP3 and the IFT-A complex to primary cilia and acts as a regulator of the PKA-dependent basal repression machinery in Shh signaling by increasing cAMP levels, leading to promote the PKA-dependent processing of GLI3 into GLI3R and repress the Shh signaling. In presence of SHH, it is removed from primary cilia and is internalized into recycling endosomes, preventing its activity and allowing activation of the Shh signaling. Its ligand is unknown (By similarity). Mainly localizes to primary cilium in a TULP3 and IFT-A complex-dependent manner. In presence of SHH, it is removed from primary cilia and is internalized into recycling endosomes and is apparently not degraded (By similarity). Belongs to the G-protein coupled receptor 1 family. +Transcription activator that recognizes two different DNA motifs: the CCAAT homology common to many promoters and the enhanced core homology common to many enhancers (PubMed:16397300). Important transcription factor regulating the expression of genes involved in immune and inflammatory responses (PubMed:1741402, PubMed:16397300). Transcriptional activator that enhances IL6 transcription alone and as heterodimer with CEBPB (PubMed:1741402). Binds DNA as a homodimer and as a heterodimer (PubMed:1741402). Can form stable heterodimers with CEBPB (PubMed:1741402). Can form stable heterodimers with CEBPA and CEBPE. Interacts with SPI1/PU.1. Interacts with PRDM16. Belongs to the bZIP family. C/EBP subfamily. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +Cytochrome P450 monooxygenase; part of the gene cluster that mediates the biosynthesis of pneumocandins, lipohexapeptides of the echinocandin family that prevent fungal cell wall formation by non-competitive inhibition of beta-1,3-glucan synthase (PubMed:27705900). The 10,12-dimethylmyristoyl side chain is synthesized by the reducing polyketide synthase gloL/GLPKS4 (PubMed:27494047). The thioesterase gloN/GLHYD exclusively interacts with gloL/GLPKS4 to maintain turnover of the polyketide side chain (PubMed:27494047). The 10R,12S-dimethylmyristic acid is then transferred to the first thiolation domain of the nonribosomal peptide synthetase gloA/GLNRPS4 by the acyl-AMP ligase gloD/GLligase, followed by its acylation to L-ornithine to trigger elongation of the cyclic hexapeptide (PubMed:27494047). L-ornithine, 4R-hydroxyl-L-proline (generated from L-proline by the dioxygenase gloF/GLOXY2), 3S-hydroxyl-L-homotyrosine (generated by gloG/GLHtyB, gloH/GLHtyA, gloI/GLHtyC, gloJ/GLHtyD and hydroxylated at C-3 by the dioxygenase gloM/GLOXY1), 3R-hydroxyl-L-glutamine (generated from L-glutamine probably by the dioxygenase gloE/GLOXY3) and 3S-hydroxyl-L-proline (generated from L-proline by the dioxygenase gloF/GLOXY2 to yield pneumocandin B0), or 3S-hydroxyl-4S-methyl-L-proline (generated from L-leucine by the dioxygenase gloC/GLOXY4 to yield pneumocandin A0) are sequentially added to the growing chain (PubMed:25270390, PubMed:25879325, PubMed:25527531). The last C domain of gloA/GLNRPS4 is proposed to be responsible for cyclization by condensation to form the peptide bond between L-ornithine and 3S-hydroxyl-4S-methyl-L-proline (for pneumocandin A0) or 3S-hydroxyl-L-proline (for pneumocandin B0). Finally, the subsequent C-4 hydroxylation of 3S-hydroxyl-L-homotyrosine and L-ornithine dihydroxylation at C-4 and C-5 are performed by the cytochrome P450 monooxygenases gloP/GLP450-1 and gloO/GLP450-2, respectively (PubMed:25879325). Mycotoxin biosynthesis. Leads to the production of pneumocandin analogs with 3S-hydroxyl-L-homotyrosine (PubMed:25879325). Pneumocandin B0 is the starting molecule for the first semisynthetic echinocandin antifungal drug, caspofungin acetate (PubMed:25527531). Pneumocandin B0 is a minor fermentation product, and its industrial production was achieved by a combination of extensive mutation and medium optimization (PubMed:25527531). Inactivation of three of gloP/GLP450-1, gloO/GLP450-2, and gloM/GLOXY1 generates 13 different pneumocandin analogs that lack one, two, three, or four hydroxyl groups on 4R,5R-dihydroxy-ornithine and 3S,4S-dihydroxy-homotyrosine of the parent hexapeptide (PubMed:25879325). All of these cyclic lipopeptides show potent antifungal activities, and two new metabolites pneumocandins F and G are more potent in vitro against Candida species and Aspergillus fumigatus than the principal fermentation products, pneumocandins A0 and B0 (PubMed:25879325). Moreover, feeding alternative side chain precursors yields acrophiarin and 4 additional pneumocandin congeners with straight C14, C15, and C16 side chains. One of those compounds, pneumocandin I, has elevated antifungal activity and similar hemolytic activity compared to pneumocandin B0, the starting molecule for caspofungin, demonstrating the potential for using gloD/GLligase for future engineering of new echinocandin analogs (PubMed:27494047). Belongs to the cytochrome P450 family. +Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling. Expressed in roots, leaf blades, leaf sheaths, shoot apex, flowers and panicles. By cytokinin in roots, shoots and leaves. Two-component system major event consists of a His-to-Asp phosphorelay between a sensor histidine kinase (HK) and a response regulator (RR). In plants, the His-to-Asp phosphorelay involves an additional intermediate named Histidine-containing phosphotransfer protein (HPt). This multistep phosphorelay consists of a His-Asp-His-Asp sequential transfer of a phosphate group between first an His and an Asp of the HK protein, followed by the transfer to a conserved His of the HPt protein and finally the transfer to an Asp in the receiver domain of the RR protein. Belongs to the ARR family. Type-A subfamily. +Component of the NOP7 complex, which is required for maturation of the 25S and 5.8S ribosomal RNAs and formation of the 60S ribosome. Component of the NOP7 complex, composed of ERB1, NOP7 and YTM1. The complex is held together by ERB1, which interacts with NOP7 via its N-terminal domain and with YTM1 via a high-affinity interaction between the seven-bladed beta-propeller domains of the 2 proteins. The NOP7 complex associates with the 66S pre-ribosome. Belongs to the WD repeat BOP1/ERB1 family. +Catalyzes the hydrolysis of the N-terminal peptide bond of an N-acetylated peptide to generate an N-acetylated amino acid and a peptide with a free N-terminus. Cleavage of an N-acetyl or N-formyl amino acid from the N-terminus of a polypeptide. Homotetramer. Belongs to the peptidase S9C family. Extended N-terminus. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL11 family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +RNA-binding protein involved in deadenylation-dependent decapping of mRNAs, leading to the degradation of mRNAs. Acts as a scaffold protein that connects deadenylation and decapping machinery. Required for cytoplasmic mRNA processing body (P-body) assembly. Interacts (via region A) with DDX6/RCK. Interacts (via region H and region C) with LSM1 and LSM4. Interacts (via region N) with DCP1A, DCP2, EDC3, EDC4 and XRN1. Interacts with the CCR4-NOT complex. Interacts with the Lsm-containing SMN-Sm protein complex. Interacts with EIF4ENIF1/4E-T. Predominantly cytoplasmic. Shuttles between the nucleus and the cytoplasm in a CRM1-dependent manner. Enriched in splicing speckles. Localization to nuclear foci and speckles requires active transcription. Excluded from the nucleolus. The region C, also named Pat-C, is required for RNA-binding and mediates the binding with the Lsm-containing SMN-Sm protein complex and the decapping machinery. It folds into an alpha-alpha superhelix, exposing conserved and basic residues on one side of the domain. Belongs to the PAT1 family. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Part of the gluconate utilization system Gnt-I; high-affinity intake of gluconate. Carbohydrate acid metabolism; D-gluconate degradation. Belongs to the GntP permease family. +Regulatory subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA and the activity is stimulated by poly(A)-binding protein PAB1. PAN deadenylation is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping and subsequent 5'-3' exonucleolytic degradation by XRN1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails. PAN3 acts as a positive regulator for PAN activity, recruiting the catalytic subunit PAN2 to mRNA via its interaction with RNA and with PAB1. Homodimer. Forms a heterotrimer with a catalytic subunit PAN2 to form the poly(A)-nuclease (PAN) deadenylation complex. Interacts (via PAM-2 motif) with poly(A)-binding protein PAB1 (via PABC domain), conferring substrate specificity of the enzyme complex. The N-terminal zinc finger binds to poly(A) RNA. Contains a pseudokinase domain. The protein kinase domain is predicted to be catalytically inactive because some of the residues important for catalytic activity are substituted and it lacks the equivalent of the binding site for a peptide substrate. However, it has retained an ATP-binding site and ATP-binding is required for mRNA degradation, stimulating the activity of the PAN2 nuclease in vitro. The nucleotide-binding site is juxtaposed to the RNase active site of PAN2 in the complex and may actually bind nucleosides of a poly(A) RNA rather than ATP, feeding the poly(A)-tail to the active site of the deadenylase and thus increasing the efficiency with which this distributive enzyme degrades oligo(A) RNAs. The pseudokinase domain, the coiled-coil (CC), and C-terminal knob domain (CK) form a structural unit (PKC) that forms an extensive high-affinity interaction surface for PAN2. Belongs to the protein kinase superfamily. PAN3 family. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Catalyzes the ATP-dependent phosphorylation of L-homoserine to L-homoserine phosphate. ATP + L-homoserine = ADP + H(+) + O-phospho-L-homoserine Amino-acid biosynthesis; L-threonine biosynthesis; L-threonine from L-aspartate: step 4/5. Belongs to the GHMP kinase family. Homoserine kinase subfamily. +Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini. Belongs to the glycosyl hydrolase 54 family. +Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. +Murein endopeptidase that cleaves the D-alanyl-meso-2,6-diamino-pimelyl amide bond that connects peptidoglycan strands. Likely plays a role in the removal of murein from the sacculus. Binds 2 Zn(2+) ions per subunit. Zn(2+) ion 1 is bound in the active site. Zn(2+) ion 2 is bound at the dimer interface by residues from both subunits. Dimer. Belongs to the peptidase M74 family. +carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family. +Belongs to the aldo/keto reductase family. +Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. ATP + NAD(+) = ADP + H(+) + NADP(+) Belongs to the NAD kinase family. +beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Binds 2 magnesium ions per subunit. Carbohydrate biosynthesis; gluconeogenesis. Homotetramer. Belongs to the FBPase class 1 family. +Catalyzes the NADH-dependent reduction of a broad spectrum of quinone substrates, generating the corresponding hydroquinones. Highly prefers NADH to NADPH as a reducing substrate. Also displays a small NADH oxidase activity. Does not exhibit nitronate monooxygenase activity; is inactive against propionate 3-nitronate, 3-nitropropionate, nitroethane, 1-nitropropane, 2-nitropropane, and the anionic forms ethylnitronate, propyl-1-nitronate, and propyl-2-nitronate. Has no azoreductase activity since it is not able to reduce the azo dye methyl red with NADH. May be required to maintain an appropriate [NAD(+)]/[NADH] ratio for the catabolism of fatty acids in P.aeruginosa PAO1. a quinone + H(+) + NADH = a quinol + NAD(+) Binds 1 FMN per subunit. kcat is 14 sec(-1) with 5,8-dihydroxy-1,4-naphthoquinone as substrate. kcat is 17 sec(-1) with 5-hydroxy-1,4-naphthoquinone as substrate. kcat is 16 sec(-1) with 2-methyl-5-hydroxy-1,4-naphthoquinone as substrate. kcat is 16 sec(-1) with 2-methyl-1,4-naphthoquinone as substrate. kcat is 6 sec(-1) with 2-methoxy-1,4-naphthoquinone as substrate. kcat is 27 sec(-1) with 1,4-benzoquinone as substrate. kcat is 24 sec(-1) with 2-methyl-5,6-dimethoxy-1,4-benzoquinone as substrate. kcat is 28 sec(-1) with 2,3,4,6-tetramethyl-1,4-benzoquinone as substrate. Monomer. The two-electron reduction of quinones by this enzyme occurs through a Ping-Pong-Bi-Bi steady-state kinetic mechanism. Belongs to the nitronate monooxygenase family. Was reported to be a 2-nitropropane dioxygenase, the previous name for nitronate monooxygenase (PubMed:16682407). However, later experiments demonstrate that this protein does not have any nitronate monooxygenase activity, the activity reported by Ha et al. was likely due to the non-enzymatic reaction of propyl-2-nitronate with oxygen (PubMed:27502282). +Part of the ABC transporter complex CysAWTP involved in sulfate/thiosulfate import. Responsible for energy coupling to the transport system. ATP + H2O + sulfate(out) = ADP + H(+) + phosphate + sulfate(in) ATP + H2O + thiosulfate(out) = ADP + H(+) + phosphate + thiosulfate(in) The complex is composed of two ATP-binding proteins (CysA), two transmembrane proteins (CysT and CysW) and a solute-binding protein (CysP). Belongs to the ABC transporter superfamily. Sulfate/tungstate importer (TC 3.A.1.6) family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. Truncated N-terminus. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate. Is involved in the anaerobic L-ascorbate utilization. L-ribulose 5-phosphate = D-xylulose 5-phosphate Binds 1 zinc ion per subunit. Cofactor degradation; L-ascorbate degradation; D-xylulose 5-phosphate from L-ascorbate: step 4/4. Induced by L-ascorbate. Repressed by UlaR. Belongs to the aldolase class II family. AraD/FucA subfamily. +Class I viral fusion protein that directs fusion of viral and host endosomal membranes, leading to delivery of the nucleocapsid into the cytoplasm. Membrane fusion is mediated by irreversible conformational changes induced upon acidification in the endosome. Stable signal peptide (SSP): cleaved and functions as a signal peptide. In addition, it is also retained as the third component of the GP complex. The SSP is required for efficient glycoprotein expression, post-translational maturation cleavage of GP1 and GP2, glycoprotein transport to the cell surface plasma membrane, formation of infectious virus particles, and acid pH-dependent glycoprotein-mediated cell fusion. Interacts with the host receptor. Homotetramer; disulfide-linked. Homotetramer. GP2 homotetramers bind through ionic interactions with GP1 homotetramers to form the GP complex together with the stable signal peptide. The GP-C polyprotein interacts with the host protease MBTPS1/SKI-1 resulting in the polyprotein processing. Binding to the stable signal peptide masks endogenous ER localization signals in the cytoplasmic domain of G2 to ensure that only the fully assembled, tripartite GP complex is transported for virion assembly. The cytoplasmic domain of GP2 plays a role in ER location. It also contains a zinc-binding domain that allows SSP retention in the GPC complex by accepting a cysteine from SSP as the fourth ligand. Specific enzymatic cleavages in vivo yield mature proteins. GP-C polyprotein is cleaved in the endoplasmic reticulum by the host protease MBTPS1. Only cleaved glycoprotein is incorporated into virions. The SSP remains stably associated with the GP complex following cleavage by signal peptidase and plays crucial roles in the trafficking of GP through the secretory pathway. Belongs to the arenaviridae GPC protein family. +Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA. a fatty acyl-[ACP] + phosphate = an acyl phosphate + holo-[ACP] Lipid metabolism; phospholipid metabolism. Homodimer. Probably interacts with PlsY. Associated with the membrane possibly through PlsY. Belongs to the PlsX family. +Probably involved in translation. Belongs to the SUI1 family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Belongs to the DMRL synthase family. +Sugar transporter involved in the transport of CMP-sialic acid from the cytoplasm into the Golgi. May transport important nucleotide sugars such as CMP-Kdo (2-keto-3-deoxy-D-manno-octulosonic acid) in physiological conditions. Belongs to the nucleotide-sugar transporter family. CMP-Sialate:CMP antiporter (TC 2.A.7.12) subfamily. +Cysteine protease that plays a key role in autophagy by mediating both proteolytic activation and delipidation of ATG8 family proteins. The protease activity is required for proteolytic activation of ATG8 family proteins: cleaves the C-terminal amino acid of ATG8 proteins to reveal a C-terminal glycine (By similarity). Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. In addition to the protease activity, also mediates delipidation of PE-conjugated ATG8 proteins (By similarity). [protein]-C-terminal L-amino acid-glycyl-phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine Interacts with ATG8. Belongs to the peptidase C54 family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Has a role in meiosis. +Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). H2O + O2 + pyridoxamine 5'-phosphate = H2O2 + NH4(+) + pyridoxal 5'-phosphate O2 + pyridoxine 5'-phosphate = H2O2 + pyridoxal 5'-phosphate Binds 1 FMN per subunit. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1. Homodimer. Belongs to the pyridoxamine 5'-phosphate oxidase family. +Transcription factor that binds to target promoter sequences and activates transcription upon il6st/gp130 stimulation. Mediates ventralization of embryos, at least in part via inhibition of smad2 signaling. Required for hairy2 to induce dll1/delta1 and promote neural crest cell proliferation and differentiation. Involved in TGFbeta-mediated mesoderm induction in early embryos, acting downstream of map3k7/tak1 and nlk.2. Forms a homodimer or a heterodimer with a related family member, such as stat1 (By similarity). Interacts with nlk.2. Shuttles between the nucleus and the cytoplasm. Constitutive nuclear presence is independent of tyrosine phosphorylation (By similarity). Expressed from the one-cell stage throughout embryogenesis (at protein level). Expressed fairly ubiquitously up to the gastrula stage, then restricted mainly to the nervous system later in development. Phosphorylation of both tyrosine and serine residues, together with dimerization, is required for mesoderm induction. Involved in the gp130-mediated signaling pathway. Belongs to the transcription factor STAT family. +Belongs to the immunoglobulin superfamily. BTN/MOG family. Product of a dubious gene prediction. +Phosphotransfer between the C1 and C5 carbon atoms of pentose. alpha-D-ribose 1-phosphate = D-ribose 5-phosphate 2-deoxy-alpha-D-ribose 1-phosphate = 2-deoxy-D-ribose 5-phosphate Binds 1 or 2 manganese ions. Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route II): step 1/3. Belongs to the phosphopentomutase family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. Probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. Involved in mitochondrial genome maintenance. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 divalent metal cation per subunit. Homodimer. Loss of QRI7 leads to the formation of mitochondria with abnormal morphology and no DNA. Present with 1400 molecules/cell in log phase SD medium. Belongs to the KAE1 / TsaD family. +Essential for recycling GMP and indirectly, cGMP. ATP + GMP = ADP + GDP Belongs to the guanylate kinase family. +Probably deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs), playing an important role in chemotaxis. H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Belongs to the CheD family. +Component of the outer dense fibers (ODF) of spermatozoa which could be involved in sperm tail structure, sperm movement and general organization of cellular cytoskeleton. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS8 family. +Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). +Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a lipid X + a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a lipid A disaccharide + H(+) + UDP Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Belongs to the LpxB family. +Required for the assembly of the rivet at the earliest stage of flagellar biosynthesis. Belongs to the FliQ/MopD/SpaQ family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Belongs to the class-II aminoacyl-tRNA synthetase family. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +May play a role in photosystem I and II biogenesis. Belongs to the PsbN family. Originally thought to be a component of PSII; based on experiments in Synechocystis, N.tabacum and barley, and its absence from PSII in T.elongatus and T.vulcanus, this is probably not true. +Regulatory subunit of the blood coagulation factor X-activating enzyme. Activates coagulation factor X (F10) by cleaving the Arg-Ile bond at position 234, activates coagulation factor IX (F9) by cleaving the Arg-Val bond at position 226 and is also able to activate protein C (PROC). May serve as an exosite by which the enzyme recognizes and binds to the Gla domain of factor X (F10) in a calcium-dependent manner. Heterotrimer; disulfide-linked. The heterotrimer consists of 1 heavy chain (a metalloproteinase) and 2 light chains: LC1 and LC2. Expressed by the venom gland. Calcium is required for ligand binding. Belongs to the snaclec family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Belongs to the DMRL synthase family. +Probable component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. May act as a co-chaperone that stimulate the ATP-dependent activity (By similarity). Probable component of the PAM complex at least composed of a mitochondrial HSP70 protein, Roe1, TIM44, blp/TIM16 and TIM14. Belongs to the TIM14 family. +Partially edited. RNA editing at this position consists of an insertion of one or two adenine nucleotides. The sequence displayed here is the super small secreted glycoprotein ssGP, derived from the +2A edited RNA. The unedited RNA gives rise to the small secreted glycoprotein sGP (AC P60171), the +1A edited RNA gives rise to the full-length transmembrane glycoprotein GP (AC P87666). Belongs to the filoviruses glycoprotein family. +Belongs to the SMIM8 family. +Essential for nitrogen assimilation, distribution and remobilization within the plant via the phloem. ATP + H2O + L-aspartate + L-glutamine = AMP + diphosphate + H(+) + L-asparagine + L-glutamate Amino-acid biosynthesis; L-asparagine biosynthesis; L-asparagine from L-aspartate (L-Gln route): step 1/1. Expressed in companion cells of leaf sheath vascular bundles, and phloem-parenchyma cells, nucellar projections and nucellar epidermis of dorsal vascular bundles of grains. +Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. (2S,6S)-2,6-diaminoheptanedioate = meso-2,6-diaminoheptanedioate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. Homodimer. Belongs to the diaminopimelate epimerase family. +Catalyzes the interconversion between glucose-6-phosphate and alpha-glucose-1-phosphate. This is the first step in the biosynthesis of diglucosyl-diacylglycerol (Glc2-DAG), i.e. the predominant glycolipid found in the S.aureus membrane, which is also used as a membrane anchor for lipoteichoic acid (LTA) (By similarity). alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate Binds 1 Mg(2+) ion per subunit. Glycolipid metabolism; diglucosyl-diacylglycerol biosynthesis. Belongs to the phosphohexose mutase family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Catalyzes, although with low efficiency, the sulfur transfer reaction from thiosulfate to cyanide. hydrogen cyanide + thiosulfate = 2 H(+) + sulfite + thiocyanate Belongs to the GlpE family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Belongs to the syntaxin family. +One of the non-neuronal predominant intermediate filament proteins of the visual pathway. Belongs to the intermediate filament family. +SUMO-specific isopeptidase involved in protein desumoylation. Specifically binds SUMO proteins with a higher affinity for SUMO2 and SUMO3 which it cleaves more efficiently. Also able to process full-length SUMO proteins to their mature forms (PubMed:22878415). Plays a key role in RNA polymerase-II-mediated snRNA transcription in the Cajal bodies (PubMed:24413172). Is a component of complexes that can bind to U snRNA genes (PubMed:24413172). Interacts with ELL. Belongs to the peptidase C19 family. +Catalyzes a salvage reaction resulting in the formation of IMP that is energically less costly than de novo synthesis. diphosphate + IMP = 5-phospho-alpha-D-ribose 1-diphosphate + hypoxanthine diphosphate + GMP = 5-phospho-alpha-D-ribose 1-diphosphate + guanine Purine metabolism; IMP biosynthesis via salvage pathway; IMP from hypoxanthine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. Archaeal HPRT subfamily. +Involved in the efflux of sugars. The physiological role may be the reduction of the intracellular concentration of toxic sugars or sugar metabolites. Belongs to the major facilitator superfamily. SotB (TC 2.A.1.2) family. +Can stimulate E2F-dependent transcription. Binds DNA cooperatively with E2F family members through the E2 recognition site, 5'-TTTC[CG]CGC-3', found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication (PubMed:8405995, PubMed:7739537). The E2F1:DP complex appears to mediate both cell proliferation and apoptosis. Blocks adipocyte differentiation by repressing CEBPA binding to its target gene promoters (PubMed:20176812). Component of the E2F:DP transcription factor complex. Forms heterodimers with E2F family members. The complex can interact with hypophosphorylated retinoblastoma protein RB1 and related proteins (RBL1 and RBL2) that inhibit the E2F transactivation domain. This repression involves recruitment of histone deacetylase (HDAC). During the cell cycle, from mid-to-late G1 phase, RB family members become phosphorylated, detach from the DRTF1/E2F complex to render E2F transcriptionally active. Viral oncoproteins, notably E1A, T-antigen and HPV E7, are capable of sequestering RB protein, thus releasing the active complex. Part of the E2F6.com-1 complex in G0 phase is composed of E2F6, MGA, MAX, TFDP1, CBX3, BAT8, EUHMTASE1, RING1, RNF2, MBLR, L3MBTL2 YAF2. Component of the DREAM complex (also named LINC complex) at least composed of E2F4, E2F5, LIN9, LIN37, LIN52, LIN54, MYBL1, MYBL2, RBL1, RBL2, RBBP4, TFDP1 and TFDP2. The complex exists in quiescent cells where it represses cell cycle-dependent genes. It dissociates in S phase when LIN9, LIN37, LIN52 and LIN54 form a subcomplex that binds to MYBL2. The complex TFDP1:E2F1 interacts with CEBPA; the interaction prevents CEBPA binding to target gene promoters and represses its transcriptional activity (PubMed:20176812). Shuttles between the cytoplasm and nucleus and translocates into the nuclear compartment upon heterodimerization with E2F1. Highest levels in muscle. Also expressed in brain, placenta, liver and kidney. Lower levels in lung and pancreas. Not detected in heart. Down-regulated during differentiation. Phosphorylation by E2F1-bound cyclin A-CDK2, in the S phase, inhibits E2F-mediated DNA binding and transactivation. Ubiquitinated by the BCR(KBTBD5) complex, leading to its subsequent degradation. E2F/DP transactivation can be mediated by several cofactors including TBP, TFIIH, MDM2 and CBP. Belongs to the E2F/DP family. +Required for streptomycin resistance (PubMed:3357770). Adenylates streptomycin on the O-6 residue (By similarity). ATP + streptomycin = 6-O-adenylylstreptomycin + diphosphate +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Part of the ABC transporter complex FbpABC involved in Fe(3+) ions import. Responsible for energy coupling to the transport system. ATP + Fe(3+)(out) + H2O = ADP + Fe(3+)(in) + H(+) + phosphate The complex is composed of two ATP-binding proteins (FbpC), two transmembrane proteins (FbpB) and a solute-binding protein (FbpA). Belongs to the ABC transporter superfamily. Fe(3+) ion importer (TC 3.A.1.10) family. +Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-terminal L-methionyl-[peptide] Binds 1 Fe(2+) ion. Belongs to the polypeptide deformylase family. +PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin. hnu + oxidized [2Fe-2S]-[ferredoxin] + reduced [plastocyanin] = oxidized [plastocyanin] + reduced [2Fe-2S]-[ferredoxin] P700 is a chlorophyll a/chlorophyll a' dimer, A0 is one or more chlorophyll a, A1 is one or both phylloquinones and FX is a shared 4Fe-4S iron-sulfur center. The PsaA/B heterodimer binds the P700 chlorophyll special pair and subsequent electron acceptors. PSI consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The eukaryotic PSI reaction center is composed of at least 11 subunits. Belongs to the PsaA/PsaB family. +Plays a major role in assembly, budding and uncoating of virion after membrane fusion. Completely covers the ribonucleoprotein coil and keep it in condensed bullet-shaped form. Inhibits viral transcription and stimulates replication. Plays a major role in early induction of TRAIL-mediated apoptosis in infected neurons. Homomultimer. Interacts with nucleoprotein and with the cytoplasmic domain of glycoprotein. Interacts with host ATP6V1A; this interaction plays an important role in virion uncoating after viral entry. Late-budding domains (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. Matrix protein contains one L domain: a PPXY motif which potentially interacts with the WW domain 3 of NEDD4 E3 ubiquitin ligase (Potential). Most abundant protein in the virion. Belongs to the lyssavirus matrix protein family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +One of the few identified sugar gustatory receptors identified so far and which promotes the starvation-induced increase of feeding motivation. Expressed in Gr5a-expressing sugar-sensing cells. Belongs to the insect chemoreceptor superfamily. Gustatory receptor (GR) family. Gr5a subfamily. +Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and/or repair of Fe-S clusters in biosynthetic enzymes. Belongs to the Fe(2+)-trafficking protein family. +JH esterase plays a crucial role in the decrease of JH activity in lepidopteran insects, by hydrolyzing the methyl ester of JH. It is also involved in the transport of JH. H2O + juvenile hormone I = H(+) + juvenile hormone I carboxylate + methanol H2O + juvenile hormone III = H(+) + juvenile hormone III carboxylate + methanol Fat body, the site of their biosynthesis, and the hemolymph where it is secreted. Belongs to the type-B carboxylesterase/lipase family. +Catalyzes the reduction of hydroxylamine to form NH(3) and H(2)O. A + H2O + NH4(+) = AH2 + H(+) + hydroxylamine Binds 1 [2Fe-2S] cluster. Binds 1 hybrid [4Fe-2O-2S] cluster. Belongs to the HCP family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +ATP-dependent RNA helicase. ATP + H2O = ADP + H(+) + phosphate Also detected in chromatoid bodies of round spermatids. An mRNA component of germ plasm. Localizes to the granulo-fibrillar material (GFM) of the mitochondrial cloud in stage I oocytes. Associated, at a low level, with the periphery of mature germinal granules in later stage oocytes. Localizes to the vegetal cortex in stage II oocytes and segregates with germ plasm during early embryogenesis. In adults, expression is restricted to the ovary and, at a lower level, to spermatogonia, spermatocytes and spermatids of the testis. Expressed at a constant level throughout oogenesis and in the egg. Levels decrease during gastrulation and are not detectable by the end of gastrulation. Belongs to the DEAD box helicase family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +RNA-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The eIF-3 complex interacts with pix. Belongs to the eIF-3 subunit A family. +Essential cell division protein that stabilizes the FtsZ protofilaments by cross-linking them and that serves as a cytoplasmic membrane anchor for the Z ring. Also required for the recruitment to the septal ring of downstream cell division proteins. Interacts with FtsZ via their C-terminal domains. Localizes to the Z ring in an FtsZ-dependent manner. Belongs to the ZipA family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (By similarity). Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Functions as actin-binding component of the Arp2/3 complex which is involved in regulation of actin polymerization and together with an activating nucleation-promoting factor (NPF) mediates the formation of branched actin networks. Seems to contact the mother actin filament (By similarity). Component of the Arp2/3 complex. Belongs to the ARPC2 family. +Belongs to the bacterial ribosomal protein bL33 family. +Belongs to the eukaryotic ribosomal protein eS4 family. +RNA chaperone with significant RNA binding, RNA strand exchange and RNA duplexing activities. May regulate ProP activity through an RNA-based, post-transcriptional mechanism. Belongs to the ProQ family. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homotetramer; dimer of dimers. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Probably participates in a plant defense mechanism (By similarity). Has cytotoxic activity against HUVEC cells (LC(50)= 2.17 uM) and various cancer cells including HeLa (LC(50)= 3.05 uM), MCF-7 and K562 (PubMed:32414842). Displays very weak hemolytic activity (PubMed:32414842). Binds to and induces leakage in phospholipd membranes, particularly ones containing 1-palmitoyl-2-oleophosphatidylethanolamine (POPE) (PubMed:32414842). Detected in stems (at protein level). The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. This is a cyclic peptide. Belongs to the cyclotide family. Bracelet subfamily. This peptide is cyclic. The start position was chosen by similarity to Oak1 (kalata B1) for which the DNA sequence is known. +Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin. di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available. Belongs to the UppP family. +Belongs to the UPF0145 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP (By similarity). Belongs to the Mediator complex subunit 31 family. +Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell. Homopentamer. Belongs to the MscL family. +Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). Belongs to the conotoxin O1 superfamily. +With CysN forms the ATP sulfurylase (ATPS) that catalyzes the adenylation of sulfate producing adenosine 5'-phosphosulfate (APS) and diphosphate, the first enzymatic step in sulfur assimilation pathway. APS synthesis involves the formation of a high-energy phosphoric-sulfuric acid anhydride bond driven by GTP hydrolysis by CysN coupled to ATP hydrolysis by CysD. ATP + H(+) + sulfate = adenosine 5'-phosphosulfate + diphosphate Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 1/3. Heterodimer composed of CysD, the smaller subunit, and CysN. Belongs to the PAPS reductase family. CysD subfamily. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Terpene cyclase/mutase; part of the gene cluster that mediates the biosynthesis of the meroterpenoids nectripenoids A and B, as well as cochliquninone D and isocochliquninone E (PubMed:29797385). The pathway probably begins with the HR-PKS ntnH that catalyzes two chain-extension steps to form a reduced triketide, which then primes the SAT domain in the NR-PKS ntnG to initiate three more cycles of extension to give a linear hexaketide corresponding to the polyketide part of nectripenoids (Probable). The FAD-dependent monooxygenase ntnJ then performs an oxidative decarboxylation at C11 of the ntnH/ntnG product, via an electrophilic aromatic hydroxylation with concomitant ipso-decarboxylation (Probable). The membrane-bound polyprenyl transferase ntnF then introduces a farnesyl group before the FAD-dependent monooxygenase ntnK functions as the first epoxidase on terminal C12'-C13' olefin, followed by a second epoxidation on C7'-C8' catalyzed by ntnA (Probable). The terpene cyclase/mutase ntnI then initiates the sequential tricyclic ring formation through protonation of the terminal epoxide and catalyzes the regioselective and stereoselective 6/6/6-tricyclic ring formation (Probable). The cytochrome P450 monooxygenase ntnM may then hydroxylate C1' (Probable). Secondary metabolite biosynthesis; terpenoid biosynthesis. Belongs to the terpene cyclase/mutase family. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Plays critical roles in virus replication, from virus entry and uncoating to assembly and budding of the virus particle. M1 binding to ribonucleocapsids (RNPs) in nucleus seems to inhibit viral transcription. Interaction of viral NEP with M1-RNP is thought to promote nuclear export of the complex, which is targeted to the virion assembly site at the apical plasma membrane in polarized epithelial cells. Interactions with NA and HA may bring M1, a non-raft-associated protein, into lipid rafts. Forms a continuous shell on the inner side of the lipid bilayer in virion, where it binds the RNP. During virus entry into cell, the M2 ion channel acidifies the internal virion core, inducing M1 dissociation from the RNP. M1-free RNPs are transported to the nucleus, where viral transcription and replication can take place. Determines the virion's shape: spherical or filamentous. Clinical isolates of influenza are characterized by the presence of significant proportion of filamentous virions, whereas after multiple passage on eggs or cell culture, virions have only spherical morphology. Filamentous virions are thought to be important to infect neighboring cells, and spherical virions more suited to spread through aerosol between hosts organisms. Homodimer and homomultimer. Interacts with NEP. Binds ribonucleocapsid by both interacting with genomic RNA and NP protein. May interact with HA and NA. Cannot bind NP without genomic RNA. Only the first 9 residues are shared by the 2 isoforms. Most abundant protein in virion. When expressed alone can form virus-like particles in transfected cells. Belongs to the influenza viruses Matrix protein M1 family. +ATPase subunit of a proteasome-like degradation complex; this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. By heat shock. Belongs to the ClpX chaperone family. HslU subfamily. +Belongs to the UPF0154 family. +The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), a major carbohydrate active -transport system, catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. This system is involved in fructose transport. The EIIC domain forms the PTS system translocation channel and contains the specific substrate-binding site. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA. cytidine(967) in 16S rRNA + S-adenosyl-L-methionine = 5-methylcytidine(967) in 16S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family. +Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + H(+) + holo-[ACP] Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxD subfamily. +Component of the cap-binding complex (CBC), which binds cotranscriptionally to the 5'-cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing and RNA-mediated gene silencing (RNAi). The CBC complex is involved in miRNA-mediated RNA interference via its interaction with Ars2 and is required for primary microRNAs (miRNAs) processing. Also involved in innate immunity via the short interfering RNAs (siRNAs) processing machinery by restricting the viral RNA production. In the CBC complex, Cbp80 does not bind directly capped RNAs (m7GpppG-capped RNA) but is required to stabilize the movement of the N-terminal loop of Cbp20 and lock the CBC into a high affinity cap-binding state with the cap structure (By similarity). Component of the nuclear cap-binding complex (CBC), a heterodimer composed of Cbp80 and Cbp20 that interacts with m7GpppG-capped RNA. Belongs to the NCBP1 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 1 Zn(2+) ion per subunit. In plastids the minimal PEP RNA polymerase catalytic core is composed of four subunits: alpha, beta, beta', and beta''. When a (nuclear-encoded) sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. RpoC1 subfamily. +Required for the expression of anaerobic nitric oxide (NO) reductase, acts as a transcriptional activator for at least the norVW operon. Activation also requires sigma-54. Nitrogen metabolism; nitric oxide reduction. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules. Belongs to the eukaryotic RecA-like protein family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreA releases sequences of 2 to 3 nucleotides. Belongs to the GreA/GreB family. +Probably plays a role in facilitating the assembly of multimeric protein complexes inside the ER. Belongs to the heat shock protein 70 family. +Forms a receptor complex together with receptor ilcr-1, which upon activation acts as a modulator of neuronal activity. Binding of the ligand ilc-17.1 to the ilcr-1/2 receptor complex triggers a signaling cascade that activates the downsteam signaling components actl-1, pik-1 and nfki-1, and results in increased neuronal activity in RMG interneurons in response to input from oxygen-sensing neurons. This leads to increased animal movement and promotes aggregation behavior. Component of a heterodimeric receptor complex composed of ilcr-1 and ilcr-2. The receptor complex interacts with actl-1 and ilc-17.1 with the interaction being mediated by ilcr-2. Expressed in most neurons, and in pharyngeal muscle. +Receptor for a number of inflammatory CC-chemokines including CCL3/MIP-1-alpha, CCL4/MIP-1-beta and RANTES and subsequently transduces a signal by increasing the intracellular calcium ion level. May play a role in the control of granulocytic lineage proliferation or differentiation. Participates in T-lymphocyte migration to the infection site by acting as a chemotactic receptor. Interacts with PRAF2. Efficient ligand binding to CCL3/MIP-1alpha and CCL4/MIP-1beta requires sulfation, O-glycosylation and sialic acid modifications. Glycosylation on Ser-6 is required for efficient binding of CCL4. Interacts with GRK2. Interacts with ARRB1 and ARRB2. Interacts with CNIH4. Interacts with S100A4; this interaction stimulates T-lymphocyte chemotaxis. Sulfated on at least 2 of the N-terminal tyrosines. Sulfation is required for efficient binding of the chemokines, CCL3 and CCL4 (By similarity). O-glycosylated, but not N-glycosylated. Ser-6 appears to be the major site. Also sialylated glycans present which contribute to chemokine binding. Ser-17 may also be glycosylated and, if so, with small moieties such as a T-antigen (By similarity). Palmitoylation in the C-terminal is important for cell surface expression. Phosphorylation on serine residues in the C-terminal is stimulated by binding CC chemokines especially by APO-RANTES. Belongs to the G-protein coupled receptor 1 family. +Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons. Belongs to the HrcA family. +May be involved in transcriptional regulation. Ubiquitous. Expression levels are highest in skeletal muscle and brain, intermediate in heart, pancreas, and placenta, and lowest in kidney, liver, and lung. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the krueppel C2H2-type zinc-finger protein family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Catalyzes the first step of the methylation pathway of phosphatidylcholine biosynthesis, the SAM-dependent methylation of phosphatidylethanolamine (PE) to phosphatidylmonomethylethanolamine (PMME). a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + S-adenosyl-L-methionine = 1,2-diacyl-sn-glycero-3-phospho-N-methylethanolamine + H(+) + S-adenosyl-L-homocysteine Phospholipid metabolism; phosphatidylcholine biosynthesis. Belongs to the class VI-like SAM-binding methyltransferase superfamily. CHO2 family. +Expressed in roots, crown and leaves during cold acclimation. In freezing-tolerant gramineae, by cold temperatures. Water-stress induces the expression to a similar extent in all species tested, abscisic acid (ABA) to a much lesser extent. +Belongs to the SlyX family. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Required for vesicular transport between the endoplasmic reticulum and the Golgi apparatus. Binds to SNARE complex and then recruits NSF to disassemble it (By similarity). Binds to the syntaxin SYP21 and to NSF. A number of isoforms are produced. According to EST sequences. Belongs to the SNAP family. +Regulates the transcription of several operons and genes involved in the biogenesis of Fe-S clusters and Fe-S-containing proteins. Binds 1 [2Fe-2S] cluster. +2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + ADP + H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole from N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide: step 2/2. Belongs to the AIR synthase family. +Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions. H2O + XTP = diphosphate + H(+) + XMP dITP + H2O = dIMP + diphosphate + H(+) H2O + ITP = diphosphate + H(+) + IMP Binds 1 Mg(2+) ion per subunit. Homodimer. Belongs to the HAM1 NTPase family. +Antimicrobial peptide. Active against Gram-negative bacterium E.coli (MIC=6 uM) and against Gram-positive bacterium S.aureus (MIC=12.5 uM). Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Brevinin subfamily. +Component of ATP-dependent clamp loader (RFC and RFC-like) complexes for DNA clamps. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC. The complex presumably provides bipartite ATP sites in which one subunit supplies a catalytic site for hydrolysis of ATP bound to the neighboring subunit. Dissociation of RFC from the clamp leaves the clamp encircling DNA. Component of the replication factor C (RFC or activator 1) complex which acts during elongation of primed DNA templates by DNA polymerase delta and epsilon. RFC has an essential but redundant activity in sister chromatid cohesion establishment (By similarity). Component of the replication factor C (RFC) complex. Expressed in late sporogonial stages. Present with 2760 molecules/cell in log phase SD medium. Belongs to the activator 1 small subunits family. +Catalyzes the final step of fatty acid oxidation in which acetyl-CoA is released and the CoA ester of a fatty acid two carbons shorter is formed. acetyl-CoA + an acyl-CoA = a 3-oxoacyl-CoA + CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadB) and two beta chains (FadA). Belongs to the thiolase-like superfamily. Thiolase family. +Required for insertion of 4Fe-4S clusters for at least IspG. Binds 1 iron-sulfur cluster per subunit. Homodimer. Belongs to the HesB/IscA family. +Delta-conotoxins bind to site 6 of voltage-gated sodium channels (Nav) and inhibit the inactivation process. This toxin acts on Nav1.4/SCN4A and Nav1.6/SCN8A (EC(50)=2.3 uM). Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). Monoisotopic mass. Monoisotopic mass. Does not show activity on rNav1.2/SCN2A, rNav1.3/SCN3A, hNav1.5/SCN5A, Nav1.7/SCN9A, rNav1.8/SCN10A, Kv1.1/KCNA1, Kv1.3/KCNA3, Kv1.4/KCNA4, Kv1.5/KCNA5, hKv11.1/KCNH2/ERG1, shaker and DmNav1/para. Found in the dissected venom (DV), but not in the injectable (milked) venom (IV). Belongs to the conotoxin O1 superfamily. +Belongs to the bacterial ribosomal protein bL33 family. +Uptake of L-rhamnose across the cytoplasmic membrane with the concomitant transport of protons into the cell (symport system). H(+)(in) + L-rhamnopyranose(in) = H(+)(out) + L-rhamnopyranose(out) Belongs to the L-rhamnose transporter (TC 2.A.7.6) family. +To S.pombe SpAC18G6.12c. +Anaerobic nitric oxide reductase; uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center; electrons enter from the NorW at rubredoxin and are transferred sequentially to the FMN center and the di-iron center. Also able to function as an aerobic oxygen reductase. Binds 3 Fe cations per monomer. Binds 1 FMN per monomer. Nitrogen metabolism; nitric oxide reduction. Homotetramer. In the N-terminal section; belongs to the zinc metallo-hydrolase group 3 family. +Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. (2E,6E,10E)-geranylgeranyl diphosphate + sn-glycerol 1-phosphate = diphosphate + sn-3-O-(geranylgeranyl)glycerol 1-phosphate Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the GGGP/HepGP synthase family. Group II subfamily. +Belongs to the UPF0248 family. +Inhibitory regulator of the Ras-cyclic AMP pathway. May function as a negative regulator of Ras85D/Ras1 in the sev signaling pathway. Acts cell autonomously in cone cell precursors as a negative regulator of R7 photoreceptor cell determination. Interacts with sty. In third instar larvae eye imaginal disk, expressed in cells posterior to the morphogenetic furrow, in all photoreceptor and cone cell precursors as well as in still uncommitted cells. Mutant flies display a highly irregular eye pattern, with ommatidia improperly oriented and occasionally fused. Most of these ommatidia contain extra cells that resemble R7 photoreceptor cell, characterized by small rhabdomere diameter, a central position in the distal half of the retina and expression of the R7-specific rhodopsin Rh4. The extra R7 cells are derived from cone cell precursors. In mutant wing, an additional longitudinal vein branches off the posterior crossvein, the wing veins widen at their junctions with the wing margins and wing vein material is found in between the longitudinal veins. +Expressed by the venom duct. The cysteine framework is III (CC-C-C-CC). Classified in the M-2 branch, since 2 residues stand between the fourth and the fifth cysteine residues. Belongs to the conotoxin M superfamily. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. 2 D-sedoheptulose 7-phosphate = D-glycero-alpha-D-manno-heptose 7-phosphate + D-glycero-beta-D-manno-heptose 7-phosphate Binds 1 zinc ion per subunit. Carbohydrate biosynthesis; D-glycero-D-manno-heptose 7-phosphate biosynthesis; D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate from sedoheptulose 7-phosphate: step 1/1. Homotetramer. The reaction produces a racemic mixture of D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate. Belongs to the SIS family. GmhA subfamily. +Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway. D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = beta-D-fructose 6-phosphate + D-erythrose 4-phosphate Carbohydrate degradation; pentose phosphate pathway; D-glyceraldehyde 3-phosphate and beta-D-fructose 6-phosphate from D-ribose 5-phosphate and D-xylulose 5-phosphate (non-oxidative stage): step 2/3. Homodimer. Belongs to the transaldolase family. Type 1 subfamily. Extended N-terminus. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Part of the high-affinity ABC transporter complex ScaABC involved in manganese import. Probably responsible for the translocation of the substrate across the membrane. Essential for growth under Mn(2+)-limiting conditions. The complex is composed of two ATP-binding proteins (ScaC), two transmembrane proteins (ScaB) and a solute-binding protein (ScaA). Belongs to the ABC-3 integral membrane protein family. +Purine nucleoside enzyme that catalyzes the phosphorolysis of adenosine and inosine nucleosides, yielding D-ribose 1-phosphate and the respective free bases, adenine and hypoxanthine. Also catalyzes the phosphorolysis of S-methyl-5'-thioadenosine into adenine and S-methyl-5-thio-alpha-D-ribose 1-phosphate. Also has adenosine deaminase activity. adenosine + phosphate = adenine + alpha-D-ribose 1-phosphate phosphate + S-methyl-5'-thioadenosine = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate inosine + phosphate = alpha-D-ribose 1-phosphate + hypoxanthine adenosine + H(+) + H2O = inosine + NH4(+) Homodimer. Belongs to the purine nucleoside phosphorylase YfiH/LACC1 family. +Belongs to the Mu gp47/PBSX XkdT family. +Precursor of the transcription factor form (Processed cyclic AMP-dependent transcription factor ATF-6 alpha), which is embedded in the endoplasmic reticulum membrane. Endoplasmic reticulum stress promotes processing of this form, releasing the transcription factor form that translocates into the nucleus, where it activates transcription of genes involved in the unfolded protein response (UPR). Transcription factor that initiates the unfolded protein response (UPR) during endoplasmic reticulum stress by activating transcription of genes involved in the UPR. Binds DNA on the 5'-CCAC[GA]-3'half of the ER stress response element (ERSE) (5'-CCAAT-N(9)-CCAC[GA]-3') and of ERSE II (5'-ATTGG-N-CCACG-3'). Binding to ERSE requires binding of NF-Y to ERSE. Could also be involved in activation of transcription by the serum response factor. May play a role in foveal development and cone function in the retina. Interacts with XBP1 isoform 2; the interaction occurs in a ER stress-dependent manner. Interacts with LACC1. Interacts with THBS4 (via EGF-like 3; calcium-binding domain) which facilitates its processing, activation and nuclear translocation (By similarity). Interacts (via lumenal domain) with THBS1 (By similarity). Homodimer and heterodimer with ATF6-beta. The dimer interacts with the nuclear transcription factor Y (NF-Y) trimer through direct binding to NF-Y subunit C (NF-YC). Interacts also with the transcription factors GTF2I, YY1 and SRF. Translocates from the endoplasmic reticulum to the Golgi, where it is processed. Under ER stress the cleaved N-terminal cytoplasmic domain translocates into the nucleus (PubMed:22682248). THBS4 promotes its nuclear shuttling (By similarity). The basic domain functions as a nuclear localization signal. The basic leucine-zipper domain is sufficient for association with the NF-Y trimer and binding to ERSE. During unfolded protein response, a fragment of approximately 50 kDa containing the cytoplasmic transcription factor domain is released by proteolysis. The cleavage seems to be performed sequentially by site-1 (MBTPS1, S1P) and site-2 (MBTPS2, S2P) proteases (By similarity). N-glycosylated. The glycosylation status may serve as a sensor for ER homeostasis, resulting in ATF6 activation to trigger the unfolded protein response (UPR) (By similarity). Ubiquitinated by RNF186 at Lys-139, which is required for pattern recognition receptor-induced unfolded protein response-associated outcomes. Belongs to the bZIP family. ATF subfamily. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms part of the jaw domain. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Part of the RNA polymerase complex. Belongs to the RNA polymerase beta' chain family. +Catalyzes the transfer of electrons from NADPH to thioredoxins TRX1, TRX2 and TRX3, which in turn act as reductants of disulfide containing proteins (PubMed:9368022, PubMed:11013257, PubMed:16910770, PubMed:23845423). Able to reduce nitroglutathione (GSNO), a compound involved in the transport of nitric oxide (NO); however, TRX1 is more efficient in reducing GSNO (PubMed:11013257). Has no catalytic activity towards oxidized glutathione (GSSG) (PubMed:11013257). [thioredoxin]-dithiol + NADP(+) = [thioredoxin]-disulfide + H(+) + NADPH Binds 1 FAD per subunit. kcat is 1725 min(-1) with TRX1 as substrate (at pH 7.4) (PubMed:23845423). kcat is 51.7 sec(-1) with TRX1 as substrate (at 25 degrees Celsius and at pH 7.4) (PubMed:23845423). kcat is 275.2 min(-1) with NADPH and DTNB as substrates (at pH 7.4) (PubMed:9368022). kcat is 48.3 sec(-1) with NADPH and TRX1 as substrates (at 25 degrees Celsius and at pH 7.4) (PubMed:11013257). kcat is 9.4 min(-1) with nitrosoglutathione (GSNO) as substrates (at 25 degrees Celsius and at pH 7.4) (PubMed:11013257). Homodimer. Produced by alternative initiation at Met-77 of isoform 1. In Plasmodium, the C-terminal redox center, which acts as the active site, is formed by two cysteines while in mammalian TRXR this redox center is composed of a cysteine-selenocysteine active site. Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. +Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes. Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Homodimer and homohexamer; in equilibrium. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrR subfamily. +Receptor for prostaglandin D2 (PGD2). The activity of this receptor is mainly mediated by G(s) proteins that stimulate adenylate cyclase, resulting in an elevation of intracellular cAMP. A mobilization of calcium is also observed, but without formation of inositol 1,4,5-trisphosphate (By similarity). Involved in PLA2G3-dependent maturation of mast cells. PLA2G3 is secreted by immature mast cells and acts on nearby fibroblasts upstream to PTDGS to synthesize PGD2, which in turn promotes mast cell maturation and degranulation via PTGDR (By similarity). Expressed in retinal choroid, ciliary epithelium, longitudinal and circular ciliary muscles, iris, small intestine and platelet membranes. Disease susceptibility is associated with variants affecting the gene represented in this entry. Belongs to the G-protein coupled receptor 1 family. +Has omega-amidase activity. The role of omega-amidase is to remove potentially toxic intermediates by converting 2-oxoglutaramate and 2-oxosuccinamate to biologically useful 2-oxoglutarate and oxaloacetate, respectively. 2-oxoglutaramate + H2O = 2-oxoglutarate + NH4(+) 2-oxosuccinamate + H2O = NH4(+) + oxaloacetate Homodimer. Belongs to the carbon-nitrogen hydrolase superfamily. NIT1/NIT2 family. +Belongs to the UPF0342 family. +Belongs to the UPF0282 family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Homodimer. Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways. AMP + ATP = 2 ADP Monomer. Predominantly mitochondrial. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. AK2 subfamily. +6-hydroxytryprostatin B O-methyltransferase; part of the gene cluster that mediates the biosynthesis of fumitremorgins, indole alkaloids that carry not only intriguing chemical structures, but also interesting biological and pharmacological activities (PubMed:23649274). The biosynthesis of fumitremorgin-type alkaloids begins by condensation of the two amino acids L-tryptophan and L-proline to brevianamide F, catalyzed by the non-ribosomal peptide synthetase ftmA (PubMed:16755625). Brevianamide F is then prenylated by the prenyltransferase ftmPT1/ftmB in the presence of dimethylallyl diphosphate, resulting in the formation of tryprostatin B (PubMed:16000710, PubMed:21105662, PubMed:23090579). The three cytochrome P450 monooxygenases, ftmP450-1/ftmC, ftmP450-2/ftmE and ftmP450-3/FtmG, are responsible for the conversion of tryprostatin B to 6-hydroxytryprostatin B, tryprostatin A to fumitremorgin C and fumitremorgin C to 12,13-dihydroxyfumitremorgin C, respectively (PubMed:19226505). The putative methyltransferase ftmMT/ftmD is expected for the conversion of 6-hydroxytryprostatin B to tryprostatin A (Probable). FtmPT2/FtmH catalyzes the prenylation of 12,13-dihydroxyfumitre-morgin C in the presence of dimethylallyl diphosphate, resulting in the formation of fumitremorgin B (PubMed:18683158). Fumitremorgin B is further converted to verruculogen by ftmOx1/ftmF via the insertion of an endoperoxide bond between the two prenyl moieties (PubMed:19763315). In some fungal species, verruculogen is further converted to fumitremorgin A, but the enzymes involved in this step have not been identified yet (Probable). 6-hydroxytryprostatin B + S-adenosyl-L-methionine = H(+) + S-adenosyl-L-homocysteine + tryprostatin A kcat is 8.2 sec(-1) with 6-hydroxytryprostatin B as substrate. kcat is 6.9 sec(-1) with S-adenosyl-L-methionine as substrate. Mycotoxin biosynthesis. Homodimer. Belongs to the class I-like SAM-binding methyltransferase superfamily. Cation-independent O-methyltransferase family. In contrast to other A.fumigatus strains, strain ATCC MYA-4609 does not produce indole alkaloids such as fumitremorgins and verruculogen. While the biosynthetic pathway is complete, a variation in this enzyme abolishes production of the tryprostatin A intermediate. The weak methyltransferase activity is probably due to the presence of Leu-202 instead of an Arg residue that affects the binding of 6-hydroxytryprostatin B (PubMed:23649274). +Interacts with LTBP1. Glycosylated (By similarity). Can be O-fucosylated by POFUT2 on a serine or a threonine residue found within the consensus sequence C1-X(2)-(S/T)-C2-G of the TSP type-1 repeat domains where C1 and C2 are the first and second cysteine residue of the repeat, respectively. Fucosylated repeats can then be further glycosylated by the addition of a beta-1,3-glucose residue by the glucosyltransferase, B3GALTL. Fucosylation mediates the efficient secretion of ADAMTS family members. Can also be C-glycosylated with one or two mannose molecules on tryptophan residues within the consensus sequence W-X-X-W of the TPRs, and N-glycosylated. These other glycosylations can also facilitate secretion (By similarity). The disease is caused by variants affecting the gene represented in this entry. There is a significant increase in total and active TGFB1 in the culture medium as well as nuclear localization of phosphorylated SMAD2 in fibroblasts from individuals with geleophysic dysplasia. Although strongly similar to members of the ADAMTS family it lacks the metalloprotease and disintegrin-like domains which are typical of that family. +The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). (R)-N(6)-lipoyl-L-lysyl-[dihydrolipoyllysine-residue acetyltransferase] + H(+) + pyruvate = (R)-N(6)-(S(8)-acetyldihydrolipoyl)-L-lysyl-[dihydrolipoyllysine-residue acetyltransferase] + CO2 E1 activity is regulated by phosphorylation (inactivation) and dephosphorylation (activation) of the alpha subunit. Pyruvate dehydrogenase (E1) is a tetramer of 2 alpha and 2 beta subunits. Eukaryotic pyruvate dehydrogenase (PDH) complexes are organized as a core consisting of the oligomeric dihydrolipoamide acetyl-transferase (E2), around which are arranged multiple copies of pyruvate dehydrogenase (E1), dihydrolipoamide dehydrogenase (E3) and protein X (E3BP) bound by non-covalent bonds. Phosphorylated at Ser-313 by pyruvate dehydrogenase kinases PKP1 (PDK1) and PKP2 (PDK2), and dephosphorylated by pyruvate dehydrogenase phosphatases PTC5 and PTC6. Present with 100000 molecules/cell in log phase SD medium. Extended N-terminus. +Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain. +During interphase, required for microtubule organizing and anchoring activities. During mitosis, required for the organization and stabilization of the spindle pole. May promote cell cycle arrest by enhancing the inhibition of CDK2 activity by CDKN1A. May be required for repair of DNA damage by homologous recombination in conjunction with BRCA2. May not be involved in non-homologous end joining (NHEJ). Interacts with BRCA2, CDKN1A and MTDH/LYRIC. Interacts with DCTN1/p150-glued and ACTR1A/ARP1. Interacts with alpha-, beta- and gamma-tubulins. Interacts with TENT5C; the interaction has no effect on TENT5C poly(A) polymerase function (By similarity). Colocalizes with BRCA2 in discrete nuclear foci. In interphase, preferential localizes to the mother centriole. Recruited to the spindle pole matrix and centrosome by microtubules and dynein/dynactin activity. Belongs to the BCP1 family. +Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-terminal L-methionyl-[peptide] Binds 1 Fe(2+) ion. Belongs to the polypeptide deformylase family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis. (R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) A monovalent cation. Ammonium or potassium. Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Homodimer. Belongs to the type III pantothenate kinase family. +Involved in the synthesis of meso-diaminopimelate (m-DAP or DL-DAP), required for both lysine and peptidoglycan biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate. (2S,6S)-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O + L-glutamate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route): step 1/1. Homodimer. Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. LL-diaminopimelate aminotransferase subfamily. +One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA. Homotetramer, a dimer of dimers. One homotetramer interacts with 1 SecA dimer. Belongs to the SecB family. +Involved in gross chromosomal rearrangements (GCRs) and telomere healing. Belongs to the IRC6 family. +Removes the pyruvyl group from chorismate, with concomitant aromatization of the ring, to provide 4-hydroxybenzoate (4HB) for the ubiquinone pathway. chorismate = 4-hydroxybenzoate + pyruvate Cofactor biosynthesis; ubiquinone biosynthesis. Monomer. Belongs to the UbiC family. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Optimum pH is 7.5-8.0. Optimum temperature is 42-44 degrees Celsius. Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. Homodimer. Belongs to the transketolase family. DXPS subfamily. +Involved in biosynthesis of the thiamine precursor thiazole. Catalyzes the conversion of NAD and glycine to adenosine diphosphate 5-(2-hydroxyethyl)-4-methylthiazole-2-carboxylic acid (ADT), an adenylated thiazole intermediate. The reaction includes an iron-dependent sulfide transfer from a conserved cysteine residue of the protein to a thiazole intermediate. The enzyme can only undergo a single turnover, which suggests it is a suicide enzyme. May have additional roles in adaptation to various stress conditions and in DNA damage tolerance. [ADP-thiazole synthase]-L-cysteine + glycine + NAD(+) = [ADP-thiazole synthase]-dehydroalanine + ADP-5-ethyl-4-methylthiazole-2-carboxylate + 2 H(+) + 3 H2O + nicotinamide Binds 1 Fe cation per subunit. Homooctamer. Highest expression in developing embryos and green leaves and a very low level expression seen in endosperm, roots, etiolated shoots and immature ears. During embryo development, expression increases from 15-21 days after pollination and decreases slightly at day 24 and this level is maintained until day 36. During the catalytic reaction, a sulfide is transferred from Cys-222 to a reaction intermediate, generating a dehydroalanine residue. Belongs to the THI4 family. +A member of the dormancy regulon. Induced in response to reduced oxygen tension (hypoxia), low levels of nitric oxide (NO) and carbon monoxide (CO). It is hoped that this regulon will give insight into the latent, or dormant phase of infection. In the N-terminal section; belongs to the purine/pyrimidine phosphoribosyltransferase family. In the C-terminal section; belongs to the dienelactone hydrolase family. +Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed to be not involved in catalysis. Required for proper complex I assembly. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Mammalian complex I is composed of 45 different subunits. Belongs to the complex I LYR family. +Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. ATP + NAD(+) = ADP + H(+) + NADP(+) Belongs to the NAD kinase family. +Belongs to the bacterial ribosomal protein bL28 family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. ATP + meso-2,6-diaminoheptanedioate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate Cell wall biogenesis; peptidoglycan biosynthesis. Carboxylation is probably crucial for Mg(2+) binding and, consequently, for the gamma-phosphate positioning of ATP. Belongs to the MurCDEF family. MurE subfamily. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +FAD-linked oxidoreductase; part of the gene cluster that mediates the biosynthesis of alternapyrone derivatives (PubMed:16356847). Alternapyrone is a decaketide with octa-methylation from methionine on every C2 unit except the third unit (PubMed:16356847). All the domains in the polyketide synthase alt5 are apparently involved in alternapyrone synthesis, that is, the 8 CMeT, 7 KR, 7 DH, and 4 ER reactions in the 9 KS-mediated condensation steps required for alternapyrone synthesis (PubMed:16356847). the alternapyrone produced by alt5 might be intensively modified by cytochrome P450 monooxygenases alt1, alt2 and alt3 and FAD-dependent oxidoreductase alt4 present in the alt gene cluster (PubMed:16356847). Secondary metabolite biosynthesis. Belongs to the oxygen-dependent FAD-linked oxidoreductase family. +Belongs to the UPF0145 family. +This protein is an aporepressor. When complexed with L-tryptophan it binds the operator region of the trp operon (5'-ACTAGT-'3') and prevents the initiation of transcription. The complex also regulates trp repressor biosynthesis by binding to its regulatory region. Homodimer. Belongs to the TrpR family. +Modifies, by uridylylation and deuridylylation, the PII regulatory proteins (GlnB and homologs), in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen assimilation and metabolism. [protein-PII]-L-tyrosine + UTP = [protein-PII]-uridylyl-L-tyrosine + diphosphate [protein-PII]-uridylyl-L-tyrosine + H2O = [protein-PII]-L-tyrosine + H(+) + UMP Uridylyltransferase (UTase) activity is inhibited by glutamine, while glutamine activates uridylyl-removing (UR) activity. Has four distinct domains: an N-terminal nucleotidyltransferase (NT) domain responsible for UTase activity, a central HD domain that encodes UR activity, and two C-terminal ACT domains that seem to have a role in glutamine sensing. Belongs to the GlnD family. +Plays a role in virus cell tropism, and may be required for efficient virus replication in macrophages. Belongs to the asfivirus MGF 110 family. +Belongs to the FAM222 family. +Nitrous-oxide reductase is part of a bacterial respiratory system which is activated under anaerobic conditions in the presence of nitrate or nitrous oxide. 2 Fe(III)-[cytochrome c] + H2O + N2 = 2 Fe(II)-[cytochrome c] + 2 H(+) + nitrous oxide Binds 2 calcium ions per subunit. Binds 6 Cu cations per subunit. Each subunit contains 2 copper centers; Cu(A) (binuclear) and Cu(Z) (tetranuclear). Cu(Z) is thought to be the site of nitrous oxide reduction. Nitrogen metabolism; nitrate reduction (denitrification); dinitrogen from nitrate: step 4/4. Homodimer. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the NosZ family. In the C-terminal section; belongs to the cytochrome c oxidase subunit 2 family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Belongs to the SecA family. Extended N-terminus. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA. a fatty acyl-[ACP] + phosphate = an acyl phosphate + holo-[ACP] Lipid metabolism; phospholipid metabolism. Homodimer. Probably interacts with PlsY. Associated with the membrane possibly through PlsY. Belongs to the PlsX family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Major component of the type III secretion needle structure that plays an essential role in translocation of effector toxins into host cells, facilitating the establishment and dissemination of infection. Forms a stable heterotrimeric complex with PscE and PscG in the cytoplasm, blocking it in a monomeric state and preventing its polymerization (PubMed:16115870, PubMed:17470796). Then, forms a polymeric structure at the cell surface (PubMed:16115870). Secreted via type III secretion system (TTSS). The N-terminal part (1-11) is species-specific and essential for export/assembly and the function of needle. Belongs to the MxiH/PrgI/YscF family. +An F and P subtype restriction enzyme that recognizes the double-stranded sequence 5'-GGCCN(5)GGCC-3' and cleaves before N-9. Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. +Collagen type III occurs in most soft connective tissues along with type I collagen. Trimers of identical alpha 1(III) chains. The chains are linked to each other by interchain disulfide bonds. Trimers are also cross-linked via hydroxylysines. The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity). Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains. Belongs to the fibrillar collagen family. +Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore. Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization either through clathrin-dependent endocytosis or through clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore. Homotrimer of disulfide-linked HA1-HA2. Targeted to the apical plasma membrane in epithelial polarized cells through a signal present in the transmembrane domain. Associated with glycosphingolipid- and cholesterol-enriched detergent-resistant lipid rafts. Palmitoylated. In natural infection, inactive HA is matured into HA1 and HA2 outside the cell by one or more trypsin-like, arginine-specific endoprotease secreted by the bronchial epithelial cells. One identified protease that may be involved in this process is secreted in lungs by Clara cells. Major glycoprotein, comprises over 80% of the envelope proteins present in virus particle. The extent of infection into host organism is determined by HA. Influenza viruses bud from the apical surface of polarized epithelial cells (e.g. bronchial epithelial cells) into lumen of lungs and are therefore usually pneumotropic. The reason is that HA is cleaved by tryptase clara which is restricted to lungs. However, HAs of H5 and H7 pantropic avian viruses subtypes can be cleaved by furin and subtilisin-type enzymes, allowing the virus to grow in other organs than lungs. The influenza A genome consist of 8 RNA segments. Genetic variation of hemagglutinin and/or neuraminidase genes results in the emergence of new influenza strains. The mechanism of variation can be the result of point mutations or the result of genetic reassortment between segments of two different strains. Belongs to the influenza viruses hemagglutinin family. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is composed of 13 subunits: EIF3A, EIF3B, EIF3C, EIF3D, EIF3E, EIF3F, EIF3G, EIF3H, EIF3I, EIF3J, EIF3K, EIF3L and EIF3M. The eIF-3 complex appears to include 3 stable modules: module A is composed of EIF3A, EIF3B, EIF3G and EIF3I; module B is composed of EIF3F, EIF3H, and EIF3M; and module C is composed of EIF3C, EIF3D, EIF3E, EIF3K and EIF3L. EIF3C of module C binds EIF3B of module A and EIF3H of module B, thereby linking the three modules. EIF3J is a labile subunit that binds to the eIF-3 complex via EIF3B. The eIF-3 complex may interact with RPS6KB1 under conditions of nutrient depletion. Mitogenic stimulation may lead to binding and activation of a complex composed of MTOR and RPTOR, leading to phosphorylation and release of RPS6KB1 and binding of EIF4B to eIF-3. Interacts with RRN3. Belongs to the eIF-3 subunit L family. +Transcriptional repressor that plays a role in various developmental processes. Specifically binds the consensus DNA sequence 5'-[AC]ACATCTG[GT][AC]-3' which contains the E box core, and acts by recruiting chromatin remodeling multiprotein complexes (By similarity). Belongs to the krueppel C2H2-type zinc-finger protein family. ZBTB18 subfamily. +PubMed:6313520 sequence has the D12 allotypic marker, 104-Thr, and the E14 marker, 185-Thr. PubMed:6193512 has the D11 and E15 markers and Ref.5 the E15 marker. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Belongs to the bacterial ribosomal protein bL27 family. +Probable transcription factor with a role in the retinal determination (RD) network. Regulates ato expression and is required for normal R8 induction and differentiation. Danr appears to repress Dan expression, but Dan is required for Danr expression anterior to the morphogenetic furrow (MF). Dan and Danr lie downstream of so and require dac function for highest levels of expression. Contributes to differentiation of antenna-specific characteristics; effector gene that acts downstream of homothorax (hth), Distal-less (Dll), cut (ct) and spineless (ss) genes to control differentiation of distal antennal structures. Interacts with itself, dan, ey and dac to form a complex (or complexes) containing the RD factors. Coexpressed with dan in the presumptive distal antenna, but not in the leg imaginal disk. Both proteins are also expressed in the brain and the eye region of the eye-antenna disk. First detected in early L3 eye disks in cells surrounding the newly initiated morphogenetic furrow. Highly expressed in evenly spaced clusters of cells anterior to the furrow, lower levels within and posterior to the furrow. Flies exhibit partial transformation of antenna toward leg identity. Ectopic expression causes partial transformation of distal leg structure toward antennal identity. +ATP + L-glutamate + NH4(+) = ADP + H(+) + L-glutamine + phosphate Homooctamer. Belongs to the glutamine synthetase family. +Snake venom serine protease that may act in the hemostasis system of the prey. Monomer. Expressed by the venom gland. Belongs to the peptidase S1 family. Snake venom subfamily. +May act as an important regulator of the cell cycle that participates in the maintenance of genome integrity. Excluded from nucleolus. +Specifically methylates the guanosine in position 1516 of 16S rRNA. guanosine(1516) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(2)-methylguanosine(1516) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmJ family. Extended N-terminus. +Belongs to the bacterial ribosomal protein bL27 family. +Specifically methylates the cytosine at position 1962 (m5C1962) of 23S rRNA. cytidine(1962) in 23S rRNA + S-adenosyl-L-methionine = 5-methylcytidine(1962) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RlmI family. +G-protein coupled receptor for 5-hydroxytryptamine (serotonin). Also functions as a receptor for various alkaloids and psychoactive substances. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors, such as adenylate cyclase. Signaling inhibits adenylate cyclase activity. Detected in hippocampus. Belongs to the G-protein coupled receptor 1 family. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Able to form a pore in lipid bilayers. May form trimers. Outer membrane location shown for Nine Mile phase I, but not that it actually spans the membrane. Found in the large cell variant (LCV) stage, very little is present in the small cell variant (SCV) stage (at protein level). LCVs are more metabolically active than SCVs. Might be used for vaccine production. Belongs to the Coxiella porin P1 (CPP1) (TC 1.B.43) family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Feedback inhibited by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Belongs to the ATP phosphoribosyltransferase family. Long subfamily. +(6S)-10-formyltetrahydrofolate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide = (6S)-5,6,7,8-tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide H2O + IMP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide Purine metabolism; IMP biosynthesis via de novo pathway; 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide (10-formyl THF route): step 1/1. Purine metabolism; IMP biosynthesis via de novo pathway; IMP from 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide: step 1/1. The IMP cyclohydrolase activity resides in the N-terminal region. Belongs to the PurH family. +Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ). 5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphooxyethyl)-thiazole + ADP + H(+) Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-methyl-5-(2-phosphoethyl)-thiazole from 5-(2-hydroxyethyl)-4-methylthiazole: step 1/1. Belongs to the Thz kinase family. +S-adenosyl-L-methionine-dependent methyltransferase that mediates mRNA cap1 2'-O-ribose methylation to the 5'-cap structure of mRNAs (PubMed:32504809). Methylates the ribose of the first nucleotide of a m(7)GpppG-capped mRNA to produce m(7)GpppNmp (cap1) (PubMed:32504809). Positively regulates the Ago2-dependent small RNA pathway, with roles in both siRNA biogenesis and RISC assembly (PubMed:32504809). Involved in facilitating conversion of pre-RISC into holo-RISC, possibly by promoting the unwinding of Ago2-bound siRNA duplexes and thus the retention of the guide strand in holo-RISC (PubMed:32504809). a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleoside) in mRNA + H(+) + S-adenosyl-L-homocysteine Interacts (via C-terminus) with r2d2 (via C-terminus). +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 2 subfamily. +Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore. Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization either through clathrin-dependent endocytosis or through clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore. Homotrimer of disulfide-linked HA1-HA2. Targeted to the apical plasma membrane in epithelial polarized cells through a signal present in the transmembrane domain. Associated with glycosphingolipid- and cholesterol-enriched detergent-resistant lipid rafts. Palmitoylated. In natural infection, inactive HA is matured into HA1 and HA2 outside the cell by one or more trypsin-like, arginine-specific endoprotease secreted by the bronchial epithelial cells. One identified protease that may be involved in this process is secreted in lungs by Clara cells. Major glycoprotein, comprises over 80% of the envelope proteins present in virus particle. The extent of infection into host organism is determined by HA. Influenza viruses bud from the apical surface of polarized epithelial cells (e.g. bronchial epithelial cells) into lumen of lungs and are therefore usually pneumotropic. The reason is that HA is cleaved by tryptase clara which is restricted to lungs. However, HAs of H5 and H7 pantropic avian viruses subtypes can be cleaved by furin and subtilisin-type enzymes, allowing the virus to grow in other organs than lungs. The influenza A genome consist of 8 RNA segments. Genetic variation of hemagglutinin and/or neuraminidase genes results in the emergence of new influenza strains. The mechanism of variation can be the result of point mutations or the result of genetic reassortment between segments of two different strains. Belongs to the influenza viruses hemagglutinin family. +dGTPase preferentially hydrolyzes dGTP over the other canonical NTPs. dGTP + H2O = 2'-deoxyguanosine + H(+) + triphosphate Homotetramer. Belongs to the dGTPase family. Type 1 subfamily. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +Putative toxic component of a type II toxin-antitoxin (TA) system, its cognate toxin is MaZE8. Probably an endoribonuclease (By similarity). Forms a complex with cognate antitoxin MazE8. Could be the product of a pseudogene. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln). Acts by mediating the C-terminal thiocarboxylation of sulfur carrier URM1. Its N-terminus first activates URM1 as acyl-adenylates (-COAMP), then the persulfide sulfur on the catalytic cysteine is transferred to URM1 to form thiocarboxylation (-COSH) of its C-terminus. The reaction probably involves hydrogen sulfide that is generated from the persulfide intermediate and that acts as nucleophile towards URM1. Subsequently, a transient disulfide bond is formed. Does not use thiosulfate as sulfur donor; NFS1 probably acting as a sulfur donor for thiocarboxylation reactions. Prior mcm(5) tRNA modification by the elongator complex is required for 2-thiolation. May also be involved in protein urmylation. Binds 1 zinc ion per subunit. tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis. Present with 2620 molecules/cell in log phase SD medium. In the N-terminal section; belongs to the HesA/MoeB/ThiF family. UBA4 subfamily. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine. putrescine + S-adenosyl 3-(methylsulfanyl)propylamine = H(+) + S-methyl-5'-thioadenosine + spermidine Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1. Homodimer or homotetramer. Belongs to the spermidine/spermine synthase family. +Involved in the early processing steps of the pre-rRNA in the maturation pathway leading to the 18S rRNA. Belongs to the RRP36 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Belongs to the V-ATPase E subunit family. +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Belongs to the urease beta subunit family. +The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination. The AddA nuclease domain is required for chi fragment generation; this subunit has the helicase and 3' -> 5' nuclease activities. ATP + H2O = ADP + H(+) + phosphate Heterodimer of AddA and AddB/RexB. Belongs to the helicase family. AddA subfamily. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s). Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core, while the alpha-helices form wings that extend away from the core. Belongs to the CsrA/RsmA family. +Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Involved in down-regulation of MYB- and JUN-dependent transcription. Enhances ligand-dependent transcriptional activity of nuclear hormone receptors. May play a role in cell differentiation. Homodimer. Component of the CCR4-NOT complex; distinct complexes seem to exist that differ in the participation of probably mutually exclusive catalytic subunits. Interacts with MYB, ATF2, RARA, RARB, RARG, RXRA, RXRB and RXRG. Identified in a complex with ATF2 bound to target DNA. Interacts with NANOS2. Directly interacts with ZNF335 (By similarity). NANOS2 promotes its localization to P-body. Belongs to the CNOT9 family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system. The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. Belongs to the TatA/E family. +Involved in the biosynthesis of osmoregulated periplasmic glucans (OPGs). Glycan metabolism; osmoregulated periplasmic glucan (OPG) biosynthesis. Belongs to the glycosyltransferase 2 family. OpgH subfamily. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 2 subfamily. +Belongs to the universal ribosomal protein uS9 family. +With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS5 family. +Component of the BRISC complex that specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates (PubMed:26344097). Does not have activity by itself, but the catalytic subunit BRCC3/BRCC36 needs to be associated into a heterotetramer with FAM175B for minimal in vitro activity (PubMed:26344097). May act as a central scaffold protein that assembles the various components of the BRISC complex and retains them in the cytoplasm (By similarity). Plays a role in regulating the onset of apoptosis via its role in modulating 'Lys-63'-linked ubiquitination of target proteins (By similarity). Required for normal mitotic spindle assembly and microtubule attachment to kinetochores via its role in deubiquitinating numa1 (By similarity). Component of the BRISC complex, at least composed of FAM175B/ABRO1, BRCC3/BRCC36, BABAM2 and BABAM1/NBA1. Within the complex, interacts directly with BRCC3/BRCC36. The heterodimer with BRCC3/BRCC36 assembles into a heterotetramer. The BRISC complex binds polyubiquitin. A minor proportion is detected in the nucleus. Translocates into the nucleus in response to DNA damage. Directly binds to microtubules and is detected at the minus end of K-fibers. Belongs to the FAM175 family. Abro1 subfamily. Expected to lack catalytic activity. +NADPH-dependent reductase which is a central component of the cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery. Transfers electrons from NADPH via its FAD and FMN prosthetic groups to the [2Fe-2S] cluster of dre2, another key component of the CIA machinery. In turn, this reduced cluster provides electrons for assembly of cytosolic iron-sulfur cluster proteins. Positively controls H(2)O(2)-induced cell death. NADPH + 2 oxidized [2Fe-2S]-[protein] = H(+) + NADP(+) + 2 reduced [2Fe-2S]-[protein] Interacts with dre2; as part of the cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery. Relocalizes to mitochondria after H(2)O(2) exposure. Belongs to the NADPH-dependent diflavin oxidoreductase NDOR1 family. In the N-terminal section; belongs to the flavodoxin family. In the C-terminal section; belongs to the flavoprotein pyridine nucleotide cytochrome reductase family. +Catalyzes the ferrous insertion into protoporphyrin IX. 2 H(+) + heme b = Fe(2+) + protoporphyrin IX Porphyrin-containing compound metabolism; protoheme biosynthesis; protoheme from protoporphyrin-IX: step 1/1. Belongs to the ferrochelatase family. +Component of the receptor for type I interferons, including interferons alpha, IFNB1 and IFNW1 (PubMed:1533935, PubMed:14532120, PubMed:23872679). Functions in general as heterodimer with IFNAR2 (By similarity). Type I interferon binding activates the JAK-STAT signaling cascade, and triggers tyrosine phosphorylation of a number of proteins including JAKs, TYK2, STAT proteins and the IFNR alpha- and beta-subunits themselves (PubMed:14532120). Can form an active IFNB1 receptor by itself and activate a signaling cascade that does not involve activation of the JAK-STAT pathway (PubMed:23872679). Contributes to modulate the innate immune response to bacterial lipopolysaccharide (PubMed:23872679). Heterodimer with IFNAR2. Interacts (serine-phosphorylated form) with FBXW11, the substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex (PubMed:14532120). Interacts with SHMT2; this promotes interaction with ABRAXAS2 and the BRISC complex (By similarity). Interacts with TYK2 (By similarity). Interacts with TRIM10; this interaction prevents association between IFNAR1 and TYK2 (By similarity). Interferon binding triggers internalization of the receptor from the cell membrane into endosomes and then into lysosomes. Ubiquitinated (PubMed:14532120). This leads to its internalization and lysosomal degradation. The 'Lys-63'-linked ubiquitin chains are cleaved off by the BRISC complex; this prevents receptor internalization and degradation. Probable ubiquitination sites have been identified in human, but are poorly conserved across species. Phosphorylated on serine residues in response to interferon binding; this promotes interaction with FBXW11 and ubiquitination (PubMed:14532120). Phosphorylated on tyrosine residues by TYK2 tyrosine kinase. Phosphorylated on tyrosine residues in response to interferon (By similarity). Mice are protected from the lethal septic effects of intraperitoneal LPS administration observed in wild-type mice (PubMed:23872679). Double knockout with TREX1 does not show a visible phenotype (PubMed:18724932). The interferon signaling pathway is not identical between species. Thus, the interaction with STAT1 and STAT2 may not be conserved in mouse; in human it requires phosphorylation at 'Tyr-466', but the mouse protein has a Phe at the equivalent position. Likewise, cysteine palmitoylation is required for the activation of STAT1 and STAT2 in human, but the Cys is not conserved in mouse. Belongs to the type II cytokine receptor family. +Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate. (2R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (2S)-2-acetolactate + H(+) + NADPH (2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP(+) = (S)-2-ethyl-2-hydroxy-3-oxobutanoate + H(+) + NADPH Binds 2 magnesium ions per subunit. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 2/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 2/4. Belongs to the ketol-acid reductoisomerase family. +Involved in chromosome condensation, segregation and cell cycle progression. May participate in facilitating chromosome segregation by condensation DNA from both sides of a centrally located replisome during cell division. Not required for mini-F plasmid partitioning. Probably acts via its interaction with MukB and MukE. Overexpression results in anucleate cells. It has a calcium binding activity. Interacts, and probably forms a ternary complex, with MukE and MukB via its C-terminal region. The complex formation is stimulated by calcium or magnesium. It is required for an interaction between MukE and MukB. Restricted to the nucleoid region. Belongs to the MukF family. +Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys) Binds 3 Mg(2+) ions per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + UDP-N-acetyl-alpha-D-glucosamine = a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + holo-[ACP] Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 1/6. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxA subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 30 kDa subunit family. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate. L-leucyl-tRNA(Leu) + N-terminal L-glutamyl-[protein] = H(+) + N-terminal L-leucyl-L-glutamyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-aspartyl-[protein] = H(+) + N-terminal L-leucyl-L-aspartyl-[protein] + tRNA(Leu) Belongs to the R-transferase family. Bpt subfamily. +Involved in the cyanide detoxification pathway. Has nitrilase and nitrile-hydratase activity in the ratio 4.0:1, producing both asparagine and aspartic acid from beta-cyano-L-alanine (Ala(CN)). Can also use 3-phenylpropionitrile as substrate, but not indole-3-acetonitrile. L-asparagine = 3-cyano-L-alanine + H2O 3-cyano-L-alanine + 2 H2O = L-aspartate + NH4(+) Ubiquitous. Belongs to the carbon-nitrogen hydrolase superfamily. Nitrilase family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +MCR is composed of three subunits: alpha, beta, and gamma. The function of proteins C and D is not known. There are two MCR complexes in this bacteria. MCR II is expressed in the early growth phase. Late growth cells contains mostly MCR I. +Part of the gene cluster that mediates the biosynthesis of calidodehydroaustin, a fungal meroterpenoid (PubMed:28233494, PubMed:29076725). The first step of the pathway is the synthesis of 3,5-dimethylorsellinic acid by the polyketide synthase ausA (PubMed:28233494). 3,5-dimethylorsellinic acid is then prenylated by the polyprenyl transferase ausN (PubMed:28233494). Further epoxidation by the FAD-dependent monooxygenase ausM and cyclization by the probable terpene cyclase ausL lead to the formation of protoaustinoid A (By similarity). Protoaustinoid A is then oxidized to spiro-lactone preaustinoid A3 by the combined action of the FAD-binding monooxygenases ausB and ausC, and the dioxygenase ausE (By similarity). Acid-catalyzed keto-rearrangement and ring contraction of the tetraketide portion of preaustinoid A3 by ausJ lead to the formation of preaustinoid A4 (By similarity). The aldo-keto reductase ausK, with the help of ausH, is involved in the next step by transforming preaustinoid A4 into isoaustinone which is in turn hydroxylated by the P450 monooxygenase ausI to form austinolide (By similarity). The cytochrome P450 monooxygenase ausG modifies austinolide to austinol (By similarity). Austinol is further acetylated to austin by the O-acetyltransferase ausP, which spontaneously changes to dehydroaustin (PubMed:28233494). The cytochrome P450 monooxygenase ausR then converts dehydroaustin is into 7-dehydrodehydroaustin (PubMed:28233494). The hydroxylation catalyzed by ausR permits the O-acetyltransferase ausQ to add an additional acetyl group to the molecule, leading to the formation of acetoxydehydroaustin (PubMed:28233494). The short chain dehydrogenase ausT catalyzes the reduction of the double bond present between carbon atoms 1 and 2 to convert 7-dehydrodehydroaustin into 1,2-dihydro-7-hydroxydehydroaustin (PubMed:28233494). AusQ catalyzes not only an acetylation reaction but also the addition of the PKS ausV diketide product to 1,2-dihydro-7-hydroxydehydroaustin, forming precalidodehydroaustin (PubMed:28233494). Finally, the iron/alpha-ketoglutarate-dependent dioxygenase converts precalidodehydroaustin into calidodehydroaustin (PubMed:28233494). Secondary metabolite biosynthesis; terpenoid biosynthesis. Homodimer. In A.calidoustus, the austinoid gene cluster lies on a contiguous DNA region, while clusters from E.nidulans and P.brasilianum are split in their respective genomes. Genetic rearrangements provoked variability among the clusters and E.nidulans produces the least number of austionoid derivatives with the end products austinol and dehydroaustinol, while P.brasilianum can produce until acetoxydehydroaustin, and A.calidoustus produces the highest number of identified derivatives. Belongs to the trt14 isomerase family. +(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate Belongs to the 4-hydroxy-2-oxovalerate aldolase family. +Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + UDP-N-acetyl-alpha-D-glucosamine = a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + holo-[ACP] Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 1/6. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxA subfamily. +Required for the retention of luminal endoplasmic reticulum proteins, affects glycoprotein processing in the Golgi apparatus. Belongs to the ERD1 family. +Component of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum (ER) and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis, and function in nonvesicular lipid trafficking between the ER and mitochondria. MDM34 is required for the interaction of the ER-resident membrane protein MMM1 and the outer mitochondrial membrane-resident beta-barrel protein MDM10. Component of the ER-mitochondria encounter structure (ERMES) or MDM complex, composed of MMM1, MDM10, MDM12 and MDM34. The ERMES/MDM complex localizes to a few discrete foci (around 10 per single cell), that represent mitochondria-endoplasmic reticulum junctions. These foci are often found next to mtDNA nucleoids. Lacks alpha-helical transmembrane segments, suggesting that it resides in the membrane via beta-sheet conformations similar to those predicted for other outer membrane proteins and porin. The SMP-LTD domain is a barrel-like domain that can bind various types of glycerophospholipids in its interior and mediate their transfer between two adjacent bilayers. Belongs to the MDM34 family. +Bifunctional enzyme that has both L-aspartate decarboxylase and transaminase activity. Has high activity with L-aspartate, and much lower activity with D-aspartate, L-lysine and L-glutamine. H(+) + L-aspartate = CO2 + L-alanine 2-oxoglutarate + L-aspartate = L-glutamate + oxaloacetate Inhibited by 10 mM Co(2+), Mn(2+) and Ni(2+), and by 1 mM Cu(2+) and Hg(2+). Optimum pH is 5. Optimum temperature is 45 degrees Celsius. Homododecamer. Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The archaeal alpha chain is a catalytic subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate Belongs to the ATPase alpha/beta chains family. +Binds the stem-loop structure of replication-dependent histone mRNAs. Is associated with translationally inactive histone mRNA stored in oocytes. Could be a specific translational repressor. Not involved in histone pre-mRNA processing. Binds the stem-loop structure of replication-dependent histone mRNAs. Is associated with translationally inactive histone mRNA stored in oocytes. Could be a specific translational repressor. Not involved in histone pre-mRNA processing. Oocyte. Detectable in stage I oocytes, increases through stages III and IV, then slightly declines as the oocytes mature to stage VI. Present in early embryogenesis until midblastula transition, at which point it becomes undetectable. Belongs to the SLBP family. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +Component of HBO1 complexes, which specifically mediate acetylation of histone H3 at 'Lys-14' (H3K14ac), and have reduced activity toward histone H4. Through chromatin acetylation it may function in DNA replication. Homodimer. Component of the HBO1 complex. The PHD-type zinc finger mediates the binding to H3K4me3. Belongs to the ING family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Divisome component that associates with the complex late in its assembly, after the Z-ring is formed, and is dependent on DivIC and PBP2B for its recruitment to the divisome. Together with EzrA, is a key component of the system that regulates PBP1 localization during cell cycle progression. Its main role could be the removal of PBP1 from the cell pole after pole maturation is completed. Also contributes to the recruitment of PBP1 to the division complex. Not essential for septum formation. Forms polymers through the coiled coil domains. Interacts with PBP1, MreC and EzrA. Shuttles between the lateral wall and the division site in a cell cycle-dependent manner. Belongs to the GpsB family. +Might take part in the signal recognition particle (SRP) pathway. This is inferred from the conservation of its genetic proximity to ftsY/ffh. May be a regulatory protein. Belongs to the UPF0122 family. +Shows a 3'-5' exoribonuclease activity. Belongs to the YhaM family. +Catalyzes the addition of molecular CO(2) and H(2)O to ribulose 1,5-bisphosphate (RuBP), generating two molecules of 3-phosphoglycerate (3-PGA). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Reversibly inhibited by O(2). Active from 25 to 40 degrees Celsius. Homodimer. In contrast to form I RuBisCO, the form III RuBisCO is composed solely of large subunits. Because the Archaea possessing a type III RuBisCO are all anaerobic, it is most likely that only the carboxylase activity of RuBisCO, and not the competitive oxygenase activity (by which RuBP reacts with O(2) to form one molecule of 3-phosphoglycerate and one molecule of 2-phosphoglycolate), is biologically relevant in these strains. Belongs to the RuBisCO large chain family. Type III subfamily. +Has no enzymatic activity. May serve as a target for Rho, and interact with some cytoskeletal component upon Rho binding or relay a Rho signal to other molecules. Binds specifically to GTP-Rho. Interacts with ROPN1. The PDZ domain mediates interaction with ROPN1. Belongs to the RHPN family. Intron retention. Intron retention. +Because S100A10 induces the dimerization of ANXA2/p36, it may function as a regulator of protein phosphorylation in that the ANXA2 monomer is the preferred target (in vitro) of tyrosine-specific kinase. Heterotetramer containing 2 light chains of S100A10/p11 and 2 heavy chains of ANXA2/p36 (By similarity). Interacts with SCN10A (By similarity). Interacts with TASOR (By similarity). Does not appear to bind calcium. Contains 2 ancestral calcium site related to EF-hand domains that have lost their ability to bind calcium. Belongs to the S-100 family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Feedback inhibited by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Belongs to the ATP phosphoribosyltransferase family. Long subfamily. +Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria. 3-deoxy-alpha-D-manno-oct-2-ulosonate + CTP = CMP-3-deoxy-beta-D-manno-octulosonate + diphosphate Nucleotide-sugar biosynthesis; CMP-3-deoxy-D-manno-octulosonate biosynthesis; CMP-3-deoxy-D-manno-octulosonate from 3-deoxy-D-manno-octulosonate and CTP: step 1/1. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsB family. +RNA-directed RNA polymerase that is involved in both transcription and genome replication. Together with VP3 capping enzyme, forms an enzyme complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. One copy of each of the viral (+)RNAs is also recruited during core assembly, together with newly synthesized polymerase complexes and VP2. The polymerase of these novo-formed particles catalyzes the synthesis of complementary minus-strands leading to dsRNA formation. To do so, the polymerase specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved 3'-sequence of plus-strand RNA templates. VP2 presumably activates the autoinhibited VP1-RNA complex to coordinate packaging and genome replication. Once dsRNA synthesis is complete, the polymerase switches to the transcriptional mode, thus providing secondary transcription (By similarity). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Interacts with VP3 (Potential). Interacts with VP2; this interaction activates VP1. Interacts with NSP5; this interaction is probably necessary for the formation of functional virus factories. Interacts with NSP2; this interaction is weak (By similarity). Attached inside the inner capsid as a minor component. Also found in spherical cytoplasmic structures, called virus factories, that appear early after infection and are the site of viral replication and packaging (By similarity). Belongs to the reoviridae RNA-directed RNA polymerase family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +Tubulin is the major constituent of microtubules. The gamma chain is found at microtubule organizing centers (MTOC) such as the spindle poles or the centrosome, suggesting that it is involved in the minus-end nucleation of microtubule assembly. Belongs to the tubulin family. +Hydrolyzes dipeptides containing N-terminal aspartate residues. May play a role in allowing the cell to use peptide aspartate to spare carbon otherwise required for the synthesis of the aspartate family of amino acids. Dipeptidase E catalyzes the hydrolysis of dipeptides Asp-|-Xaa. It does not act on peptides with N-terminal Glu, Asn or Gln, nor does it cleave isoaspartyl peptides. Belongs to the peptidase S51 family. +Mono-ADP-ribosyltransferase that mediates mono-ADP-ribosylation of target proteins (PubMed:25043379, PubMed:25673562). Plays a role in nuclear envelope stability and nuclear remodeling during spermiogenesis (By similarity). L-aspartyl-[protein] + NAD(+) = 4-O-(ADP-D-ribosyl)-L-aspartyl-[protein] + nicotinamide L-cysteinyl-[protein] + NAD(+) = H(+) + nicotinamide + S-(ADP-D-ribosyl)-L-cysteinyl-[protein] L-glutamyl-[protein] + NAD(+) = 5-O-(ADP-D-ribosyl)-L-glutamyl-[protein] + nicotinamide L-lysyl-[protein] + NAD(+) = H(+) + N(6)-(ADP-D-ribosyl)-L-lysyl-[protein] + nicotinamide Colocalizes with NUP153 at nuclear pores. Auto-mono-ADP-ribosylated. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the ARTD/PARP family. Truncated N-terminus. Truncated N-terminus. +One of the components of the core complex of photosystem II (PSII), required for its stability and/or assembly. PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, numerous small proteins, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbH family. +The electron transfer flavoprotein serves as a specific electron acceptor for other dehydrogenases. It transfers the electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase (ETF dehydrogenase). Binds 1 FAD per dimer. Heterodimer of an alpha and a beta subunit. Belongs to the ETF alpha-subunit/FixB family. +Displays ATPase and GTPase activities. Belongs to the RapZ-like family. +One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS17 family. +Catalyzes the methylation of C-1 in cobalt-precorrin-5B to form cobalt-precorrin-6A. Co-precorrin-5B + S-adenosyl-L-methionine = Co-precorrin-6A + S-adenosyl-L-homocysteine Cofactor biosynthesis; adenosylcobalamin biosynthesis; cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route): step 6/10. Belongs to the CbiD family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +5' to 3' DNA replicative helicase recruited to paused replisomes to promote fork progression throughout nonhistone protein-DNA complexes, naturally occurring impediments that are encountered in each S phase where replication forks pauses. Needed for normal fork progression through over 1000 discrete sites scattered throughout the genome, like rDNA, tRNA genes, centromeres, active replication origins, or transcriptional silencers. Required for timely replication of the telomere and subtelomeric DNA and for wild-type levels of telomeric silencing. Involved in regulation of Ty1 transposition and protects the genome from instability at nascent sites of retrotransposition. Involved in DNA repair during stalled replication fork, regulation of fragile sites expression and essential for genome stability. Also plays a role in mtDNA replication. Has G-quadruplex (G4) unwinding activity and can suppress G4-induced genome instability when PIF1 levels are low. ATP + H2O = ADP + H(+) + phosphate Interacts with DEF1 and POL30. The N-terminal part (residues 1 to 249) is essential for function and confers locus specificity. Present with 656 molecules/cell in log phase SD medium. Belongs to the helicase family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 1 Zn(2+) ion per subunit. In cyanobacteria the RNAP catalytic core is composed of 2 alpha, 1 beta, 1 beta', 1 gamma and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. RpoC1 subfamily. +Catalyzes the excretion of spermidine. Forms a complex with MdtI. Belongs to the drug/metabolite transporter (DMT) superfamily. Small multidrug resistance (SMR) (TC 2.A.7.1) family. MdtJ subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 30 kDa subunit family. +Belongs to the protein-tyrosine phosphatase family. PTP-H1 does not appear to be a functional PTP. +Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. This function is generally fulfilled by the C-terminal part of HisG, which is missing in some bacteria such as this one. Belongs to the class-II aminoacyl-tRNA synthetase family. HisZ subfamily. +Catalyzes the attachment of tryptophan to tRNA(Trp). ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + H(+) + L-tryptophanyl-tRNA(Trp) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell. Homopentamer. Belongs to the MscL family. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Acts redundantly with SPR1 in maintaining the cortical microtubules organization essential for anisotropic cell growth. A number of isoforms are produced. According to EST sequences. Ubiquitous. Preferentially expressed in above-ground organs. Belongs to the SPIRAL1 family. +May be involved in signal transduction. Participates in the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria, via its interaction with KaiC. Required for robustness of the circadian rhythm of gene expression and is involved in clock outputs. ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. Interacts with KaiC. Participates in the KaiABC complex, whose core is composed of a KaiC homohexamer, a KaiB dimer and two KaiA dimers. +Responsible for synthesis of pseudouridine from uracil at positions 955, 2504 and 2580 in 23S ribosomal RNA. uridine(955/2504/2580) in 23S rRNA = pseudouridine(955/2504/2580) in 23S rRNA Belongs to the pseudouridine synthase RluA family. +In conjunction with KorB, inhibits the transcription of kilA, trfA and korAB operons. In conjunction with KorC is responsible for the negative control of kilC and kilE operons. +Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III. 4 H(+) + uroporphyrinogen III = 4 CO2 + coproporphyrinogen III Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 4/4. Homodimer. Belongs to the uroporphyrinogen decarboxylase family. +Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Belongs to the Abd-B homeobox family. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. (2S,6S)-2,6-diaminoheptanedioate = meso-2,6-diaminoheptanedioate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. Homodimer. Belongs to the diaminopimelate epimerase family. +The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination. The AddA nuclease domain is required for chi fragment generation; this subunit has the helicase and 3' -> 5' nuclease activities. ATP + H2O = ADP + H(+) + phosphate Heterodimer of AddA and AddB/RexB. Belongs to the helicase family. AddA subfamily. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +2 ATP + H2O + hydrogencarbonate + L-glutamine = 2 ADP + carbamoyl phosphate + 2 H(+) + L-glutamate + phosphate Amino-acid biosynthesis; L-arginine biosynthesis; carbamoyl phosphate from bicarbonate: step 1/1. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 1/3. Composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate. Belongs to the CarA family. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Catalyzes the formation of a hydroxyacyl-CoA by addition of water on enoyl-CoA. Also exhibits 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities. a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O a 4-saturated-(3S)-3-hydroxyacyl-CoA = a (3E)-enoyl-CoA + H2O a (3S)-3-hydroxyacyl-CoA + NAD(+) = a 3-oxoacyl-CoA + H(+) + NADH (3S)-3-hydroxybutanoyl-CoA = (3R)-3-hydroxybutanoyl-CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadJ) and two beta chains (FadI). In the N-terminal section; belongs to the enoyl-CoA hydratase/isomerase family. In the central section; belongs to the 3-hydroxyacyl-CoA dehydrogenase family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. ATP + meso-2,6-diaminoheptanedioate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate Cell wall biogenesis; peptidoglycan biosynthesis. Carboxylation is probably crucial for Mg(2+) binding and, consequently, for the gamma-phosphate positioning of ATP. Belongs to the MurCDEF family. MurE subfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Belongs to the V-ATPase E subunit family. +Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain. acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine Binds 1 Mg(2+) ion per subunit. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; N-acetyl-alpha-D-glucosamine 1-phosphate from alpha-D-glucosamine 6-phosphate (route II): step 2/2. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; UDP-N-acetyl-alpha-D-glucosamine from N-acetyl-alpha-D-glucosamine 1-phosphate: step 1/1. Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. In the N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family. In the C-terminal section; belongs to the transferase hexapeptide repeat family. +Belongs to the SH3BGR family. +Protein phosphatase with specificity for serine, threonine, and tyrosine residues; has a role in the DNA synthesis phase of the cell cycle. H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Belongs to the protein-tyrosine phosphatase family. Non-receptor class dual specificity subfamily. +Spectrin is the major constituent of the cytoskeletal network underlying the erythrocyte plasma membrane. It associates with band 4.1 and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. Composed of nonhomologous chains, alpha and beta, which aggregate to form dimers, tetramers, and higher polymers. This complex is anchored to the cytoplasmic face of the plasma membrane via another protein, ankyrin, which binds to beta-spectrin and mediates the binding of the whole complex to a transmembrane protein band 3. The interaction of erythrocyte spectrin with other proteins through specific binding domains lead to the formation of an extensive subplasmalemmal meshwork which is thought to be responsible for the maintenance of the biconcave shape of human erythrocytes, for the regulation of plasma membrane components and for the maintenance of the lipid asymmetry of the plasma membrane. Belongs to the spectrin family. +Auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'-5' exonuclease and 3'-phosphodiesterase, but not apurinic-apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2. Plays a key role in DNA damage response (DDR) by being conveniently positioned at the replication fork to coordinate DNA replication with DNA repair and DNA damage tolerance pathways. Acts as a loading platform to recruit DDR proteins that allow completion of DNA replication after DNA damage and promote postreplication repair: Monoubiquitinated PCNA leads to recruitment of translesion (TLS) polymerases, while 'Lys-63'-linked polyubiquitination of PCNA is involved in error-free pathway and employs recombination mechanisms to synthesize across the lesion (By similarity). Homotrimer. Interacts with p300/EP300; the interaction occurs on chromatin in UV-irradiated damaged cells. Interacts with CREBBP (via transactivation domain and C-terminus); the interaction occurs on chromatin in UV-irradiated damaged cells. Directly interacts with POLD1, POLD3 and POLD4 subunits of the DNA polymerase delta complex, POLD3 being the major interacting partner; the interaction with POLD3 is inhibited by CDKN1A/p21(CIP1). Forms a complex with activator 1 heteropentamer in the presence of ATP. Interacts with EXO1, POLH, POLK, DNMT1, ERCC5, FEN1, CDC6 and POLDIP2. Interacts with APEX2; this interaction is triggered by reactive oxygen species and increased by misincorporation of uracil in nuclear DNA. Forms a ternary complex with DNTTIP2 and core histone (By similarity). Interacts with KCTD10 and PPP1R15A (By similarity). Interacts with SMARCA5/SNF2H (By similarity). Interacts with BAZ1B/WSTF; the interaction is direct and is required for BAZ1B/WSTF binding to replication foci during S phase (By similarity). Interacts with HLTF and SHPRH. Interacts with NUDT15; this interaction is disrupted in response to UV irradiation and acetylation. Interacts with CDKN1A/p21(CIP1) and CDT1; interacts via their PIP-box which also recruits the DCX(DTL) complex. The interaction with CDKN1A inhibits POLD3 binding. Interacts with DDX11. Interacts with EGFR; positively regulates PCNA. Interacts with PARPBP. Interacts (when ubiquitinated) with SPRTN; leading to enhance RAD18-mediated PCNA ubiquitination. Interacts (when polyubiquitinated) with ZRANB3. Interacts with SMARCAD1. Interacts with CDKN1C. Interacts with PCLAF (via PIP-box). Interacts with RTEL1 (via PIP-box); the interaction is direct and essential for the suppression of telomere fragility. Interacts with FAM111A (via PIP-box); the interaction is direct and required for PCNA loading on chromatin binding. Interacts with LIG1. Interacts with SETMAR. Interacts with ANKRD17. Interacts with FBXO18/FBH1 (via PIP-box); the interaction recruits the DCX(DTL) complex and promotes ubiquitination and degradation of FBXO18/FBH1. Interacts with POLN (By similarity). Interacts with SDE2 (via PIP-box); the interaction is direct and prevents ultraviolet light induced monoubiquitination (By similarity). Component of the replisome complex composed of at least DONSON, MCM2, MCM7, PCNA and TICRR; interaction at least with PCNA occurs during DNA replication (By similarity). Interacts with MAPK15; the interaction is chromatin binding dependent and prevents MDM2-mediated PCNA destruction by inhibiting the association of PCNA with MDM2. Interacts with PARP10 (via PIP-box) (By similarity). Interacts with DDI2 (By similarity). Interacts with HMCES (via PIP-box) (By similarity). Interacts with TRAIP (via PIP-box) (By similarity). Interacts with UHRF2 (By similarity). Interacts with ALKBH2; this interaction is enhanced during the S-phase of the cell cycle. Interacts with ATAD5; the interaction promotes USP1-mediated PCNA deubiquitination (By similarity). Forms nuclear foci representing sites of ongoing DNA replication and vary in morphology and number during S phase. Together with APEX2, is redistributed in discrete nuclear foci in presence of oxidative DNA damaging agents. Colocalizes with CREBBP, EP300 and POLD1 to sites of DNA damage (By similarity). Phosphorylated. Phosphorylation at Tyr-211 by EGFR stabilizes chromatin-associated PCNA (By similarity). Acetylated by CREBBP and p300/EP300; preferentially acetylated by CREBBP on Lys-80, Lys-13 and Lys-14 and on Lys-77 by p300/EP300 upon loading on chromatin in response to UV irradiation. Lysine acetylation disrupts association with chromatin, hence promoting PCNA ubiquitination and proteasomal degradation in response to UV damage in a CREBBP- and EP300-dependent manner. Acetylation disrupts interaction with NUDT15 and promotes degradation (By similarity). Ubiquitinated. Following DNA damage, can be either monoubiquitinated to stimulate direct bypass of DNA lesions by specialized DNA polymerases or polyubiquitinated to promote recombination-dependent DNA synthesis across DNA lesions by template switching mechanisms. Following induction of replication stress, monoubiquitinated by the UBE2B-RAD18 complex on Lys-164, leading to recruit translesion (TLS) polymerases, which are able to synthesize across DNA lesions in a potentially error-prone manner. An error-free pathway also exists and requires non-canonical polyubiquitination on Lys-164 through 'Lys-63' linkage of ubiquitin moieties by the E2 complex UBE2N-UBE2V2 and the E3 ligases, HLTF, RNF8 and SHPRH. This error-free pathway, also known as template switching, employs recombination mechanisms to synthesize across the lesion, using as a template the undamaged, newly synthesized strand of the sister chromatid. Monoubiquitination at Lys-164 also takes place in undamaged proliferating cells, and is mediated by the DCX(DTL) complex, leading to enhance PCNA-dependent translesion DNA synthesis. Sumoylated during S phase (By similarity). Methylated on glutamate residues by ARMT1. Belongs to the PCNA family. +Is able to catalyze the biosynthesis of dTMP using dUMP, tetrahydrofolate and formaldehyde in vitro, i.e. a reaction equivalent to that catalyzed by bacterial thymidylate synthases (EC 2.1.1.45). However, M.jannaschii like most methanogenic Archaea lacks folates, thus the physiological cosubstrate is unknown but is likely one of the non-methylated methanopterin biosynthetic intermediates. Pyrimidine metabolism; dTTP biosynthesis. +Component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. Component of the PAM complex, at least composed of mtHsp70 (SSC1), MGE1, TIM44, PAM16, PAM17 and PAM18. Belongs to the PAM17 family. +Catalyzes the O-sulfation of tyrosine residues within acidic motifs of polypeptides, using 3'-phosphoadenylyl sulfate (PAPS) as cosubstrate. 3'-phosphoadenylyl sulfate + L-tyrosyl-[protein] = adenosine 3',5'-bisphosphate + H(+) + O-sulfo-L-tyrosine-[protein] Belongs to the protein sulfotransferase family. +Catalyzes the transfer of L-fucose, from a guanosine diphosphate-beta-L-fucose, to the N-acetyl glucosamine (GlcNAc) of a distal alpha2,3 sialylated lactosamine unit of a glycoprotein- or a glycolipid-linked sialopolylactosamines chain or of a distal or internal lactosamine unit of a neutral glycoprotein- or a glycolipid-linked polylactosamines chain through an alpha-1,3 glycosidic linkage and participates in surface expression of the sialyl Lewis X (sLe(x)), Lewis X (Le(x)) and non sialylated VIM2 determinants (PubMed:9451035, PubMed:1520296, PubMed:1339443, PubMed:7650030, PubMed:17604274, PubMed:9363434, PubMed:10728707, PubMed:29593094). Moreover transfers fucose to H-type 2 (Fucalpha1-2Galbeta1-4GlcNAc) chain acceptor substrates and participates in difucosylated sialyl Lewis x determinants (PubMed:17604274, PubMed:1339443). Also fucosylates a polylactosamine substrate having a 6 sulfate modification at the GlcNAc moiety and gives rise to sialyl and non-sialyl 6-sulfo lewis X (PubMed:10728707). Does not have activity towards type 1 ((Galbeta1-3GlcNAc)) and H-type 1 chain (Fucalpha1-2Galbeta1-3GlcNAc) acceptors substrates (PubMed:1339443, PubMed:17604274, PubMed:9363434). Does not have alpha(1,3)-fucosyltransferase activity. a beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + GDP-beta-L-fucose = a beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl derivative + GDP + H(+) an N-acetyl-alpha-neuraminyl-(2->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + GDP-beta-L-fucose = an alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-beta-D-GlcNAc derivative + GDP + H(+) an alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-beta-D-GlcNAc derivative + GDP-beta-L-fucose = an alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-beta-D-GlcNAc derivative + GDP + H(+) beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + GDP-beta-L-fucose = beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + GDP + H(+) beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + GDP-beta-L-fucose = beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide + GDP + H(+) GDP-beta-L-fucose + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide = GDP + H(+) + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide beta-D-galactosyl-(1->4)-N-acetyl-D-glucosamine + GDP-beta-L-fucose = beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-D-glucosamine + GDP + H(+) GDP-beta-L-fucose + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosamine = GDP + H(+) + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosamine GDP-beta-L-fucose + lactose = beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-D-glucose + GDP + H(+) alpha-L-Fuc-(1->2)-beta-D-Gal-(1->4)-D-Glc + GDP-beta-L-fucose = alpha-L-Fuc-(1->2)-beta-D-Gal-(1->4)-[alpha-L-Fuc-(1->3)]-D-Glc + GDP + H(+) a beta-D-galactosyl-(1->4)-N-acetyl-beta-D-6-sulfooxy-glucosaminyl derivative + GDP-beta-L-fucose = a beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-6-sulfooxy-glucosaminyl derivative + GDP + H(+) Protein modification; protein glycosylation. Homodimer and monomer (PubMed:9451035). Monomer (secreted form) (PubMed:9451035). Membrane-bound form in trans cisternae of Golgi. Kidney, liver, colon, small intestine, bladder, uterus and salivary gland. N-glycosylated. Proteolytic cleavage releases a secreted glycoform of 43 kDa. Expression of alpha(1,3)-fucosyltransferase in plasma can vary among different populations. 9% of individuals on the isle of Java (Indonesia) do not express this enzyme. Ninety-five percent of plasma alpha(1,3)-fucosyltransferase-deficient individuals have Lewis negative phenotype on red cells, suggesting strong linkage disequilibrium between these two traits. Variations in FUT6 are responsible for plasma alpha(1,3)-fucosyltransferase deficiency [MIM:613852]. Belongs to the glycosyltransferase 10 family. Probable cloning artifact. Fucosyltransferase 6 +Pore-forming protein that forms cations-selective hydrophilic pores of around 1 nm and causes cardiac stimulation and hemolysis. Pore formation is a multi-step process that involves specific recognition of membrane sphingomyelin (but neither cholesterol nor phosphatidylcholine) using aromatic rich region and adjacent phosphocholine (POC) binding site, firm binding to the membrane (mainly driven by hydrophobic interactions) accompanied by the transfer of the N-terminal region to the lipid-water interface and finally pore formation after oligomerization of monomers. Tetramer in the presence of a lipidic interface. Monomer, in soluble state. Forms an alpha-helical membrane channel in the prey. The N-terminal region, before the pore is formed, is bound to the lipid membrane. It partitions into the lipid-water interface and stabilizes the monomeric molecule on the membrane. Finally, it traverses the bilayer, thus forming the transmembrane pore. Belongs to the actinoporin family. Sea anemone subfamily. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homodimer. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 2 subfamily. +PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin. hnu + oxidized [2Fe-2S]-[ferredoxin] + reduced [plastocyanin] = oxidized [plastocyanin] + reduced [2Fe-2S]-[ferredoxin] P700 is a chlorophyll a/chlorophyll a' dimer, A0 is one or more chlorophyll a, A1 is one or both phylloquinones and FX is a shared 4Fe-4S iron-sulfur center. The PsaA/B heterodimer binds the P700 chlorophyll special pair and subsequent electron acceptors. PSI consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The eukaryotic PSI reaction center is composed of at least 11 subunits. Belongs to the PsaA/PsaB family. +GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Toroid-shaped homodecamer, composed of two pentamers of five dimers. Belongs to the GTP cyclohydrolase I family. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Cysteine protease inhibitor which inhibits members of the peptidase C1 family (PubMed:12704112, PubMed:15664654). Does not inhibit asparaginyl endopeptidase (PubMed:15664654). Required for the uptake and/or processing of yolk proteins during the development of oocytes, probably by regulating the catalytic activity of cysteine proteases cpl-1 and cpz-1 (PubMed:16857685). May play a protective role against exogenous cysteine proteases derived from soil bacteria or fungi, or rotting fruits and vegetation (PubMed:24001183). Localizes to the sheath cell cytoplasm surrounding germ cells and oocytes. Localizes to yolk granules in the developing oocyte. Expressed in germ cells, developing oocytes and sperm, sheath cells surrounding germ cells and oocytes and in the eggshell (at protein level) (PubMed:16857685). Expressed in the pharyngeal gland, pharyngeal muscles and some hypodermal cells in the tail (PubMed:16857685). Expressed in embryos, larvae and adults (at protein level) (PubMed:15664654, PubMed:16857685). Expressed in the ecdysed cuticle during molting (at protein level) (PubMed:16857685). In embryos and larvae, expressed in intestinal, hypodermal and pharyngeal cells (PubMed:16857685). Expression transiently increases during early embryonic stages and prior to the larval L1/L2, L2/L3, L3/L4 and L4/adult molts (PubMed:16857685). Belongs to the cystatin family. +Recognizes and binds in the vacant E-site of ribosomes stalled by some peptidyltransferase center (PTC)-targeting antibiotics. Makes contact with the PTC and both ribosomal subunits. Induces conformational changes in the P-site, which allows it to dislodge the antibiotic from its PTC binding site. Binds to ribosomes either directly following translation initation or subsequent to E tRNA release during elongation (PubMed:30126986). Involved in resistance to a narrow spectrum of antibiotics (the streptogramin A antibiotic virginiamycin M, the lincosamide antibiotic lincomycin and the pleuromutilin antibiotic tiamulin) (PubMed:16109936, PubMed:30126986). Binds within the E-site of the 70S ribosome, where it contacts ribosomal proteins L1, L5, L33-1, S7, S11, the 16 and 23S rRNAs and the acceptor arm of the P-site tRNA. Does not stably associate with ribosomes. Expressed during all growth phases; expression is higher during early log phase and decreases as growth continues. Expression is dramatically increased in the presence of antibiotics virginiamycin M and lincomycin. A monocistronic operon. The antibiotic resistance domain (ARD) is packed between the 23S rRNA and the acceptor arm of the P-site tRNA and inserts into the peptidyltransferase center (PTC). The C-terminal extension (CTE) contacts the small ribosomal subunit, positioned in the Shine-Dalgarno-anti-Shine-Dalgarno cavity. Hypersensitivity toward the antibiotics virginiamycin M and lincomycin, mildly increased sensitivity to erythromycin, clindamycin and oleandomycin (PubMed:16109936). Hypersensitivity toward the antibiotics virginiamycin M, lincomycin and tiamulin, in this study has no effect on sensitivity to erythromycin, chloramphenicol or linezolid (PubMed:30126986). Belongs to the ABC transporter superfamily. ABCF family. ARE2 subfamily. +A non-essential component of RNA polymerase (RNAP). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) RNAP is composed of a core of 2 alpha, a beta and a beta' subunit. The core is associated with a delta subunit, and at least one of epsilon or omega. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit epsilon family. +Plays a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as the collagens and fibronectin. Can mediate the interaction of chondrocytes with the cartilage extracellular matrix through interaction with cell surface integrin receptors. Could play a role in the pathogenesis of osteoarthritis. Potent suppressor of apoptosis in both primary chondrocytes and transformed cells. Suppresses apoptosis by blocking the activation of caspase-3 and by inducing the IAP family of survival proteins (BIRC3, BIRC2, BIRC5 and XIAP) (By similarity). Essential for maintaining a vascular smooth muscle cells (VSMCs) contractile/differentiated phenotype under physiological and pathological stimuli. Maintains this phenotype of VSMCs by interacting with ITGA7 (By similarity). Binds 11-14 calcium ions per subunit. Pentamer; disulfide-linked. Exists in a more compact conformation in the presence of calcium and shows a more extended conformation in the absence of calcium. Interacts with ITGB3, ITGA5 and FN1. Binding to FN1 requires the presence of divalent cations (Ca(2+), Mg(2+) or Mn(2+)). The greatest amount of binding is seen in the presence of Mn(2+). Interacts with MATN1, MATN3, MATN4 and ACAN (By similarity) (PubMed:15075323). Binds heparin, heparan sulfate and chondroitin sulfate. EDTA dimishes significantly its binding to ACAN and abolishes its binding to MATN3, MATN4 and chondroitin sulfate. Interacts with collagen I, II and IX, and interaction with these collagens is dependent on the presence of zinc ions. Interacts with ADAMTS12 (By similarity). Interacts with ITGA7 (By similarity). The cell attachment motif mediates the attachment to chondrocytes. It mediates the induction of both the IAP family of survival proteins and the antiapoptotic response. The TSP C-terminal domain mediates interaction with FN1 and ACAN. Each of the eight TSP type-3 repeats binds two calcium ions. The TSP C-terminal domain binds three calcium ions. Belongs to the thrombospondin family. +Required for precocious cardiac adaptation to stress through integrated regulation of the AKT/mTOR pathways and FOXO1. Regulates cardiac homeostasis and plays an important role in protection against cardiac hypertrophy (PubMed:22343712, PubMed:26436652). Acts as a transcriptional cofactor, represses transactivator activity of ISL1 and MYOCD (By similarity). Interacts with LMNA. Interacts with ISL1 (via N-terminal domain); the interaction represses ISL1 transactivator activity. Expressed in cardiomyoctes. Expression is highly reduced in hypertrophic cardiomyocytes. Extended N-terminus. +Forms oligomers. Belongs to the MraZ family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a(1), b(1), b'(1) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta, b and b' chains. Belongs to the ATPase delta chain family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +Belongs to the UPF0234 family. +Probable cell surface metalloreductase. May be involved in iron or copper homeostasis (By similarity). Interacts with ribosomes. Belongs to the ferric reductase (FRE) family. AIM14 subfamily. +Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + H2O + oxidized [flavodoxin] = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + reduced [flavodoxin] Binds 1 [4Fe-4S] cluster. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 5/6. Belongs to the IspG family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-methyl-D-erythritol + diphosphate Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. Belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Belongs to the UPF0312 family. Type 1 subfamily. +May be involved in the ribosome maturation process. Found in the dense fibrillar compartment region of the nucleolus. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 1 family. +This clone was isolated from a cytotoxic T lymphocyte. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvP family. +Part of the AP-3 complex, an adaptor-related complex which is essential for the compartmentalization of the endocytic pathway. Adaptor protein complex 3 (AP-3) is a heterotetramer composed of two large adaptins (delta-type subunit and beta-type subunit), a medium adaptin (mu-type subunit) and a small adaptin (sigma-type subunit). Belongs to the adaptor complexes large subunit family. The gene for this protein is duplicated in strains AX3 and AX4. These strains contain a duplication of a segment of 750 kb of chromosome 2 compared to the corresponding sequence in strain AX2. +Actins are highly conserved proteins that are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells. Polymerization of globular actin (G-actin) leads to a structural filament (F-actin) in the form of a two-stranded helix. Each actin can bind to 4 others. Predominantly expressed in heart. Lower levels in skeletal muscle and skin. Oxidation of Met-46 and Met-49 by MICALs (MICAL1, MICAL2 or MICAL3) to form methionine sulfoxide promotes actin filament depolymerization. MICAL1 and MICAL2 produce the (R)-S-oxide form. The (R)-S-oxide form is reverted by MSRB1 and MSRB2, which promotes actin repolymerization. Monomethylation at Lys-86 (K86me1) regulates actin-myosin interaction and actomyosin-dependent processes. Demethylation by ALKBH4 is required for maintaining actomyosin dynamics supporting normal cleavage furrow ingression during cytokinesis and cell migration. In vertebrates 3 main groups of actin isoforms, alpha, beta and gamma have been identified. The alpha actins are found in muscle tissues and are a major constituent of the contractile apparatus. The beta and gamma actins coexist in most cell types as components of the cytoskeleton and as mediators of internal cell motility. There are three genes coding for cardiac actin in Fugu. Belongs to the actin family. +This protein strongly inhibits papain and ficin, partially inhibits stem bromelain and bovine cathepsin C, but does not inhibit porcine cathepsin B or clostripain. Papain is inhibited non-competitively. Found in saliva, tears, urine and seminal fluid. Belongs to the cystatin family. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Probable regulator of exocrine pancreas development. Belongs to the PPDPF family. +The glycine decarboxylase (GDC) or glycine cleavage system catalyzes the degradation of glycine. (6S)-5,6,7,8-tetrahydrofolate + (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[protein] = (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + NH4(+) The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvT family. +Belongs to the DNA glycosylase MPG family. +Involved in GM1/GD1B/GA1 ganglioside biosynthesis. ganglioside GM2 (d18:1(4E)) + UDP-alpha-D-galactose = ganglioside GM1 (d18:1(4E)) + H(+) + UDP ganglioside GM2 + UDP-alpha-D-galactose = ganglioside GM1 + H(+) + UDP ganglioside GD2 (d18:1(4E)) + UDP-alpha-D-galactose = ganglioside GD1b (d18:1(4E)) + H(+) + UDP ganglioside GA2 (d18:1(4E)) + UDP-alpha-D-galactose = ganglioside GA1 (d18:1(4E)) + H(+) + UDP Protein modification; protein glycosylation. Expressed in heart, brain, spleen, kidney, lung and testis. First expressed at embryonic day 3. Maintained at high levels between days 4 and 7 and declines thereafter to stabilize at low levels after day 10. Belongs to the glycosyltransferase 31 family. b3GalT4 +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Nuclear receptor that exhibits a ligand-dependent transcriptional activation activity (PubMed:18055760, PubMed:19520913, PubMed:20427281). Interaction with retinoic acid receptor (RXR) shifts RXR from its role as a silent DNA-binding partner to an active ligand-binding subunit in mediating retinoid responses through target genes defined by LXRES. LXRES are DR4-type response elements characterized by direct repeats of two similar hexanuclotide half-sites spaced by four nucleotides. Plays an important role in the regulation of cholesterol homeostasis, regulating cholesterol uptake through MYLIP-dependent ubiquitination of LDLR, VLDLR and LRP8. Interplays functionally with RORA for the regulation of genes involved in liver metabolism (By similarity). Induces LPCAT3-dependent phospholipid remodeling in endoplasmic reticulum (ER) membranes of hepatocytes, driving SREBF1 processing and lipogenesis (PubMed:28846071, PubMed:25806685). Via LPCAT3, triggers the incorporation of arachidonate into phosphatidylcholines of ER membranes, increasing membrane dynamics and enabling triacylglycerols transfer to nascent very low-density lipoprotein (VLDL) particles (PubMed:25806685). Via LPCAT3 also counteracts lipid-induced ER stress response and inflammation, likely by modulating SRC kinase membrane compartmentalization and limiting the synthesis of lipid inflammatory mediators (PubMed:24206663). Heterodimer of NR1H3 and RXR (retinoic acid receptor). Interacts with CCAR2 (via N-terminus) in a ligand-independent manner. Interacts with SIRT1 and this interaction is inhibited by CCAR2 (By similarity). Ubiquitinated leading to its degradation by the proteasome. Belongs to the nuclear hormone receptor family. NR1 subfamily. +Involved in iron-sulfur cluster biogenesis. Binds a 4Fe-4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe/S proteins. Could also act as a scaffold/chaperone for damaged Fe/S proteins. Binds 1 [4Fe-4S] cluster per subunit. The cluster is presumably bound at the interface of two monomers. Homodimer. Belongs to the NfuA family. +Has an antimicrobial activity. Belongs to the LEAP2 family. +Functions as a negative regulator of TP53/P53 in the cellular response to telomere erosion and probably also DNA damage. Belongs to the TAPR1 family. +Represses ulaG and the ulaABCDEF operon. +(2R)-O-phospho-3-sulfolactate + H2O = (2R)-3-sulfolactate + phosphate Belongs to the ComB family. +Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair. Hydrolysis of Ala-|-Gly bond in repressor LexA. Homodimer. Belongs to the peptidase S24 family. +Belongs to the eukaryotic ribosomal protein eL43 family. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Belongs to the thiamine-phosphate synthase family. +Catalyzes the formation of 5-methyl-uridine at position 747 (m5U747) in 23S rRNA. S-adenosyl-L-methionine + uridine(747) in 23S rRNA = 5-methyluridine(747) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmC subfamily. +Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P). D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate from glycerone phosphate: step 1/1. Homodimer. Belongs to the triosephosphate isomerase family. +Involved in redox-control of magnetite formation; oxidizes Fe(2+) to Fe(3+) or to mixed-valent Fe(2+)-Fe(3+) oxide minerals (PubMed:25775527). May control magnetite crystal size and number (Probable). Overproduction of MamP leads to more crystals than normal during exponential growth of normal size; in stationary phase crystal numbers become wild-type (PubMed:25048532). Binds 2 heme groups via the 2 magnetochrome (MCR) motifs. E(0) is -89 +/- 11 mV for Fe(3+)-Fe(2+) at pH 7.5. Homodimer. Not seen in magnetosome membranes. Constitutively expressed, levels are high for 24 hours after innoculation then decrease in stationary phase (up to 144 hours) (at protein level) (PubMed:25048532). Part of the probable 18 gene mamAB operon (Probable). The dimer forms a pocket of about 8 X 15 Angstroms, lined with acidic residues, which may bind 2 Fe(2+) ions. Subject to proteolytic cleavage which requires both MamE and MamO. Cells have a weak magnetic response and make magnetosome membranes. Has fewer but larger magnetite crystals (PubMed:20212111). Makes small, flaky magnetite crystals, does not alter subcellular localization of MamC, MamF, MamI or MmsF (PubMed:25775527). Deletion of genes mamH to mamV (amb0961 to amb0978) gives cells with no magnetosomes and no magnetic response (PubMed:20212111). This bacteria makes up to 20 cubo-octahedral magnetosomes of about 45 nm in diameter which contain membrane-bound crystals of magnetite (Fe(3)O(4)). Expression of just the minimal mamAB gene cluster (amb0961 to amb0978), including this gene, is sufficient to form a minimal magnetosome chain with small magnetite particles. Belongs to the magnetosome MamP family. +Located at the top of the head of the small subunit, it contacts several helices of the 18S rRNA. Part of the small ribosomal subunit. Belongs to the universal ribosomal protein uS13 family. +Destroys radicals which are normally produced within the cells and which are toxic to biological systems. 2 H(+) + 2 superoxide = H2O2 + O2 Binds 1 copper ion per subunit. Binds 1 zinc ion per subunit. Homodimer. Belongs to the Cu-Zn superoxide dismutase family. +Detected mainly on membrane-like structures within viral factories (By similarity). Probably part of the inner envelope (By similarity). Expressed in the late phase of the viral replicative cycle. Belongs to the asfivirus H108R family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +Cysteine methyltransferase effector that inhibits host cell NF-kappa-B activation by preventing nuclear translocation of host protein RELA/p65. Acts by mediating cysteine methylation of host proteins TAB2 and TAB3: methylation of a conserved cysteine residue of the RanBP2-type zinc finger (NZF) of TAB2 and TAB3 disrupts zinc-binding, thereby inactivating the ubiquitin chain-binding activity of TAB2 and TAB3, leading to NF-kappa-B inactivation. Also mediates cysteine methylation of host protein ZRANB3, inactivating its ability to bind ubiquitin chains. L-cysteinyl-[protein] + S-adenosyl-L-methionine = H(+) + S-adenosyl-L-homocysteine + S-methyl-L-cysteinyl-[protein] Monomer. Secreted via the type III secretion system (TTSS). Localizes in the nucleus of the infected cells. Belongs to the NleE/OspZ family. +Essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep and/or Rep' binds a specific hairpin at the genome origin of replication. Introduces an endonucleolytic nick within the conserved sequence 5'-AGTATTAC-3' in the intergenic region of the genome, thereby initiating the rolling circle replication (RCR). Following cleavage, binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication. Displays origin-specific DNA cleavage, nucleotidyl transferase, ATPase and helicase activities. ATPase activity is probably carried by the isoform Rep (By similarity). ATP + H2O = ADP + H(+) + phosphate Divalent metal cations, possibly Mg(2+) or Mn(2+). Interacts with the capsid protein; this interaction relocates Rep into the nucleus. There are 3 rolling circle replication (RCR) motifs. RCR-2 is probably involved in metal coordination. RCR-3 is required for phosphodiester bond cleavage for initiation of RCR. Belongs to the nanoviruses/circoviruses replication-associated protein family. +Activates the tRNA-splicing ligase complex by facilitating the enzymatic turnover of catalytic subunit RtcB. Acts by promoting the guanylylation of RtcB, a key intermediate step in tRNA ligation. Can also alter the NTP specificity of RtcB such that ATP, dGTP or ITP is used efficiently (By similarity). Belongs to the archease family. +Bifunctional enzyme that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP) (IspD), and catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (IspF). 2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-methyl-D-erythritol + diphosphate 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 4/6. In the N-terminal section; belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily. In the C-terminal section; belongs to the IspF family. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +Present with 319 molecules/cell in log phase SD medium. +Type II topoisomerase. Processively relaxes supercoiled DNA. Displays DNA-supercoiling activity only when associated with the viral histone-like protein. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+). Localizes throughout the cytoplasmic viral factories at 16 hpi. Expressed in the early phase of the viral replicative cycle. Belongs to the type II topoisomerase family. +One of the components of the core complex of photosystem II (PSII), required for its stability and/or assembly. PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, numerous small proteins, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Phosphorylation is a light-dependent reaction catalyzed by a membrane-bound kinase; phosphorylation occurs on Thr residue(s) in the N-terminus of the protein. Belongs to the PsbH family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP). 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP Binds 1 divalent metal cation per subunit. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 4/6. Homotrimer. Belongs to the IspF family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +Contributes to tetrahydrofolate metabolism and photorespiration through the regulation of serine hydroxymethyltransferase. Prefers the pentalutamyl to the monoglutamyl form of 5-formyltetrahydrofolate. (6S)-5-formyl-5,6,7,8-tetrahydrofolate + ATP = 5,10-methenyltetrahydrofolate + ADP + phosphate Optimum pH is 8.5. Monomer. Reduced growth rate and delayed flowering. Belongs to the 5-formyltetrahydrofolate cyclo-ligase family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 13 different subunits. Subunits NuoB, CD, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishment of the nucleosome following the passage of RNA polymerase II (By similarity). Forms a stable heterodimer with ctc-2/spt16. The dimer of ctc-1 and ctc-2 weakly associates with multiple molecules of nhp-1/nhp6 to form the FACT complex (By similarity). Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci. In contrast to the orthologous protein in animals and plants, this protein does not contain a HMG box DNA-binding domain. This function may instead be provided by the HMG box of the associated nhp-1 protein in the FACT complex of fungi. Belongs to the SSRP1 family. +Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Binds 1 potassium ion per subunit. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. +Amidohydrolase that hydrolyzes specifically one of the carboamide linkages in D-pantetheine thus recycling pantothenic acid (vitamin B5) and releasing cysteamine. (R)-pantetheine + H2O = (R)-pantothenate + cysteamine Monomer. Widely expressed with higher expression in spleen, kidney and blood. Overexpressed in lesional psoriatic skin. By Th17/Th1 type cytokines, but not by Th2-type. Belongs to the carbon-nitrogen hydrolase superfamily. BTD/VNN family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Probable rhomboid-type serine protease that catalyzes intramembrane proteolysis. Probably essential for the meiosis stage-specific callose accumulation and pollen exine formation. Expressed in pollen mother cell. Belongs to the peptidase S54 family. Might be an inactive rhomboid-type serine protease due to mismatches with the consensus active sites. Wrong choice of frame. +Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O Binds 1 Mg(2+) ion per subunit. Homooctamer; tetramer of dimers. Reaction proceeds via a syn dehydration. Belongs to the mandelate racemase/muconate lactonizing enzyme family. RhamD subfamily. +Belongs to the bacterial ribosomal protein bL34 family. +Induces host cell lysis. Inhibits host MurA activity thereby blocking the synthesis of murein precursors necessary for the host cell wall biosynthesis. May be responsible for the attachment to the host pilus. Interacts with host MurA; this interaction inhibits the first step in host cell wall synthesis. Interacts with the capsid protein dimers. A single copy of the maturation protein is present in the virion. Belongs to the Levivirus maturation protein family. +Required for spatial organization of the terminus region of the chromosome (Ter macrodomain) during the cell cycle. Prevents early segregation of duplicated Ter macrodomains during cell division. Binds specifically to matS, which is a 13 bp signature motif repeated within the Ter macrodomain. Homodimer. Belongs to the MatP family. +Catalyzes the oxidation of oleanolate at the C-23 position to form hederagenin. O2 + oleanolate + reduced [NADPH--hemoprotein reductase] = H(+) + H2O + hederagenin + oxidized [NADPH--hemoprotein reductase] Belongs to the cytochrome P450 family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Belongs to the peptidase M50B family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. In this organism, the P 'protein' is a heterodimer of two subunits. Belongs to the GcvP family. N-terminal subunit subfamily. +Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones. Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines. 2 a quinone + H(+) + NADH = 2 a 1,4-benzosemiquinone + NAD(+) anthranilate + N,N-dimethyl-1,4-phenylenediamine + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 H(+) + 2 NADH Binds 1 FMN per subunit. Homodimer. Belongs to the azoreductase type 1 family. +Repressed by silencing mediated by polycomb group (PcG) protein complex containing EMF1 and EMF2. Belongs to the disease resistance NB-LRR family. RPP8/HRT subfamily. Could be the product of a pseudogene. In strain cv. Columbia, a stop codon at position 117 and a naturally occurring frameshift at position 846 result in a truncated LOV1 protein. A complete sequence for LOV1 can be found in strain cv. Cl-0 (AC A7XGN8). Functional and comparative genomics of disease resistance gene homologs +E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of SIN3B (By similarity). Independently of its E3 ligase activity, acts as a CTNNB1 stabilizer through USP7-mediated deubiquitination of CTNNB1 promoting Wnt signaling (PubMed:25266658). S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Interacts with SIN3B (By similarity). Interacts with CTNNB1 (via Armadillo repeats 2-8) (PubMed:25266658). Interacts with USP7 (via MATH domain) (PubMed:25266658). Auto-ubiquitinated; leads to proteasomal degradation. Truncated N-terminus. +Heterotetramer of two alpha and two beta subunits. Paraxonemal body. And paraxonemal bodies (PABs). The FB strain is deficient in phototaxis. It is not known if this is due to defective adenylate cyclase activity or defective BLUF domains in this protein. In wild-type E.gracilis, photoactivated adenylate cyclase is found in the paraxonemal bodies (PABs). PABs are not visible in all cells in this strain, and are smaller than in wild-type. Belongs to the adenylyl cyclase class-4/guanylyl cyclase family. +Required for RNA-mediated gene silencing (RNAi). Binds to short RNAs such as microRNAs (miRNAs) and represses the translation of mRNAs which are complementary to them. Lacks endonuclease activity and does not appear to cleave target mRNAs. Belongs to the argonaute family. Ago subfamily. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Component of the ESCRT-0 complex which is the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB) and recruits ESCRT-I to the MVB outer membrane. Component of the ESCRT-0 complex composed of HSE1 and VPS27. The FYVE domain is involved in the binding to phosphatidylinositol 3-phosphate (PtdIns(3)P) which is required for the association to endosomal membranes. Both IUM domains are necessary for efficient binding to ubiquitin. Belongs to the VPS27 family. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Phosphatidylserine (PS) lipase that mediates the hydrolysis of phosphatidylserine to generate lysophosphatidylserine (LPS) (By similarity). LPS constitutes a class of signaling lipids that regulates immunological and neurological processes (By similarity). Has no activity towards diacylglycerol, triacylglycerol or lysophosphatidylserine lipase (PubMed:25290914). Also has monoacylglycerol lipase activity, with preference for 1-(9Z,12Z-octadecadienoyl)-glycerol (1-LG) and 2-glyceryl-15-deoxy-Delta(12,14)-prostaglandin J2 (15d-PGJ(2)-G) (PubMed:25290914). 1-heptadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphoserine + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + 1-heptadecanoyl-sn-glycero-3-phosphoserine + H(+) 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-L-serine + H2O = (9Z)-octadecenoate + 1-hexadecanoyl-sn-glycero-3-phospho-L-serine + H(+) 1-octadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphoserine + H2O = (9Z,12Z)-octadecadienoate + 1-octadecanoyl-sn-glycero-3-phosphoserine + H(+) 1-heptadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + 1-heptadecanoyl-sn-glycero-3-phosphocholine + H(+) 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-glycerol + H2O = (9Z)-octadecenoate + 1-hexadecanoyl-sn-glycero-3-phospho-glycerol + H(+) 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1D-myo-inositol) + H2O = (9Z)-octadecenoate + 1-hexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + H(+) 1-heptadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphoethanolamine + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + 1-heptadecanoyl-sn-glycero-3-phosphoethanolamine + H(+) 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1'-sn-glycerol) + H2O = (9Z)-octadecenoate + 1-hexadecanoyl-sn-glycero-3-phospho-(1'-sn-glycerol) + H(+) Hydrolyzes glycerol monoesters of long-chain fatty acids. 1-tetradecanoylglycerol + H2O = glycerol + H(+) + tetradecanoate 2-hexadecanoylglycerol + H2O = glycerol + H(+) + hexadecanoate 1-(9Z-octadecenoyl)-glycerol + H2O = (9Z)-octadecenoate + glycerol + H(+) 2-(9Z-octadecenoyl)-glycerol + H2O = (9Z)-octadecenoate + glycerol + H(+) 2-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)-octadecadienoate + glycerol + H(+) 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + glycerol + H(+) 2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-glycerol + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + glycerol + H(+) H2O + prostaglandin D2-1-glycerol ester = glycerol + H(+) + prostaglandin D2 11-oxo-5Z,9,12E,14E-prostatetraenoate + H2O = 15-deoxy-Delta(12,14)-prostaglandin J2 + glycerol + H(+) 1-(9Z,12Z-octadecadienoyl)-glycerol + H2O = (9Z,12Z)-octadecadienoate + glycerol + H(+) Inhibited by beta-lactone-based lipid inhibitors, such as beta-lactone palmostatin-B. Optimum pH is 7.2-8.0. Belongs to the AB hydrolase superfamily. ABHD16 family. +Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate. ATP + formate + N(1)-(5-phospho-beta-D-ribosyl)glycinamide = ADP + H(+) + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (formate route): step 1/1. Homodimer. Belongs to the PurK/PurT family. +Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Belongs to the Antp homeobox family. +Protein that inhibits host translation while promoting late viral translation by ribosome shunting. Blocks host cap-dependent translation by binding to eIF4G, displacing MKNK1 from cap initiation complexes and preventing EIF4E phosphorylation. Binds to the tripartite leader sequence of viral late mRNAs and recruits host eIF4G, PABPC1/poly-A binding protein and 40S ribosomes subunits on viral mRNAs, allowing ribosome shunting and efficient translation of late viral mRNAs even though conventional translation via ribosome scanning from the cap has been shut off in the host cell. During assembly, acts as a chaperone protein that helps hexon proteins assembly into trimers. Monomer. Interacts with hexon protein; this interaction allows chaperoning and trimerization of hexon proteins. Interacts (via N-terminus) with host initiation factor EIF4G (via C-terminus). Interacts (via RRM domain) with viral mRNAs that contain the tripartite leader; this interaction allows ribosome shunting and expression of viral late mRNAs. Expressed in the late phase of the viral replicative cycle. Might be cleaved by the viral protease. Phosphorylated. Tyrosine phosphorylation enhances preferential binding to tripartite leader mRNAs and allows ribosome shunting. Methylated. Asymmetric dimethylation by host PRMT1 of the Arg/Gly-rich region may regulate shutoff protein binding to hexon and promote the capsid assembly in the nucleus. All late proteins expressed from the major late promoter are produced by alternative splicing and alternative polyadenylation of the same gene giving rise to non-overlapping ORFs. A leader sequence is present in the N-terminus of all these mRNAs and is recognized by the viral shutoff protein to provide expression although conventional translation via ribosome scanning from the cap has been shut off in the host cell. Belongs to the adenoviridae shutoff protein family. +Serine/threonine protein kinase involved in the cytoplasm to vacuole transport (Cvt) and found to be essential in autophagy, where it is required for the formation of autophagosomes. Involved in the clearance of protein aggregates which cannot be efficiently cleared by the proteasome. Required for selective autophagic degradation of the nucleus (nucleophagy) as well as for mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. Also involved in endoplasmic reticulum-specific autophagic process, in selective removal of ER-associated degradation (ERAD) substrates. Plays a key role in ATG9 and ATG23 cycling through the pre-autophagosomal structure and is necessary to promote ATG18 binding to ATG9 through phosphorylation of ATG9. Catalyzes phosphorylation of ATG4, decreasing the interaction between ATG4 and ATG8 and impairing deconjugation of PE-conjugated forms of ATG8. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Homodimer. Forms a ternary complex with ATG13 and ATG17. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. APG1/unc-51/ULK1 subfamily. +ATP-binding RNA helicase involved in translation initiation. Remodels RNA in response to ADP and ATP concentrations by facilitating disruption, but also formation of RNA duplexes (By similarity). ATP + H2O = ADP + H(+) + phosphate The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis. Belongs to the DEAD box helicase family. DDX3/DED1 subfamily. +Salivary tick protein that acts by scavenging histamine at the wound site, outcompeting histamine receptors for histamine, thereby overcoming host inflammatory responses (PubMed:10360182). Binds histamine with a high-affinity (Kd=1.2 nM) (PubMed:10360182). Contains two binding histamine sites (H and L), that appear to bind histamine with differing affinities (By similarity). Homodimer; disulcde-linked. Expressed by salivary glands. Exclusively secreted by larvae, nymphs and adult male ticks. Contains 2 sites/pockets that bind histamine with different affinities. Site H (high affinity) is indicated here as binding to histamine 1, and site L (low affinity) is indicated as binding to histamine 2. N-glycosylated. Belongs to the calycin superfamily. Histamine-binding salivary protein family. +Catalyzes, although with low efficiency, the sulfur transfer reaction from thiosulfate to cyanide. hydrogen cyanide + thiosulfate = 2 H(+) + sulfite + thiocyanate Belongs to the GlpE family. +Protein phosphatase that associates with over 200 regulatory proteins to form highly specific holoenzymes which dephosphorylate hundreds of biological targets. Protein phosphatase 1 (PP1) is essential for cell division, and participates in the regulation of glycogen metabolism, muscle contractility and protein synthesis. Dephosphorylates RPS6KB1. Involved in regulation of ionic conductances and long-term synaptic plasticity. May play an important role in dephosphorylating substrates such as the postsynaptic density-associated Ca(2+)/calmodulin dependent protein kinase II. Component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase (By similarity). H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 manganese ions per subunit. Inactivated by binding to URI1. PP1 comprises a catalytic subunit, PPP1CA, PPP1CB or PPP1CC, which is folded into its native form by inhibitor 2 and glycogen synthetase kinase 3, and then complexed to one or several targeting or regulatory subunits. PPP1R12A, PPP1R12B and PPP1R12C mediate binding to myosin. PPP1R3A (in skeletal muscle), PPP1R3B (in liver), PPP1R3C, PPP1R3D and PPP1R3F (in brain) mediate binding to glycogen. PPP1R15A and PPP1R15B mediate binding to EIF2S1. Part of a complex containing PPP1R15B, PP1 and NCK1/2. Interacts with PPP1R3B, PPP1R7 and CDCA2. Interacts with IKFZ1; the interaction targets PPP1CC to pericentromeric heterochromatin, dephosphorylates IKAROS, stabilizes it and prevents it from degradation. Interacts with NOM1 and PPP1R8. Component of the PTW/PP1 phosphatase complex, composed of PPP1R10/PNUTS, TOX4, WDR82, and PPP1CA or PPP1CB or PPP1CC. Interacts with PPP1R8. Interacts with NEK2. Interacts with PPP1R42; the interaction is direct. Interacts with URI1; the interaction is phosphorylation-dependent and occurs in a growth factor-dependent manner. Interacts with FOXP3. Interacts with TMEM225 (via RVxF motif). Interacts with MKI67. Interacts with RRP1B; this targets PPP1CC to the nucleolus (By similarity). Interacts with DYNLT4 (By similarity). Colocalizes with SPZ1 in the nucleus. Colocalizes with URI1 at mitochondrion. Rapidly exchanges between the nucleolar, nucleoplasmic and cytoplasmic compartments. Highly mobile in cells and can be relocalized through interaction with targeting subunits. In the presence of PPP1R8 relocalizes from the nucleolus to nuclear speckles. Shows a dynamic targeting to specific sites throughout the cell cycle. Highly concentrated in nucleoli of interphase cells and localizes at kinetochores early in mitosis. Relocalization to chromosome-containing regions occurs at the transition from early to late anaphase. Also accumulates at the cleavage furrow and midbody by telophase. Phosphorylated by NEK2. Belongs to the PPP phosphatase family. PP-1 subfamily. The things we forget - Issue 32 of March 2003 +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 2 subfamily. +Destroys radicals which are normally produced within the cells and which are toxic to biological systems. 2 H(+) + 2 superoxide = H2O2 + O2 Binds 1 copper ion per subunit. Binds 1 zinc ion per subunit. Homodimer. Palmitoylation helps nuclear targeting and decreases catalytic activity. Succinylation, adjacent to copper catalytic site, probably inhibits activity. Desuccinylation by SIRT5 enhances activity. Belongs to the Cu-Zn superoxide dismutase family. +Picornain 3C-like protease is a thiol protease that cleaves the P1 and P2 polyproteins. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Specific enzymatic cleavages by picornain 3C-like protease in vivo yield mature proteins. Picornain 3C-like protease is autocatalytically processed (By similarity). VPg is uridylylated by the polymerase and is covalently linked to the 5'-end of genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase (By similarity). Belongs to the nepoviruses RNA1 polyprotein family. +Catalyzes the first step of the '4S' desulfurization pathway that removes covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. Sulfur dioxygenase which converts DBT to DBT-sulfone (DBTO2 or DBT 5,5-dioxide) probably in a stepwise manner. In addition to FMNH2 can also use FAD (although FAD is less efficient). dibenzothiophene + 2 FMNH2 + 2 O2 = dibenzothiophene 5,5-dioxide + 2 FMN + 2 H(+) + 2 H2O dibenzothiophene + FMNH2 + O2 = dibenzothiophene 5-oxide + FMN + H(+) + H2O dibenzothiophene 5-oxide + FMNH2 + O2 = dibenzothiophene 5,5-dioxide + FMN + H(+) + H2O Reduced flavin is provided by flavin reductase DszD; in a coupled DszC-DszD reaction both FMNH2 and FADH2 can be used, maximal DBTO2 production is seen with 5 uM FMN or with 35 uM FAD. Inhibited at high concentrations of FMN or FAD. Sulfur metabolism; dibenzothiophene degradation. Homotetramer. The lid loop assumes one of 2 conformations allowing opening and closing of the active site. Belongs to the DszC flavin monooxygenase family. +Belongs to the allatostatin family. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +Part of prostatein which is the major secretory glycoprotein of ventral prostate gland. Prostatein is composed of three different peptides called C1, C2 and C3. These form covalent C1:C3 (F) and C2:C3 (S) heterodimers whose noncovalent association forms tetrameric (C1:C3/C3:C2) prostatein molecules. Linked by three disulfide bonds to C3. The N-terminus is blocked. The heterodimer can bind non-polar steroids, cholesterol and a group of small proline-rich peptides. Belongs to the secretoglobin family. Lipophilin subfamily. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +May be part of a membrane-spanning permease system necessary for the transport of pigment precursors into pigment cells responsible for eye color. Belongs to the ABC transporter superfamily. ABCG family. Eye pigment precursor importer (TC 3.A.1.204) subfamily. +Ribonucleoside-diphosphate reductase holoenzyme that provides the precursors necessary for viral DNA synthesis. Allows virus growth in non-dividing cells, as well as reactivation from latency in infected hosts. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity). The N-terminal region confers antiapoptotic activity in differentiated cells such as neurons and is important for viral reactivation to increase neural survivability. Prevents host necroptosis by targeting host RIPK1 and RIPK3, thereby hampering the formation of necroptotic RIPK1-RIPK3 complexes (By similarity). May form hetero-amyloid structures with host proteins RIPK3 or ZBP1, thereby preventing RIPK3- and ZBP1-mediated necroptosis (By similarity). In addition, inhibits extrinsic apoptosis by targeting host CASP8 (By similarity). [thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-diphosphate Genetic information processing; DNA replication. Heterotetramer composed of a homodimer of the large subunit (R1) and a homodimer of the small subunit (R2). Larger multisubunit protein complex are also active, composed of (R1)n(R2)n (By similarity). May self-assemble (via RIP homotypic interaction motif/RHIM) into homomeric fibrillar amyloid structures (By similarity). Interacts (via RHIM) with human RIPK1 (via RHIM). Interacts (via RHIM) with human RIPK3 (via RHIM) (By similarity). May interact (via RHIM) with human ZBP1 (via RHIM) (By similarity). Interacts (via C-terminus) with host CASP8 (By similarity). The RIP homotypic interaction motif/RHIM may drive self-assembly into homomeric amyloid structures and mediates interaction with the RHIM motif of host proteins RIPK3 and ZBP1 to form heteromeric amyloid structures. Belongs to the ribonucleoside diphosphate reductase large chain family. +Catalyzes a trans-dehydration via an enolate intermediate. 3-dehydroquinate = 3-dehydroshikimate + H2O Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 3/7. Homododecamer. Belongs to the type-II 3-dehydroquinase family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +May help in the organization of the PsaE and PsaF subunits. Belongs to the PsaJ family. +Nucleoside triphosphate pyrophosphatase. May have a dual role in cell division arrest and in preventing the incorporation of modified nucleotides into cellular nucleic acids. a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-phosphate + diphosphate + H(+) a 2'-deoxyribonucleoside 5'-triphosphate + H2O = a 2'-deoxyribonucleoside 5'-phosphate + diphosphate + H(+) Belongs to the Maf family. +Carrier protein involved in the D-alanylation of lipoteichoic acid (LTA). The loading of thioester-linked D-alanine onto DltC is catalyzed by D-alanine--D-alanyl carrier protein ligase DltA. The DltC-carried D-alanyl group is further transferred to cell membrane phosphatidylglycerol (PG) by forming an ester bond, probably catalyzed by DltD. D-alanylation of LTA plays an important role in modulating the properties of the cell wall in Gram-positive bacteria, influencing the net charge of the cell wall. Cell wall biogenesis; lipoteichoic acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-DCP. Belongs to the DltC family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) Binds 1 [4Fe-4S] cluster. NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I 20 kDa subunit family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity and assembly of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 4 family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) Binds 1 [4Fe-4S] cluster. NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I 20 kDa subunit family. +Acts in a DNA repair pathway for removal of UV-induced DNA damage that is distinct from classical nucleotide excision repair and in repair of ionizing radiation damage. Functions in homologous recombination repair of DNA double strand breaks and in recovery of stalled replication forks. Plays a critical role in meiosis. Two subcomplexes smc5-smc6-nse2 and nse1-nse3-nse4 exist. These subcomplexes are then brought together via a number of interactions, forming the Smc5-Smc6 complex. Belongs to the NSE4 family. +Belongs to the UPF0235 family. +D-galactose specific lectin. Binds in decreasing order of affinity: melibiose, methyl-alpha-D-galactoside, D-galactose, methyl-beta-D-galactoside, N-acetyl-D-galactosamine. Similar to plant lectins in its selective (carbohydrate-specific) hemagglutinating activity. Low exposure on the cell surface. Belongs to the LecA/PllA lectin family. +Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and/or repair of Fe-S clusters in biosynthetic enzymes. Belongs to the Fe(2+)-trafficking protein family. +Plays a major role in protein secretion by helping the post-translocational extracellular folding of several secreted proteins. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the PrsA family. +Component of the 90S pre-ribosome involved in the maturation of rRNAs. Required for early cleavages of the pre-RNAs in the 40S ribosomal subunit maturation pathway (By similarity). Associates with 90S and pre-40S pre-ribosomal particles. Belongs to the RRP36 family. +Acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. Suppresses the host RNA silencing by inhibiting adenosine kinase 2 (ADK2), a kinase involved in a general methylation pathway. Also suppresses the host basal defense by interacting with and inhibiting SNF1 kinase, a key regulator of cell metabolism implicated in innate antiviral defense. Determines pathogenicity (By similarity). Monomer. Suppress local silencing by interacting with and inactivating host adenosine kinase 2 (ADK2) in the cytoplasm. Interacts with and inhibits host SNF1 kinase (By similarity). The zinc finger is involved in PTGS suppression. Belongs to the geminiviridae transcriptional activator protein family. +Catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 2/4. Belongs to the GPI family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Odorant receptor. Olfactory epithelium. Belongs to the G-protein coupled receptor 1 family. +RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. Also part of the exosome, which is a complex involved in RNA degradation. Acts as a poly(A)-binding protein that enhances the interaction between heteromeric, adenine-rich transcripts and the exosome. ssDNA + n NTP = ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate. Binds two Mg(2+) per subunit. Forms a ternary complex with MCM helicase and DNA. Component of the archaeal exosome complex. Belongs to the archaeal DnaG primase family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Dicer-like endonuclease involved in cleaving double-stranded RNA in the RNA interference (RNAi) pathway. Produces 21 to 25 bp dsRNAs (siRNAs) which target the selective destruction of homologous RNAs leading to sequence-specific suppression of gene expression, called post-transcriptional gene silencing (PTGS). Part of a broad host defense response against viral infection and transposons (By similarity). Belongs to the helicase family. Dicer subfamily. +Belongs to the bacterial ribosomal protein bS21 family. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Catalytic subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (By similarity). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (By similarity). ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate ATP hydrolysis occurs at the interface between the nucleotide-binding domains of subunits A and B (By similarity). ATP hydrolysis triggers a conformational change in the subunits D and F, which induces a shift of subunit d (By similarity). The c-ring is subsequently rotated and results in a continuous proton translocation across the membrane (By similarity). V-ATPase is a heteromultimeric enzyme made up of two complexes: the ATP-hydrolytic V1 complex and the proton translocation V0 complex (By similarity). The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H (By similarity). The proton translocation complex V0 consists of the proton transport subunit a, a ring of proteolipid subunits c9c'', rotary subunit d, subunits e and f, and the accessory subunits VhaAC45 and ATP6AP2 (By similarity). Belongs to the ATPase alpha/beta chains family. +Catalyzes the conversion of pppGpp to ppGpp. Guanosine pentaphosphate (pppGpp) is a cytoplasmic signaling molecule which together with ppGpp controls the 'stringent response', an adaptive process that allows bacteria to respond to amino acid starvation, resulting in the coordinated regulation of numerous cellular activities. guanosine 3'-diphosphate 5'-triphosphate + H2O = guanosine 3',5'-bis(diphosphate) + H(+) + phosphate Purine metabolism; ppGpp biosynthesis; ppGpp from GTP: step 2/2. Belongs to the GppA/Ppx family. GppA subfamily. +Putative component of the fimbrium tip. Fimbriae are filamentous appendages on the cell surface that mediate cell adhesion and biofilm formation. May be part of the fimbrial tip. Belongs to the bacteroidetes fimbrillin superfamily. Mfa-like family. Lacks the lipidation signal found in other family members, suggesting it may not be exported to the cell surface, and may not be part of the fimbriae. +Plays a role in primary oral infection of the host. +Binds to the inner side of the nucleosomal DNA thus altering the interaction between the DNA and the histone octamer. May be involved in the process which maintains transcribable genes in a unique chromatin conformation (By similarity). Cytoplasmic enrichment upon phosphorylation. Phosphorylation favors cytoplasmic localization. Belongs to the HMGN family. +To U.parvum UU089.1. +Belongs to the UPF0702 family. +Synthesizes alpha-1,4-glucan chains using ADP-glucose. [(1->4)-alpha-D-glucosyl](n) + ADP-alpha-D-glucose = [(1->4)-alpha-D-glucosyl](n+1) + ADP + H(+) Glycan biosynthesis; glycogen biosynthesis. Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily. +Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Binds 2 divalent ions per subunit. Binds 1 potassium ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Homotetramer; dimer of dimers. Belongs to the AdoMet synthase family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 4L family. +Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and probably mediates its effects by recruiting and clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. May also play a role in glia-glia or glia-neuron interactions in the developing peripheral nervous system (By similarity). Interacts with NRXN1, NRXN2 and NRXN3. Interacts (via its C-terminus) with DLG4/PSD-95 (via PDZ domain 3) (By similarity). Homodimer, and heterodimer with NLGN1 and NLGN2 (By similarity). Detected at both glutamatergic and GABAergic synapses. Belongs to the type-B carboxylesterase/lipase family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Homodimer and monomer. In vivo most of the ribosomes are in complex with monomeric TF. Uncomplexed TF, however, is in a monomer-dimer equilibrium with approximately two thirds of TF existing in a dimeric state. About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +In the Western Reserve strain (WR), the A39R protein is intracellular and not secreted as observed in other vaccinia strains such as Copenhagen strain (COP). The WR equivalent of the semaphorin-like protein is split into two ORFs which are likely to be truncated and non-functional. This ORF would be the N-terminal part. Belongs to the semaphorin family. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway. D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = beta-D-fructose 6-phosphate + D-erythrose 4-phosphate Carbohydrate degradation; pentose phosphate pathway; D-glyceraldehyde 3-phosphate and beta-D-fructose 6-phosphate from D-ribose 5-phosphate and D-xylulose 5-phosphate (non-oxidative stage): step 2/3. Homodimer. Belongs to the transaldolase family. Type 1 subfamily. +Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds directly to 7S RNA and mediates binding of the 54 kDa subunit of the SRP. Part of the signal recognition particle protein translocation system, which is composed of SRP and FtsY. Archaeal SRP consists of a 7S RNA molecule of 300 nucleotides and two protein subunits: SRP54 and SRP19. Belongs to the SRP19 family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Transcription factor which binds to enhancer elements in the promoter region of genes (PubMed:26234645). Regulates the expression of the transcription factor bed-3 to control vulval development (PubMed:26234645, PubMed:32417234). Promotes terminal differentiation in the hypodermis and is involved in regulation of gonadal outgrowth and entry into the dauer stage (PubMed:24613396). Regulates the timing of dorsalward migration of the distal tip cells of the hermaphrodite gonad by inhibiting precocious unc-5 and lin-29 expression which in turn prevents early dorsalward turning (PubMed:24968003). Plays a role in male tail tip morphogenesis (PubMed:21408209). Interacts with dre-1; the interaction targets blmp-1 for proteasomal degradation (PubMed:24613396, PubMed:24968003). Interacts with ldb-1 and ham-3 (PubMed:32417234). Localizes to the nucleus and cytoplasm in hyp8-11 tail tip cells throughout development, but cytoplasmic localization is most prominent during male tail tip retraction. Expressed in hypodermal, vulval, intestinal and distal tip cells. In distal tip cells, expressed from mid-L2 when gonadal outgrowth initiates (PubMed:24613396). By mid-L3, just prior to the dorsal gonadal turn, levels drop dramatically (PubMed:24968003). In seam and hypodermal cells, levels are largely constant throughout larval development except for a transient peak early in L4 (PubMed:24613396). Ubiquitinated by the SCF(dre-1) complex, leading to its degradation by the proteasome. Gonadal migration defects with premature dorsal turning of distal tip cells in the hermaphrodite gonad (PubMed:24613396, PubMed:24968003). Defective dauer formation, shortened lifespan and retarded terminal differentiation of seam cells with incomplete adult alae synthesis (PubMed:24613396). Suppresses the precocious seam cell terminal differentiation and gonadal migration defects seen in dre-1 mutants (PubMed:24613396). Weak dumpy phenotype and partially penetrant embryonic lethality (PubMed:24968003). Reduced expression of the transcription factor bed-3 which is involved in vulval development and failed division of vulval precursor cell descendents (PubMed:26234645). RNAi-mediated knockdown impairs the expression of several hypodermis-specific genes; reduces levels of clo-124 mRNA and increases levels of lin-29 mRNA (PubMed:32417234). RNAi-mediated knockdown results in the precocious onset of tail tip retraction resulting in over-retracted and shortened adult male tails (also known as the Ore phenotype) (PubMed:21408209). +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +May be a regulator of keratinocyte proliferation or differentiation. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +May be involved in transcriptional regulation. Modulates various viral and cellular promoters in a promoter context-dependent manner. For example, transcription from the FOS promoter is increased, while Rous sarcoma virus (RSV) long terminal repeat (LTR) promoter activity is repressed. Does not bind DNA directly. Expressed in all tissues examined. Highly expressed in heart, ovary, prostate and skeletal muscle. Moderately expressed in brain, placenta, testis and small intestine. Weakly expressed in lung, liver and spleen. Expressed in several cancer cell lines. Phosphorylation of Ser-38 and Ser-39 is critical for transcriptional repression. Belongs to the TFS-II family. TFA subfamily. +Mediates both low-affinity uptake and efflux of sugar across the plasma membrane. Forms homooligomers and/or heterooligomers. Belongs to the SWEET sugar transporter family. +Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing (By similarity). a 3'-end 3'-phospho-ribonucleotide-RNA + ATP = a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + AMP + diphosphate Belongs to the RNA 3'-terminal cyclase family. Type 1 subfamily. +Belongs to the bacterial ribosomal protein bL27 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Belongs to the TACO1 family. +Belongs to the bacterial ribosomal protein bL32 family. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +Tooth-associated epithelia protein that probably plays a role in odontogenesis, the complex process that results in the initiation and generation of the tooth. May be incorporated in the enamel matrix at the end of mineralization process. Involved in the induction of RHOA activity via interaction with ARHGEF and expression of downstream factors such as ROCK. Plays a role in attachment of the junctional epithelium to the tooth surface. Interacts (via C-terminus) with ARHGEF5. O-glycosylated. Belongs to the ODAM family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Required for resistance to DNA-damaging agents. Homodimer. Belongs to the universal stress protein A family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the PetN family. +Belongs to the UPF0758 family. +May constitute a novel regulatory system for basal transcription. Negatively regulates ABT1 (By similarity). Interacts with ABT1. Forms a complex with ABT1 and suppresses the ABT1-induced activation of polymerase II-directed transcription in mammalian cells (By similarity). Belongs to the ESF1 family. Contaminating sequence. Potential poly-A sequence. +Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. A number of isoforms are produced. According to EST sequences. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single-stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates (By similarity). Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing (By similarity). Regulation of gene expression levels depends on the balance between methylation and acetylation levels of tha CTD-lysines (PubMed:26687004). Initiation or early elongation steps of transcription of growth-factors-induced immediate early genes are regulated by the acetylation status of the CTD (PubMed:24207025). Methylation and dimethylation have a repressive effect on target genes expression (PubMed:26687004). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. Component of a complex which is at least composed of HTATSF1/Tat-SF1, the P-TEFb complex components CDK9 and CCNT1, RNA polymerase II, SUPT5H, and NCL/nucleolin. The large PER complex involved in the repression of transcriptional termination is composed of at least PER2, CDK9, DDX5, DHX9, NCBP1 and POLR2A (active). Interacts (via the C-terminal domain (CTD)) with U2AF2; recruits PRPF19 and the Prp19 complex to the pre-mRNA and may couple transcription to pre-mRNA splicing. Interacts (via the C-terminal domain (CTD)) with SMN1/SMN2; recruits SMN1/SMN2 to RNA Pol II elongation complexes. Interacts via the phosphorylated C-terminal domain with WDR82 and with SETD1A and SETD1B only in the presence of WDR82. When phosphorylated at 'Ser-5', interacts with MEN1; the unphosphorylated form, or phosphorylated at 'Ser-2' does not interact. When phosphorylated at 'Ser-2', interacts with SUPT6H (via SH2 domain). Interacts with RECQL5 and TCEA1; binding of RECQL5 prevents TCEA1 binding. The phosphorylated C-terminal domain interacts with FNBP3 and SYNCRIP. Interacts with ATF7IP. Interacts with DDX5. Interacts with WWP2. Interacts with SETX. Interacts (phosphorylated) with PIH1D1. Interacts (via the C-terminal domain (CTD)) with TDRD3. Interacts with PRMT5. Interacts with XRN2. Interacts with SAFB/SAFB1. Interacts with CCNL1. Interacts with CCNL2, MYO1C, PAF1 and SFRS19. Interacts (via C-terminus) with CMTR1, CTDSP1 and SCAF8. Interacts (via the C-terminal domain (CTD)) with CCNT2 (By similarity). Interacts with FUS (By similarity). Interacts with MCM3AP (By similarity). Interacts with kinase SRPK2; the interaction occurs during the co-transcriptional formation of inappropriate R-loops (By similarity). Hypophosphorylated form is mainly found in the cytoplasm, while the hyperphosphorylated and active form is nuclear (By similarity). Co-localizes with kinase SRPK2 and helicase DDX23 at chromatin loci where unscheduled R-loops form (By similarity). The C-terminal domain (CTD) serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. The tandem heptapeptide repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapeptide repeat and is mediated, at least, by CDK7 and CDK9. CDK7 phosphorylation of POLR2A associated with DNA promotes transcription initiation by triggering dissociation from DNA. Phosphorylation also takes place at 'Ser-7' of the heptapeptide repeat, which is required for efficient transcription of snRNA genes and processing of the transcripts. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatases, and a 'CTD code' that specifies the position of Pol II within the transcription cycle has been proposed. Dephosphorylated by the protein phosphatase CTDSP1. Among tandem heptapeptide repeats of the C-terminal domain (CTD) some do not match the Y-S-P-T-S-P-S consensus, the seventh serine residue 'Ser-7' being replaced by a lysine. 'Lys-7' in these non-consensus heptapeptide repeats can be alternatively acetylated, methylated and dimethylated. EP300 is one of the enzyme able to acetylate 'Lys-7'. Acetylation at 'Lys-7' of non-consensus heptapeptide repeats is associated with 'Ser-2' phosphorylation and active transcription. It may regulate initiation or early elongation steps of transcription specially for inducible genes. Ubiquitinated by WWP2 leading to proteasomal degradation (PubMed:17526739). Following UV treatment, the elongating form of RNA polymerase II (RNA pol IIo) is ubiquitinated on UV damage sites without leading to degradation: ubiquitination is facilitated by KIAA1530/UVSSA and promotes RNA pol IIo backtracking to allow access to the nucleotide excision repair machinery (By similarity). Methylated at Arg-1810 prior to transcription initiation when the CTD is hypophosphorylated, phosphorylation at Ser-1805 and Ser-1808 preventing this methylation. Symmetrically or asymmetrically dimethylated at Arg-1810 by PRMT5 and CARM1 respectively. Symmetric or asymmetric dimethylation modulates interactions with CTD-binding proteins like SMN1/SMN2 and TDRD3. SMN1/SMN2 interacts preferentially with the symmetrically dimethylated form while TDRD3 interacts with the asymmetric form. Through the recruitment of SMN1/SMN2, symmetric dimethylation is required for resolving RNA-DNA hybrids created by RNA polymerase II, that form R-loop in transcription terminal regions, an important step in proper transcription termination. CTD dimethylation may also facilitate the expression of select RNAs. Among tandem heptapeptide repeats of the C-terminal domain (CTD) some do not match the Y-S-P-T-S-P-S consensus, the seventh serine residue 'Ser-7' being replaced by a lysine. 'Lys-7' in these non-consensus heptapeptide repeats can be alternatively acetylated, methylated, dimethylated and trimethylated. Methylation occurs in the earliest transcription stages and precedes or is concomitant to 'Ser-5' and 'Ser-7' phosphorylation. Dimethylation and trimehtylation at 'Lys-7' of non-consensus heptapeptide repeats are exclusively associated with phosphorylated CTD. The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucleotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion. Belongs to the RNA polymerase beta' chain family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Binds 1 zinc ion per subunit. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. Zinc-binding uS14 subfamily. +Belongs to the UPF0060 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Catalyzes the formation of 5-methyl-uridine at position 747 (m5U747) in 23S rRNA. S-adenosyl-L-methionine + uridine(747) in 23S rRNA = 5-methyluridine(747) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmC subfamily. +Has low D-gluconate dehydratase activity (in vitro), suggesting that it has no significant role in D-gluconate degradation in vivo. Has no detectable activity with a panel of 70 other acid sugars (in vitro). D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O Binds 1 Mg(2+) ion per subunit. kcat is 0.02 sec(-1) with D-gluconate. Belongs to the mandelate racemase/muconate lactonizing enzyme family. GalD subfamily. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I 30 kDa subunit family. +Mediates visceral muscle contractile activity (myotropic activity). Belongs to the periviscerokinin family. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +Adenosine deaminase that may contribute to the degradation of extracellular adenosine, a signaling molecule that controls a variety of cellular responses. Requires elevated adenosine levels for optimal enzyme activity. Binds to cell surfaces via proteoglycans and may play a role in the regulation of cell proliferation and differentiation, independently of its enzyme activity (By similarity). adenosine + H(+) + H2O = inosine + NH4(+) Binds 1 zinc ion per subunit. Homodimer. Interacts with adenosine receptors. Binds heparin (By similarity). The PRB domain is involved in receptor binding, and may be responsible for the cytokine-like growth factor activity due to it's sharing of several structural properties with chemokines. High-affinity binding to heparin/glycosaminoclycan (GAG) is mediated by a large, highly positively charged surface at the interface of dimer's subunits involving approximately residues 25-40, 386-393, and 419-425. Belongs to the metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. ADGF subfamily. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. +Catalyzes the phosphorylation of N-acetylmannosamine (ManNAc) to ManNAc-6-P. an N-acyl-D-mannosamine + ATP = ADP + an N-acyl-D-mannosamine 6-phosphate + H(+) Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 2/5. Homodimer. Belongs to the ROK (NagC/XylR) family. NanK subfamily. +Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Plays a role in endocytic trafficking. Required for receptor recycling from endosomes, both to the trans-Golgi network and the plasma membrane. Forms homodimers and heterodimers with PHETA1. Interacts with OCRL and INPP5B. Also found on macropinosomes. Not detected in late endosomes, nor in lysosomes. The F&H motif, an approximately 12-13 amino-acid sequence centered around Phe and His residues, is essential for binding to OCRL and INPP5B. Was named after 'sesquipedalian', an unnecessarily long description of a simple thing. Belongs to the sesquipedalian family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Sul-ATPase is composed of six (or maybe five) subunits: alpha, beta, delta, gamma, C (proteolipid), and possibly epsilon. The N-terminus is blocked. Belongs to the V-ATPase E subunit family. Was originally reported as originating from S.acidocaldarius. +Transpeptidase that anchors surface proteins to the cell wall. Recognizes both Leu-Ala-x-Thr-Gly and Leu-Pro-x-Thr-Gly, with a preference for the former. Unlike the S.aureus sortase it cleaves not only the Thr-Gly motif but also the Ala-X bond; Ala-Glu and Ala-His bonds are better substrates than the Thr-Gly motif in vitro (PubMed:22296345, PubMed:27936128). Among its possible substrates are the chaplins ChpA, ChpB and ChpC; this enzyme is less important for ChpC attachment than is SrtE2. A double knockout mutant of srtE1 and srtE2 shows a developmental defect in aerial hyphae formation more dramatic than that due to chaplin deletion (PubMed:22296345). The enzyme catalyzes a cell wall sorting reaction in which a surface protein with a sorting signal containing a LPXTG motif is cleaved between the Thr and Gly residue. The resulting threonine carboxyl end of the protein is covalently attached to a pentaglycine cross-bridge of peptidoglycan. Transcribed independently of the operon's upstream, overlapping gene (SCO3851); transcribed with srtE2 over the first 72 hours of growth. Part of the strE1-srtE2 operon. The probably cytoplasmic N-terminus cannot be deleted without destabilizing the protein. A single srtE1 deletion, has a significant delay in aerial hyphae formation when grown on minimal medium, but no delay on rich medium. Nearly wild-type levels of ChpC are attached to the cell wall. A double srtE1-srtE2 knockout grown on minimal medium has a more severe delay in aerial hyphae formation and does not make spores, on rich medium initiates aerial hyphae formation later than wild-type and does not make spores. In the double mutant no ChpC is attached to the cell wall in liquid medium, on solid minimal medium chpD, chpF (SCO2699), rdlA and nepA are transcribed poorly or not at all (with no change in chpH), while very few spore chains or rodlets are seen on the aerial hyphae. Belongs to the bacterial sortase family. Class E subfamily. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Causes abnormal twist followed by immobility when injected into C.elegans. Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). +Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. Belongs to the glycosyl hydrolase 5 (cellulase A) family. +Antimicrobial peptide that acts against Gram-positive bacteria (Listeria spp., Enterococcus spp., B.subtilis, B.anthracis, P.aeruginosa) (PubMed:25342741, PubMed:28825809). Is not active against Gram-negative bacteria (PubMed:25342741). It selectively inhibits peptidoglycan biosynthesis through complex formation with the cell wall precursor lipid II (1:1 molar ratio), probably anchoring lipid II to the membrane, thus inhibiting cell wall synthesis (PubMed:25342741, PubMed:28825809). The interaction with lipid II involves the third position of the pentapeptide (PubMed:25342741). Shows bactericidal activity at about 2-fold minimal inhibitory concentrations (MIC), but does not form pore across the membrane (PubMed:25342741). Optimum pH is 1-8. Optimum temperature is 4-90 degrees Celsius. specific localization at active cell wall synthesis sites. Contains a unique connectivity of 6 cysteine bonds in contrast to most other CS-alpha-beta defensins which are linked by 3 or 4 disulfide bonds. Disulfide bonds are essential for structural integrity and antibacterial activity, since activity is lost after treatment with reducing agents. Thanks to disulfide bonds and N-terminal pyroglutamate, the protein is extremely stable in a wide pH and temperature range and insensitive toward proteases. Belongs to the invertebrate defensin family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-48-linked is involved in protein degradation via the proteasome. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity). Ribosomal protein S27a is a component of the 40S subunit of the ribosome. Ribosomal protein S27a is part of the 40S ribosomal subunit. Ubiquitin is synthesized as a polyubiquitin precursor with exact head to tail repeats, the number of repeats differs between species. In some species there is a final amino-acid after the last repeat. Some ubiquitin genes contain a single copy of ubiquitin fused to a ribosomal protein (either L40 or S27A). In the N-terminal section; belongs to the ubiquitin family. In the C-terminal section; belongs to the eukaryotic ribosomal protein eS31 family. +This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA. dUTP + H2O = diphosphate + dUMP + H(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 2/2. Belongs to the dUTPase family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +ATP + L-aspartate + NH4(+) = AMP + diphosphate + H(+) + L-asparagine Amino-acid biosynthesis; L-asparagine biosynthesis; L-asparagine from L-aspartate (ammonia route): step 1/1. Belongs to the class-II aminoacyl-tRNA synthetase family. AsnA subfamily. +Functions as an electroneutral and bidirectional ammonium transporter. May regulate transepithelial ammonia secretion (By similarity). Homotrimer. Also detected at the basolateral membrane and in subapical vesicles. Chronic acidosis induces relocalization to the apical cell membrane. Expressed by connecting tubule cells and intercalated cells of the collecting duct in kidney (at protein level). N-glycosylated. Belongs to the ammonium transporter (TC 2.A.49) family. Rh subfamily. +Involved in postreplication mismatch repair. Binds specifically to DNA containing mismatched nucleotides thus providing a target for the excision repair processes characteristic of postreplication mismatch repair (By similarity). Heterodimer of MSH2 and MSH6 (GTBP). Belongs to the DNA mismatch repair MutS family. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +Self-assembles to form the virion icosahedral capsid with a T=1 symmetry. This very small capsid (17 - 22 nm in diameter) allows the virus to be very stable in the environment and resistant to some disinfectants, including detergents. Essential for the initial attachment to heparan sulfate moieties and chondroitin sulfate B of the host cell surface proteoglycans. After attachment, the virus is endocytosed and traffics to the nucleus. The capsid protein binds and transports the viral genome and Rep across the nuclear envelope (By similarity). Homomultimer. Assembles in the nucleus, presumably in an immature form, then migrates to the cytoplasm once assembled as mature virion. Interacts with Rep; this interaction relocates Rep into the nucleus (By similarity). Belongs to the circoviridae capsid protein family. +Signal-transducing molecule. The receptor systems for IL6, LIF, OSM, CNTF, IL11, CTF1 and BSF3 can utilize IL6ST for initiating signal transmission. Binding of IL6 to IL6R induces IL6ST homodimerization and formation of a high-affinity receptor complex, which activates the intracellular JAK-MAPK and JAK-STAT3 signaling pathways. That causes phosphorylation of IL6ST tyrosine residues which in turn activates STAT3 (By similarity). In parallel, the IL6 signaling pathway induces the expression of two cytokine receptor signaling inhibitors, SOCS1 and SOCS3, which inhibit JAK and terminate the activity of the IL6 signaling pathway as a negative feedback loop. Also activates the yes-associated protein 1 (YAP) and NOTCH pathways to control inflammation-induced epithelial regeneration, independently of STAT3 (By similarity). Mediates signals which regulate immune response, hematopoiesis, pain control and bone metabolism (By similarity). Has a role in embryonic development (By similarity). Essential for survival of motor and sensory neurons and for differentiation of astrocytes (By similarity). Required for expression of TRPA1 in nociceptive neurons (By similarity). Required for the maintenance of PTH1R expression in the osteoblast lineage and for the stimulation of PTH-induced osteoblast differentiation (By similarity). Required for normal trabecular bone mass and cortical bone composition (By similarity). Component of a hexamer of two molecules each of IL6, IL6R and IL6ST; associates with the complex IL6:IL6R but does not interact with IL6 (By similarity). Forms heterodimers composed of LIFR and IL6ST (type I OSM receptor) which are activated by LIF and OSM. Also forms heterodimers composed of OSMR and IL6ST (type II receptor) which are activated by OSM but not by LIF. Interacts with HCK (By similarity). Interacts with INPP5D/SHIP1 (By similarity). Interacts with SRC and YES (By similarity). Found in hepatocytes, astrocytes, fibroblasts and endothelial cells. The WSXWS motif appears to be necessary for proper protein folding and thereby efficient intracellular transport and cell-surface receptor binding. The box 1 motif is required for JAK interaction and/or activation. Phosphorylation of Ser-781 down-regulates cell surface expression. Heavily N-glycosylated. Glycosylation is required for protein stability and localization in plasma membrane but not for ligand binding. Belongs to the type I cytokine receptor family. Type 2 subfamily. +Inhibits a wide spectrum of lactic acid bacteria. Belongs to the bacteriocin class IIA/YGNGV family. +Nuclear transcriptional activator of viral gene expression, that is essential for viral transcription from the LTR promoter and replication. Acts as a sequence-specific molecular adapter, directing components of the cellular transcription machinery to the viral RNA to promote processive transcription elongation by the RNA polymerase II (RNA pol II) complex, thereby increasing the level of full-length transcripts. In the absence of Tat, the RNA Pol II generates short or non-processive transcripts that terminate at approximately 60 bp from the initiation site. Tat associates with the CCNT1/cyclin-T1 component of the P-TEFb complex (CDK9 and CCNT1), which promotes RNA chain elongation. This binding increases Tat's affinity for a hairpin structure at the 5'-end of all nascent viral mRNAs referred to as the transactivation responsive RNA element (TAR RNA) and allows Tat/P-TEFb complex to bind cooperatively to TAR RNA. The CDK9 component of P-TEFb and other Tat-activated kinases hyperphosphorylate the C-terminus of RNA Pol II that becomes stabilized and much more processive (By similarity). Extracellular circulating Tat can be endocytosed by surrounding uninfected cells via the binding to several surface receptors. Endosomal low pH allows Tat to cross the endosome membrane to enter the cytosol and eventually further translocate into the nucleus, thereby inducing severe cell dysfunctions ranging from cell activation to cell death. Through (By similarity). Interacts with host CCNT1. Associates with the P-TEFb complex composed at least of Tat, P-TEFb (CDK9 and CCNT1), TAR RNA, RNA Pol II. Interacts with CCNT2; the resulting complex is unable to bind to TAR RNA (By similarity). The Arg-rich RNA-binding region binds the TAR RNA. This region also mediates the nuclear localization (By similarity). The phosphorylation by CDK9 does not seem to be important for transactivation function. Expressed in the late stage of the infection cycle, when unspliced viral RNAs are exported to the cytoplasm by the viral Rev protein. Belongs to the lentiviruses Tat family. +Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+) Binds 1 dipyrromethane group covalently. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. Monomer. The porphobilinogen subunits are added to the dipyrromethane group. Belongs to the HMBS family. +Involved in the export of mRNA from the nucleus to the cytoplasm. Interacts with NXT1, NXT2, E1B-AP5, the REF proteins and with nucleoporins, Nup62, Nup153 and Nup214. Interacts with LUZP4. Localized in the nucleoplasm and at the nuclear envelope. Shuttles between the nucleus and the cytoplasm. Expressed almost exclusively in testis. Also expressed in several cancers. The NTF2 domain heterodimerizes with NXT1 and NXT2. The formation of NXF1/NXT1 heterodimers is required for NXF2-mediated nuclear mRNA export. The leucine-rich repeats and the NTF2-domain are essential for the export of mRNA from the nucleus. The C-terminal fragment, containing the TAP domain (also called UBA-like domain) and part of the NTF2-like domain, named the NPC-binding domain, mediates direct interactions with nucleoporin-FG-repeats and is necessary and sufficient for localization of NXF2 to the nuclear rim. The RNA-binding domain is a non-canonical RNP-type domain. Belongs to the NXF family. The sequence differs from that shown due to either intron retention or a splicing event. +Plays a role in fertilization by controlling binding of sperm to zona pellucida and migration of spermatozoa into the oviduct (By similarity). May play a role in signal transduction and promote protein tyrosine phosphorylation (By similarity). Interacts with VAMP3. Interacts with LY6K. Interacts with DPEP3; co-localized on the cell surface of spermatocytes, spermatids, and testicular spermatozoa, co-localized only in cytoplasmic droplets of caput and corpus epididymal sperm. Interacts with ADAM5. Located on plasma membrane of spermatocytes, round and elongated spermatids, and testicular spermatozoa. N-glycosylated; by high mannose and/or biantennary complex and/or certain types of hybrid oligosaccharides; possesses different oligosaccharides chains according to its subcellular localization in the testis. Sheds from membrane raft by ACE and released from the cell surface of epididymal sperm while it passes through the caput epididymis leading to disappearance of TEX101 on spermatozoa; is essential to produce fertile spermatozoa. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Plays an essential role in the assembly of succinate dehydrogenase (SDH), an enzyme complex (also referred to as respiratory complex II) that is a component of both the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. Required for flavinylation (covalent attachment of FAD) of the flavoprotein subunit of the SDH catalytic dimer. Interacts with the flavoprotein subunit within the SDH catalytic dimer. Belongs to the SDHAF2 family. +Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +May be involved in transcriptional regulation. Belongs to the krueppel C2H2-type zinc-finger protein family. +The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. The coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated with ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity). Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits. The coatomer is cytoplasmic or polymerized on the cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it. Polyubiquitinated by RCHY1 in the presence of androgen, leading to proteasomal degradation. Belongs to the COPE family. +Partially overlaps RPP0. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +This alpha-adrenergic receptor mediates its action by association with G proteins that activate a phosphatidylinositol-calcium second messenger system. Its effect is mediated by G(q) and G(11) proteins. Nuclear ADRA1A-ADRA1B heterooligomers regulate phenylephrine (PE)-stimulated ERK signaling in cardiac myocytes (By similarity). Homo- and heterooligomer. Heterooligomerizes with ADRA1B homooligomers in cardiac myocytes. Interacts with CAVIN4. Location at the nuclear membrane facilitates heterooligomerization and regulates ERK-mediated signaling in cardiac myocytes. Colocalizes with GNAQ, PLCB1 as well as LAP2 at the nuclear membrane of cardiac myocytes (By similarity). Belongs to the G-protein coupled receptor 1 family. Adrenergic receptor subfamily. ADRA1A sub-subfamily. Truncated N-terminus. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Pycsar (pyrimidine cyclase system for antiphage resistance) provides immunity against bacteriophage. The pyrimidine cyclase (PycC) synthesizes cyclic nucleotides in response to infection; these serve as specific second messenger signals. The signals activate the adjacent effector, leading to bacterial cell death and abortive phage infection. A clade A Pycsar system. The pyrimidine cyclase gene of a two-gene Pycsar system, generates cyclic UMP (cUMP) from UTP, has little to no activity on ATP, CTP or GTP (PubMed:34644530). Expression of this and adjacent effector PaPycTIR (AC P0DV41) probably confers resistance to bacteriophage. The genes are probably only expressed in response to bacteriophage infection (Probable). Does not have adenylyl or guanylyl cyclase activity (PubMed:32454240). UTP = 3',5'-cyclic UMP + diphosphate When crystallized with (non-physiological) ATP it binds both Ca(2+) and Mn(2+) (PubMed:32454240). The enzyme assay showing cUMP synthase activity has Mn(2+) and Mg(2+) (PubMed:34644530). Monomer. The 2 guanylate cyclase domains fold into a pseudo-dimeric structure; the second domain binds metal while the first provides most of the nucleotide-binding residues. Belongs to the adenylyl cyclase class-4/guanylyl cyclase family. Pyrimidine cyclase subfamily. +Ensures chromosome alignment and accurate chromosome segregation during mitosis. Promotes proper kinetochore-microtubule (k-MT) interactions during anaphase B. The phosphorylation status of nsk1 affects the proper k-MT coupling, ensuring that it interacts stably only at the correct time during mitosis. Interacts with dlc1. The dlc1-nsk1 complex seems to oligomerize in chain-like structures. Also binds directly to spindle microtubules. Undergoes cell cycle-dependent localization changes, nucleolar during interphase, distributed in the nucleoplasm during metaphase, and increased at kinetochores and the spindle during anaphase. Phosphorylated by cdk1 at prometaphase arrest. Phosphorylation prevents nsk1 kinetochore and spindle targeting. Dephosphorylated by clp1 at anaphase onset controls its relocalization. +Homohexamer. Belongs to the GTP cyclohydrolase I type 2/NIF3 family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +Belongs to the UPF0637 family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain and the peripheric stalk, which acts as a stator to hold the catalytic alpha(3)beta(3) subcomplex and subunit a/ATP6 static relative to the rotary elements (By similarity). F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. In yeast, the dimeric form of ATP synthase consists of 17 polypeptides: alpha, beta, gamma, delta, epsilon, 4 (B), 5 (OSCP), 6 (A), 8, 9 (C), d, E (Tim11), f, g, h, i/j and k (By similarity). Belongs to the eukaryotic ATPase B chain family. +Disrupting the ure2 operon has no effect on urease activity or pathogen survival in BALB/c mice when administered orally. 2 H(+) + H2O + urea = CO2 + 2 NH4(+) Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Belongs to the urease gamma subunit family. +May function in innate immunity through activation of the lectin complement pathway. Calcium-dependent and GlcNAc-binding lectin (By similarity). Homotrimer. Interacts with elastin. Interacts with MASP1 and MASP2. The fibrinogen-like domain (FBG) contains calcium-binding sites that may be involved in carbohydrate binding. Belongs to the ficolin lectin family. +Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). diphosphate + N-(5-phospho-beta-D-ribosyl)anthranilate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate Binds 2 magnesium ions per monomer. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 2/5. Homodimer. Belongs to the anthranilate phosphoribosyltransferase family. +Catalyzes the transfer of the AMP portion of ATP to flavin mononucleotide (FMN) to produce flavin adenine dinucleotide (FAD) coenzyme. ATP + FMN + H(+) = diphosphate + FAD Cofactor biosynthesis; FAD biosynthesis; FAD from FMN: step 1/1. Homodimer. Belongs to the archaeal FAD synthase family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel. Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL. Belongs to the GroES chaperonin family. +Catalyzes the hydrolysis of 1-phosphatidylinositol 4,5-bisphosphate into diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) and mediates intracellular signaling downstream of G protein-coupled receptors. Regulates the function of the endothelial barrier. a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate) + H2O = 1D-myo-inositol 1,4,5-trisphosphate + a 1,2-diacyl-sn-glycerol + H(+) a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + H2O = 1D-myo-inositol 1-phosphate + a 1,2-diacyl-sn-glycerol + H(+) Interacts with DGKQ. Colocalizes with the adrenergic receptors, ADREN1A and ADREN1B, at the nuclear membrane of cardiac myocytes. Highest expression in brain. Also expressed in parotid gland, liver, uterus, lung, heart, adrenal gland and ovary. Not detected in spleen, pancreas, intestine, thymus or kidney. Palmitoylated. Palmitoylation at Cys-17 by ZDHHC21 regulates the signaling activity of PLCB1 and the function of the endothelial barrier. Palmitoylation by ZDHHC21 is stimulated by inflammation. The receptor-mediated activation of PLC-beta-1 is mediated by two G-protein alpha subunits, alpha-Q and alpha-11. +Ras proteins bind GDP/GTP and possess intrinsic GTPase activity. Plays a role in eye development by regulating cell growth, survival of postmitotic ommatidial cells and differentiation of photoreceptor cells. During larval development, mediates Ptth/tor signaling leading to the production of ecdysone, a hormone required for the initiation of metamorphosis. GTP + H2O = GDP + H(+) + phosphate Alternates between an inactive form bound to GDP and an active form bound to GTP. Activated by a guanine nucleotide-exchange factor (GEF) and inactivated by a GTPase-activating protein (GAP). Belongs to the small GTPase superfamily. Ras family. +Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. (2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 4/5. Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface. Belongs to the enolase family. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Belongs to the SfsA family. +Belongs to the UPF0145 family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 magnesium or manganese ions per subunit. Belongs to the PP2C family. +Probable metal transporter. Probably acts redundantly with the other metal transport proteins cnnm-1, cnnm-2, cnnm-4 and cnnm-5 to regulate Mg(2+) homeostasis. Promotes postembryonic gonad development by regulating Mg(2+) levels, probably via AMPK signaling. Highly expressed in the intestine and in neurons, but it is also expressed in a variety of tissues including the pharynx, hypodermis, rectum and in muscles. No visible phenotype. Double knockout with cnnm-1 results in increased levels of intestinal Mg(2+) and reduced levels in other tissues. This Mg(2+) deficiency in tissues leads to a reduced lifespan, 100% sterility, and smaller animals that exhibit a developmental delay with defective gonad development and which therefore do not produce oocytes or form vulva. In addition, the gonad development defect in the cnnm-1 and cnnm-3 double knockout is rescued when the AMPK alpha subunit aak-2 is also knocked out. Double knockout with cnnm-2 results in 22% sterility. Quintuple knockout with cnnm-1, cnnm-2, cnnm-4 and cnnm-5 results in a reduced lifespan and 100% sterility. Belongs to the ACDP family. +Belongs to the universal ribosomal protein uS2 family. +Forms a heterodimer, consisting of a large extracellular region non-covalently linked to a seven-transmembrane moiety. Proteolytically cleaved into 2 subunits, an extracellular subunit and a seven-transmembrane subunit. Belongs to the G-protein coupled receptor 2 family. LN-TM7 subfamily. +GTPase-activating protein (GAP) for the ADP ribosylation factor 1 (ARF1). Involved in membrane trafficking and /or vesicle transport. Promotes hydrolysis of the ARF1-bound GTP and thus, is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles, a prerequisite for vesicle's fusion with target compartment. Probably regulates ARF1-mediated transport via its interaction with the KDELR proteins and TMED2. Overexpression induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, as when ARF1 is deactivated. Its activity is stimulated by phosphoinosides and inhibited by phosphatidylcholine (By similarity). Interacts with ARF1. Interacts with the COPI coat proteins, KDELR1 and TMED2. It is probably a component of the COPI coat protein complex. The interaction with TMED2 inhibits the GAP activity (By similarity). Associates with the Golgi complex. The region downstream of Arf-GAP domain is essential to GAP activity in vivo. This region may be required for its targeting to Golgi membranes (By similarity). +Belongs to the UPF0316 family. +One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. Binds multiple chlorophylls and provides some of the ligands for the Ca-4Mn-5O cluster of the oxygen-evolving complex. It may also provide a ligand for a Cl- that is required for oxygen evolution. PSII binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbB/PsbC family. PsbC subfamily. +Catalyzes the calcium-dependent formation of isopeptide cross-links between glutamine and lysine residues in various proteins, as well as the conjugation of polyamines to proteins. Involved in the formation of the cornified envelope (CE), a specialized component consisting of covalent cross-links of proteins beneath the plasma membrane of terminally differentiated keratinocytes. Catalyzes small proline-rich proteins (SPRR1 and SPRR2) and LOR cross-linking to form small interchain oligomers, which are further cross-linked by TGM1 onto the growing CE scaffold (By similarity). In hair follicles, involved in cross-linking structural proteins to hardening the inner root sheath. L-glutaminyl-[protein] + L-lysyl-[protein] = [protein]-L-lysyl-N(6)-5-L-glutamyl-[protein] + NH4(+) Binds 3 Ca(2+) cations per subunit. Binds 1 Ca(2+) as a zymogen, and binds 2 more Ca(2+) cations, or other divalent metal cations, after proteolytic processing. Consists of two polypeptide chains, which are synthesized as a precursor form of a single polypeptide. Activated by proteolytic processing. In vitro activation is commonly achieved by cleavage with dispase, a neutral bacterial protease. Dispase cleavage site was proposed to lie between Ser-470 and Ser-471 (PubMed:8099584) or between Pro-465 and Phe-466 (PubMed:16565075). Physiological activation may be catalyzed by CTSL and, to a lesser extent, by CTSS, but not by CTSB, CTSD nor CTSV (PubMed:16565075). The disease is caused by variants affecting the gene represented in this entry. Belongs to the transglutaminase superfamily. Transglutaminase family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a, b, b' and c. Belongs to the ATPase gamma chain family. +Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules (By similarity). COPII is composed of at least 5 proteins: the SEC23/24 complex, the SEC13/31 complex and SAR1. SEC13 and SEC31 make a 2:2 tetramer that forms the edge element of the COPII outer coat. The tetramer self-assembles in multiple copies to form the complete polyhedral cage. Interacts (via WD 8) with SEC13 (By similarity). Associates with membranes in a GTP-dependent manner. Localizes to endoplasmic reticulum exit sites (ERES), also known as transitional endoplasmic reticulum (tER). Belongs to the WD repeat SEC31 family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Required for chromosome condensation and partitioning. Homodimer. Contains large globular domains required for ATP hydrolysis at each terminus and a third globular domain forming a flexible SMC hinge near the middle of the molecule. These domains are separated by coiled-coil structures. Belongs to the SMC family. +Cytochrome c oxidase subunit which plays a role in assembly of respiratory supercomplexes. Associates with the respiratory chain complex III/complex IV supercomplex. Belongs to the RCF1 family. +Putative adhesion molecule that mediates sialic-acid dependent binding to cells. Preferentially binds to alpha-2,3-linked sialic acid. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface. Predominantly expressed by immature monocytic/myeloid lineage cells in bone marrow. Also found at lower levels in mature neutrophils and monocytes. Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases. Belongs to the immunoglobulin superfamily. SIGLEC (sialic acid binding Ig-like lectin) family. Siglec-F +Required for determination of left/right asymmetry in nervous system. Acts together with unc-40 to control an initial left-right asymmetric polarization of the Q neuroblasts. Mig-21 and unc-40 may control the asymmetry in Wnt signaling response by restricting posterior polarization to one of the 2 Q neuroblasts. Involved in left-side QL posterior migration. In right-side QR, unc-40 and mig-21 pathways mutually inhibit each other in posterior migration, allowing anterior QR migration. Glycosylated via C-mannosylation by dpy-19 at Trp-58 and Trp-61. +Belongs to the bacterial ribosomal protein bL33 family. +Belongs to the UPF0102 family. +Encapsidates the viral DNA into characteristic twinned ('geminate') particles. Binds the genomic viral ssDNA and shuttles it into and out of the cell nucleus. The CP of bipartite geminiviruses is not required for cell-to-cell or systemic movement. Homomultimer. Binds to single-stranded and double-stranded viral DNA. Interacts (via nuclear localization signals) with host importin alpha-1a (By similarity). It is actively transported into the host cell nucleus. It may be exported out of the nucleus through a nuclear export signal for cell-to-cell movement and spread (By similarity). Belongs to the geminiviridae capsid protein family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell. Homopentamer. Belongs to the MscL family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +E3 ubiquitin ligase essential for DNA replication origin activation during S phase (PubMed:31160578). Acts as a replication origin selector which selects the origins to be fired and catalyzes the multi-mono-ubiquitination of a subset of chromatin-bound ORC3 and ORC5 during S-phase (PubMed:31160578). S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Associates with ORC complex (PubMed:31160578). Binds to chromatin; association is cell cycle-regulated, absent from mitotic chromosomes, is associated with chromatin from G1 and partially released from chromatin from mid S-phase (PubMed:31160578). Association to chromatin is cell cycle-regulated, absent from mitotic chromosomes, is associated with chromatin from G1 and partially released from chromatin from mid S-phase. Auto-ubiquitinated. Truncated N-terminus. +Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell. Belongs to the MinE family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Plays a role in virus cell tropism, and may be required for efficient virus replication in macrophages. Expressed in the early phase of the viral replicative cycle. Belongs to the asfivirus MGF 360 family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +D-serine = NH4(+) + pyruvate Belongs to the serine/threonine dehydratase family. DsdA subfamily. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides. Belongs to the glycosyl hydrolase 32 family. +L-histidine = NH4(+) + trans-urocanate Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 1/3. Contains an active site 4-methylidene-imidazol-5-one (MIO), which is formed autocatalytically by cyclization and dehydration of residues Ala-Ser-Gly. Belongs to the PAL/histidase family. The gene for this protein is duplicated in strains AX3 and AX4. These strains contain a duplication of a segment of 750 kb of chromosome 2 compared to the corresponding sequence in strain AX2. +Catalyzes the reversible interconversion of serine and glycine with a modified folate serving as the one-carbon carrier. Also exhibits a pteridine-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Reduces the physiological low-potential two-electron acceptor coenzyme F420, and the artificial one-electron acceptor methylviologen. H(+) + H2 + oxidized coenzyme F420-(gamma-L-Glu)(n) = reduced coenzyme F420-(gamma-L-Glu)(n) There are 12-13 Fe atoms/(alpha(1)beta(1)gamma(1)) unit of the FRH. Heterocomplex of the form (alpha(1)beta(1)gamma(1))(8). Belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit family. +Belongs to the bacterial ribosomal protein bL34 family. +Belongs to the CNPPD1 family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase. Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Prokaryotic type I sub-subfamily. +Component of the INA complex (INAC) that promotes the biogenesis of mitochondrial F(1)F(0)-ATP synthase. INAC facilitates the assembly of the peripheral stalk and promotes the assembly of the catalytic F(1)-domain with the membrane-embedded F(0)-domain. Component of the inner membrane assembly (INA) complex, composed of INA17 and INA22. Interacts with a subset of F(1)F(0)-ATP synthase subunits of the F(1)-domain and the peripheral stalk. Belongs to the INA17 family. +Belongs to the hssA/B family. +Participates in the translocation of lipoproteins from the inner membrane to the outer membrane. Only forms a complex with a lipoprotein if the residue after the N-terminal Cys is not an aspartate (The Asp acts as a targeting signal to indicate that the lipoprotein should stay in the inner membrane). Monomer. Belongs to the LolA family. +Probably involved in the RNA silencing pathway. May bind to short RNAs such as microRNAs (miRNAs) or short interfering RNAs (siRNAs), and represses the translation of mRNAs which are complementary to them (By similarity). Belongs to the argonaute family. Ago subfamily. +Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide. 6-carboxyhexanoyl-[ACP] + H(+) + L-alanine = (8S)-8-amino-7-oxononanoate + CO2 + holo-[ACP] Cofactor biosynthesis; biotin biosynthesis. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase delta chain family. +(R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Belongs to the prokaryotic pantothenate kinase family. +Involved in cell cycle regulation. May be a regulatory subunit of CDKD-1/CAK-R2. Interacts specifically with CDKD-1/CAK-R2. Expressed in roots, nodes and internodes, and at lower levels in shoots and leaves. Expressed in the intercalary meristem of internodes and at lower levels in the elongation zone and differentiation zone. Expressed in the S and G2 phases. By submergence in the meristematic zone of internodes. Belongs to the cyclin family. Cyclin F subfamily. +Belongs to the bacterial ribosomal protein bL32 family. +Catalyzes the isomerization of 5-dehydro-4-deoxy-D-glucuronate to 3-deoxy-D-glycero-2,5-hexodiulosonate. 5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate Binds 1 zinc ion per subunit. Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-gluconate from pectin: step 4/5. Belongs to the KduI family. +May catalyze the cis-trans isomerization of proline imidic peptide bonds in oligopeptides thereby assisting the folding of proteins. May also function as a chaperone, playing a role in intracellular transport of proteins. May also have a protein ubiquitin ligase activity acting as an E3 ubiquitin protein ligase or as a ubiquitin-ubiquitin ligase promoting elongation of ubiquitin chains on proteins. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Expressed in leaves, flower buds and stems. Lower levels of expression in roots. Belongs to the cyclophilin-type PPIase family. PPIL2 subfamily. +Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia. ATP + L-glutamate + NH4(+) = ADP + H(+) + L-glutamine + phosphate Binds 2 Mg(2+) ions per subunit. The activity of this enzyme could be controlled by adenylation under conditions of abundant glutamine. Oligomer of 12 subunits arranged in the form of two hexameric ring. Belongs to the glutamine synthetase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Negative feedback regulator that controls excessive innate immune responses. Regulates both Toll-like receptor 4 (TLR4) and DDX58/RIG1-like helicases (RLH) pathways. May inhibit the LTR pathway by direct interaction with TRAF6 and attenuation of NF-kappa-B activation. May negatively regulate the RLH pathway downstream from MAVS and upstream of NF-kappa-B and IRF3 (By similarity). Interacts with MAVS, TICAM1, TRAF1, TRAF2, TRAF3 (By similarity). Interacts with TRAF6. +NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. a ubiquinone + H(+) + n Na(+)(in) + NADH = a ubiquinol + n Na(+)(out) + NAD(+) Composed of six subunits; NqrA, NqrB, NqrC, NqrD, NqrE and NqrF. Belongs to the NqrDE/RnfAE family. +Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)). 7-carboxy-7-deazaguanine + ATP + NH4(+) = 7-cyano-7-deazaguanine + ADP + H(+) + H2O + phosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. Belongs to the QueC family. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Bifunctional serine/threonine kinase and phosphorylase involved in the regulation of the pyruvate, phosphate dikinase (PPDK) by catalyzing its phosphorylation/dephosphorylation. ADP + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] = AMP + H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] + phosphate = diphosphate + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] Belongs to the pyruvate, phosphate/water dikinase regulatory protein family. PDRP subfamily. +Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Complex I is composed of 45 different subunits. Acetylation of Lys-64 and Lys-75 is observed in liver mitochondria from fasted mice but not from fed mice. Belongs to the complex I NDUFA2 subunit family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate. Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate. D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+) GTP + 4 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + formate + 3 H(+) + 2 phosphate Binds 2 divalent metal cations per subunit. Magnesium or manganese. Binds 1 zinc ion per subunit. Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-ribitylamino)uracil from GTP: step 1/4. In the N-terminal section; belongs to the DHBP synthase family. In the C-terminal section; belongs to the GTP cyclohydrolase II family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units. Binds 2 calcium ions per subunit. Calcium is inhibitory at high concentrations. Alpha-amylase expression underlies catabolite repression by glucose. Belongs to the glycosyl hydrolase 13 family. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +Catalyzes the addition of 3 molecules of isopentenyl diphosphate (IPP) onto dimethylallyl diphosphate (DMAPP) to form geranylgeranyl pyrophosphate (GGPP). Catalyzes the synthesis of geranylgeranyl pyrophosphate as a major product and of farnesyl pyrophosphate in smaller amounts. dimethylallyl diphosphate + isopentenyl diphosphate = (2E)-geranyl diphosphate + diphosphate (2E)-geranyl diphosphate + isopentenyl diphosphate = (2E,6E)-farnesyl diphosphate + diphosphate (2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = (2E,6E,10E)-geranylgeranyl diphosphate + diphosphate Binds 2 Mg(2+) ions per subunit. Isoprenoid biosynthesis; geranyl diphosphate biosynthesis; geranyl diphosphate from dimethylallyl diphosphate and isopentenyl diphosphate: step 1/1. Isoprenoid biosynthesis; farnesyl diphosphate biosynthesis; farnesyl diphosphate from geranyl diphosphate and isopentenyl diphosphate: step 1/1. Isoprenoid biosynthesis; geranylgeranyl diphosphate biosynthesis; geranylgeranyl diphosphate from farnesyl diphosphate and isopentenyl diphosphate: step 1/1. Homodimer. Belongs to the FPP/GGPP synthase family. +Serine endopeptidase which hydrolyzes a range of fluorogenic peptide substrates containing the basic residues arginine or lysine at the P1 position and prefers paired basic resides. Also hydrolyzes clupeine and salmine, activates plasminogen and converts trypsinogen to trypsin. Binds 1 Ca(2+) ion per subunit. Inhibited by antipain and leupeptin. The highest catalytic efficiency is observed for Boc-Leu-Lys-Arg-MCA. Optimum pH is 4.0. Inactive below pH 3.0 and above pH 6.5. The half-life (t1/2) values for activity loss at 30 degrees Celsius are 150 min at pH 6.6, 5.5 min at pH 6.8 and 14 min at pH 2.4. Remains fully active after heating at 50 degrees Celsius and pH 4.0 for 10 min. Retains 65% of its activity after heating at 55 degrees Celsius for 10 min. The half-life value for loss of activity at 60 degrees Celsius and pH 4.0 is 3.5 min. Activity found in solid culture only. Increases at the initial growth stage and decreases in the late growth stage. N-glycosylated. O-glycosylated. +Part of the ABC transporter complex AraFGH involved in arabinose import. Responsible for energy coupling to the transport system. ATP + H2O + L-arabinose(out) = ADP + H(+) + L-arabinose(in) + phosphate The complex is composed of two ATP-binding proteins (AraG), two transmembrane proteins (AraH) and a solute-binding protein (AraF). Belongs to the ABC transporter superfamily. Arabinose importer (TC 3.A.1.2.2) family. +May be a pheromone carrier. Acts as a kairomone, detected by the prey vomeronasal organ and inducing fear reactions in mice. Abundant in urine (at protein level). Causes an allergic reaction in human. Binds to IgE. Belongs to the calycin superfamily. Lipocalin family. +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Involved in iron-sulfur cluster biogenesis. Binds a 4Fe-4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe/S proteins. Could also act as a scaffold/chaperone for damaged Fe/S proteins. Binds 1 [4Fe-4S] cluster per subunit. The cluster is presumably bound at the interface of two monomers. Homodimer. Belongs to the NfuA family. +Belongs to the SfsA family. +Catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation. Cofactor biosynthesis; adenosylcobalamin biosynthesis. Belongs to the CobB/CobQ family. CobQ subfamily. +Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. (2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 4/5. Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface. Belongs to the enolase family. +Belongs to the herpesviridae US22 family. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + UDP-N-acetyl-alpha-D-glucosamine = beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +Possesses 5'->3' exoribonuclease activity. Required for the processing of nuclear mRNA and rRNA precursors. May promote termination of transcription by RNA polymerase II (By similarity). Belongs to the 5'-3' exonuclease family. XRN2/RAT1 subfamily. +a (3S)-3-hydroxyacyl-CoA + NAD(+) = a 3-oxoacyl-CoA + H(+) + NADH On the 2D-gel the determined pI of this protein is: 6.00, its MW is: 83 kDa. Belongs to the 3-hydroxyacyl-CoA dehydrogenase family. +Partially overlaps DST1. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Catalyzes the desulfonation of aliphatic sulfonates. an alkanesulfonate + FMNH2 + O2 = an aldehyde + FMN + 2 H(+) + H2O + sulfite Homotetramer. FMNH(2) which is absolutely required for this enzymatic reaction, is provided by SsuE. Belongs to the SsuD family. +Glutathione S-transferase that catalyzes the nucleophilic attack of the sulfur atom of glutathione on the electrophilic groups of a wide range of exogenous and endogenous compounds. Involved in the formation of glutathione conjugates of both prostaglandin A2 (PGA2) and prostaglandin J2 (PGJ2). It also catalyzes the isomerization of D5-androstene-3,17-dione (AD) into D4-androstene-3,17-dione and may therefore play an important role in hormone biosynthesis. Through its glutathione-dependent peroxidase activity toward the fatty acid hydroperoxide (13S)-hydroperoxy-(9Z,11E)-octadecadienoate/13-HPODE it is also involved in the metabolism of oxidized linoleic acid. glutathione + RX = a halide anion + an S-substituted glutathione + H(+) glutathione + prostaglandin A2 = prostaglandin A2-S-(R)-glutathione glutathione + prostaglandin J2 = prostaglandin J2-S-(R)-glutathione (13S)-hydroperoxy-(9Z,11E)-octadecadienoate + 2 glutathione = (13S)-hydroxy-(9Z,11E)-octadecadienoate + glutathione disulfide + H2O androst-5-ene-3,17-dione = androst-4-ene-3,17-dione Homodimer or heterodimer of GSTA1 and GSTA2. Belongs to the GST superfamily. Alpha family. +Covalent carrier of the coenzyme of citrate lyase. Oligomer with a subunit composition of (alpha,beta,gamma)6. Belongs to the CitD family. +DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease (By similarity). a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 divalent metal cations. Magnesium or manganese. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII' complex. PolIII' associates with the gamma complex (composed of gamma, delta, delta', psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex (By similarity). +Probably required for nitrate uptake under anoxic conditions. Also possibly involved in excretion of nitrite produced by the dissimilatory reduction of nitrate (By similarity). Positively regulated by the two-component system NreB/NreC. Belongs to the major facilitator superfamily. Nitrate/nitrite porter (TC 2.A.1.8) family. +Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF-1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. PrfC subfamily. +Belongs to the bacterial ribosomal protein bL32 family. +Inhibits the enzymatic activity of phospholipase A2 (PA2) (PubMed:10924158). Binds to the major PLA2 toxin of D.russelli siamensis (Daboiatoxin, AC Q7T2R1, and AC Q7T3T5) at 1-2-fold molar excess of inhibitor to toxin (PubMed:10924158). It exhibits broad spectra in neutralizing the toxicity of various snake venoms and toxins and inhibits the formation of edema in mice (PubMed:10924158). May bind to PLA2 through its proline-rich hydrophobic core region (Probable). Homohexamer. Secreted in blood plasma. Expressed by the liver. Glycosylated. Belongs to the CNF-like-inhibitor family. +Together with LptE, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Component of the lipopolysaccharide transport and assembly complex. Interacts with LptE and LptA. Belongs to the LptD family. +Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). Component of the Mediator complex. Belongs to the Mediator complex subunit 7 family. +Serine/threonine-protein phosphatase that plays an important role in controlling colony morphology, filament extension and agar invasion. Down-regulates expression of NRG1 and affects the expression of multiple filament-specific transcripts in response to serum and 37 degrees Celsius. Plays a crucial role in virulence in a mouse model of systemic candidiasis. H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 manganese ions per subunit. Inhibited by okadaic acid, a specific inhibitor of serine/threonine phosphatases of types 1, 2A and 2B. Leads to defect in morphogenesis and reduced virulence. Belongs to the PPP phosphatase family. PP-2A subfamily. +ATP + D-gluconate = 6-phospho-D-gluconate + ADP + H(+) Carbohydrate acid metabolism; D-gluconate degradation. Belongs to the gluconokinase GntK/GntV family. +Catalytic component of the GSH degradosomal complex involved in the degradation of glutathione (GSH) and other peptides containing a gamma-glu-X bond. Has a Gly-Cys dipeptidase activity. Homodimer. Component of the GSH degradosomal complex. Belongs to the peptidase M20A family. +Belongs to the bacterial ribosomal protein bL35 family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Protamines substitute for histones in the chromatin of sperm during the haploid phase of spermatogenesis. They compact sperm DNA into a highly condensed, stable and inactive complex (By similarity). Testis. Belongs to the protamine P1 family. +Dermonecrotic toxins cleave the phosphodiester linkage between the phosphate and headgroup of certain phospholipids (sphingolipid and lysolipid substrates), forming an alcohol (often choline) and a cyclic phosphate (By similarity). This toxin acts on sphingomyelin (SM) (By similarity). It may also act on ceramide phosphoethanolamine (CPE), lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE), but not on lysophosphatidylserine (LPS), and lysophosphatidylglycerol (LPG) (By similarity). It acts by transphosphatidylation, releasing exclusively cyclic phosphate products as second products (By similarity). Induces dermonecrosis, hemolysis, increased vascular permeability, edema, inflammatory response, and platelet aggregation (By similarity). an N-(acyl)-sphingosylphosphocholine = an N-(acyl)-sphingosyl-1,3-cyclic phosphate + choline an N-(acyl)-sphingosylphosphoethanolamine = an N-(acyl)-sphingosyl-1,3-cyclic phosphate + ethanolamine a 1-acyl-sn-glycero-3-phosphocholine = a 1-acyl-sn-glycero-2,3-cyclic phosphate + choline a 1-acyl-sn-glycero-3-phosphoethanolamine = a 1-acyl-sn-glycero-2,3-cyclic phosphate + ethanolamine Binds 1 Mg(2+) ion per subunit. Expressed by the venom gland. Belongs to the arthropod phospholipase D family. Class I subfamily. The most common activity assay for dermonecrotic toxins detects enzymatic activity by monitoring choline release from substrate. Liberation of choline from sphingomyelin (SM) or lysophosphatidylcholine (LPC) is commonly assumed to result from substrate hydrolysis, giving either ceramide-1-phosphate (C1P) or lysophosphatidic acid (LPA), respectively, as a second product. However, two studies from Lajoie and colleagues (2013 and 2015) report the observation of exclusive formation of cyclic phosphate products as second products, resulting from intramolecular transphosphatidylation. Cyclic phosphates have vastly different biological properties from their monoester counterparts, and they may be relevant to the pathology of brown spider envenomation. +Non-hemorrhagic snake venom zinc metalloprotease that hydrolyzes the Aalpha-chain of fibrinogen, more slowly the Bbeta-chain and shows no effect on the gamma chain. Has no coagulant activity on bovine plasma and fibrinogen. Binds 1 zinc ion per subunit. Inhibited by EDTA, 1,10-phenanthroline and beta-mercaptoethanol. Not inhibited by the serine protease inhibitors aprotinin and benzamidin. Highest activity at neutral to basic pH. Reduced activity at pH 3.0. Activity is highest at 4 degrees Celsius, decreases with increasing temperatures and is lost at 60 degrees Celsius. Monomer. Expressed by the venom gland. Belongs to the venom metalloproteinase (M12B) family. P-I subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex (Probable). No functional NADH-quinone oxidoreductase complex. Cells lacking this gene have a nearly normal respiratory growth phenotype on lactate, however they are unable to perform anaerobic photosynthesis. It is suggested that in R.capsulatus this complex may function in reverse flow under physiological conditions. Belongs to the complex I subunit 2 family. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. WEE1 subfamily. +Required for leukotriene biosynthesis by ALOX5 (5-lipoxygenase). Anchors ALOX5 to the membrane. Binds arachidonic acid, and could play an essential role in the transfer of arachidonic acid to ALOX5. Binds to MK-886, a compound that blocks the biosynthesis of leukotrienes (By similarity). Homotrimer. Interacts with LTC4S and ALOX5 (By similarity). The C-terminal part after residue 140 is mostly disordered. Belongs to the MAPEG family. +Cortical patch protein involved in endocytosis. May serve as an adapter to link INP52 and INP53 to the cortical actin cytoskeleton. Interacts with CAP1, RVS167, SLA1, INP52 and INP53. The INP52 and INP53 C-terminal Sac1 domains are required for the binding with BSP1. Peripheral membrane protein in a PtdIns(4)P and PtdIns(4,5)P2 manner. Phosphorylated by CDC28. Present with 704 molecules/cell in log phase SD medium. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Component of the coenzyme Q biosynthetic pathway. May play a role in organizing a multi-subunit COQ enzyme complex required for coenzyme Q biosynthesis. Required for steady-state levels of other COQ polypeptides. Cofactor biosynthesis; ubiquinone biosynthesis. Component of a multi-subunit COQ enzyme complex, composed of at least coq3, coq4, coq5, coq6, coq7 and coq9. Belongs to the COQ4 family. +Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP (PubMed:12297000, PubMed:17976651). Can also efficiently hydrolyze 2'-deoxy-N-6-hydroxylaminopurine triphosphate (dHAPTP) (PubMed:17090528). Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions (PubMed:12297000, PubMed:12730170, PubMed:17090528). To a much lesser extent, is also able to hydrolyze GTP, dGTP and dUTP, but shows very low activity toward the canonical nucleotides dATP, dCTP and dTTP and toward 8-oxo-dGTP, purine deoxyribose triphosphate, 2-aminopurine deoxyribose triphosphate and 2,6-diaminopurine deoxyribose triphosphate (PubMed:12297000, PubMed:17090528). H2O + XTP = diphosphate + H(+) + XMP dITP + H2O = dIMP + diphosphate + H(+) H2O + ITP = diphosphate + H(+) + IMP Binds 1 divalent metal cation per subunit. Maximum activity is obtained with Mg(2+). Activity with Mn(2+) or Ni(2+) makes up 60-75% of the maximum rate. Vmax values are similar for XTP, dITP and ITP. Activity toward dATP, dCTP and dTTP is less than 1% of the rate of XTP hydrolysis. dGTP and dUTP are hydrolyzed at 10-12% of the rate of XTP hydrolysis (PubMed:12297000). kcat is 5.7 sec(-1) with ITP or dHAPTP as substrate. kcat is 1.5 sec(-1) with dGTP as substrate (at pH 9.5 and 37 degrees Celsius) (PubMed:17090528). kcat is 19.9 sec(-1) with XTP as substrate. kcat is 13.2 sec(-1) with dITP as substrate. kcat is 18.9 sec(-1) with ITP as substrate. kcat is 0.85 sec(-1) with GTP as substrate. kcat is 0.37 sec(-1) with dGTP as substrate. kcat is 0.26 sec(-1) with TTP as substrate (at pH 9.0 and 37 degrees Celsius) (PubMed:17976651). Optimum pH is 10-10.5 (PubMed:12297000). Optimum pH is 9.0 (PubMed:17976651). Reaction rates under neutral conditions are <40% of the maximum (PubMed:12297000). Homodimer. Inactivation of this gene in a moa background (cells deficient in molybdopterin biosynthesis) results in increased N-6-hydroxylaminopurine (HAP) sensitivity, an increase in the level of mutagenesis, and increased recombination and SOS induction upon HAP exposure. Modified or damaged nucleotides such as 6-chloropurine deoxyribose triphosphate, 8-Br-dGTP, 5-Br-dCTP, 5-Br-dUTP, 7-deaza-dGTP, 7-methyl-GTP, N6-etheno-ATP, NAD, NADH, FAD, ADP-ribose, UPD-glucose, AppA and ApppA are not hydrolyzed by the enzyme. The aberrant nucleotides XTP and dITP can be produced by oxidative deamination from purine nucleotides in cells; they are potentially mutagenic. Belongs to the HAM1 NTPase family. +ATP + shikimate = 3-phosphoshikimate + ADP + H(+) Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 5/7. Belongs to the GHMP kinase family. Archaeal shikimate kinase subfamily. +Catalytic subunit of the essential mitochondrial processing protease (MPP), which cleaves the mitochondrial sequence off newly imported precursors proteins (By similarity). Preferentially, cleaves after an arginine at position P2 (By similarity). Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2. Binds 1 zinc ion per subunit. Binding to the alpha subunit is required for catalytic activity. Heterodimer of an alpha subunit and a beta subunit subunits, forming the mitochondrial processing protease (MPP) in which the alpha subunit is involved in substrate recognition and binding and the beta subunit is the catalytic subunit. Belongs to the peptidase M16 family. +Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. Binds two Mg(2+) per subunit. Monomer. Belongs to the type IA topoisomerase family. +Involved in the biosynthesis of the O-methyl phosphoramidate (MeOPN) group found on the capsular polysaccharide (CPS) of C.jejuni (PubMed:17675288). Catalyzes the ATP-dependent phosphorylation of the amide nitrogen of L-glutamine to form L-glutamine phosphate, the first committed step in MeOPN biosynthesis (PubMed:28650156, PubMed:30142271). Catalyzes also the phosphorylation of D-glutamine, gamma-L-glutamyl hydroxamate, gamma-L-glutamyl-hydrazide and beta-L-aspartyl hydroxamate (PubMed:30142271). Does not phosphorylate L-glutamate or L-asparagine (PubMed:28650156, PubMed:30142271). Does not act on L-glutamine derivatives with removed alpha-amino or alpha-carboxy groups (PubMed:30142271). ATP + H2O + L-glutamine = AMP + 2 H(+) + N(5)-phospho-L-glutamine + phosphate kcat is 2.5 sec(-1) with L-glutamine as substrate (PubMed:28650156, PubMed:30142271). kcat is 1.5 sec(-1) with D-glutamine as substrate. kcat is 2.1 sec(-1) with gamma-L-glutamyl hydroxamate as substrate. kcat is 0.41 sec(-1) with gamma-L-glutamyl-hydrazide as substrate (PubMed:30142271). Capsule biogenesis; capsule polysaccharide biosynthesis. Contains an N-terminal ATP-grasp domain, a specialized central substrate-binding domain for L-glutamine and a C-terminal phospho-histidine domain. Mutant does not express the MeOPN CPS modification. The reaction mechanism comprises three steps. First, a histidine residue of the enzyme attacks ATP at the beta-phosphoryl group to form AMP and a pyrophosphorylated enzyme intermediate. Next, the pyrophosphorylated enzyme intermediate is hydrolyzed to generate inorganic phosphate and a phosphorylated enzyme intermediate. Finally, the phosphorylated enzyme intermediate transfers the phosphate to the amide nitrogen of the acceptor substrate L-glutamine. In this mechanism, the gamma-phosphoryl group of ATP is converted to phosphate and the beta-phosphoryl group is utilized in the phosphorylation of L-glutamine. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +Part of the ABC transporter complex ModABC involved in molybdenum import. Responsible for energy coupling to the transport system. ATP + H2O + molybdate(out) = ADP + H(+) + molybdate(in) + phosphate The complex is composed of two ATP-binding proteins (ModC), two transmembrane proteins (ModB) and a solute-binding protein (ModA). Belongs to the ABC transporter superfamily. Molybdate importer (TC 3.A.1.8) family. +(6S)-10-formyltetrahydrofolate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide = (6S)-5,6,7,8-tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide H2O + IMP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide Purine metabolism; IMP biosynthesis via de novo pathway; 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide (10-formyl THF route): step 1/1. Purine metabolism; IMP biosynthesis via de novo pathway; IMP from 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide: step 1/1. The IMP cyclohydrolase activity resides in the N-terminal region. Belongs to the PurH family. +Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophobic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system (By similarity). Involved in PLA2G3-dependent maturation of mast cells. PLA2G3 is secreted by immature mast cells and acts on nearby fibroblasts upstream to PTDGS to synthesize PGD2, which in turn promotes mast cell maturation and degranulation via PTGDR (By similarity). prostaglandin H2 = prostaglandin D2 Monomer. Detected on rough endoplasmic reticulum of arachnoid and menigioma cells. Localized to the nuclear envelope, Golgi apparatus, secretory vesicles and spherical cytoplasmic structures in arachnoid trabecular cells, and to circular cytoplasmic structures in meningeal macrophages and perivascular microglial cells. In oligodendrocytes, localized to the rough endoplasmic reticulum and nuclear envelope. In retinal pigment epithelial cells, localized to distinct cytoplasmic domains including the perinuclear region. Also secreted. Forms a beta-barrel structure that accommodates hydrophobic ligands in its interior. Belongs to the calycin superfamily. Lipocalin family. +H2O + L-glutamine = L-glutamate + NH4(+) Homotetramer. Belongs to the glutaminase family. +RNA-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the eIF-3 subunit B family. +May regulate an early stage of the zoospore pathway. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Catalyzes the hydrolysis of esters. a carboxylic ester + H2O = a carboxylate + an alcohol + H(+) Belongs to the FrsA family. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +Involved in the degradation of chitin. ChbG is essential for growth on the acetylated chitooligosaccharides chitobiose and chitotriose but is dispensable for growth on cellobiose and chitosan dimer, the deacetylated form of chitobiose. Deacetylation of chitobiose-6-P and chitotriose-6-P is necessary for both the activation of the chb promoter by the regulatory protein ChbR and the hydrolysis of phosphorylated beta-glucosides by the phospho-beta-glucosidase ChbF. Catalyzes the removal of only one acetyl group from chitobiose-6-P to yield monoacetylchitobiose-6-P, the inducer of ChbR and the substrate of ChbF. H2O + N,N'-diacetylchitobiose = acetate + N-acetyl-beta-D-glucosaminyl-(1->4)-D-glucosamine diacetylchitobiose-6'-phosphate + H2O = acetate + N'-monoacetylchitobiose-6'-phosphate Glycan degradation; chitin degradation. Homodimer. Belongs to the YdjC deacetylase family. ChbG subfamily. +Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP). diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 1/2. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrE subfamily. +Additional isoforms seem to exist. The adjacent MYZAP and POLR2M genes are part of a complex transcription unit. The respective transcripts derive from different promoters and are alternatively spliced. In human, some transcripts of the upstream promoter of MYZAP use exons of the downstream POLR2M gene. +Belongs to the AIM9 family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. Belongs to the RecF family. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +May function as antiviral protein and may contribute to the defense against retroviral infections. Homotrimer. Interacts (via the B30.2/SPRY domain) with HIV-1 capsid complexes (PubMed:17156811). Interacts (via B-box and SPRY domain) with TRIM5 (PubMed:21680743, PubMed:17156811). Is the most abundant form. It is highly expressed in the placenta, spleen, colon and peripheral blood leukocytes. Up-regulated by interferons. Belongs to the TRIM/RBCC family. The in vivo relevance of this transcript of the TRIM6 (AC Q9C030) and TRIM34 genes creating a chimeric protein of 842 residues is uncertain. +Guanine nucleotide exchange factor (GEF) that catalyzes the exchange of GDP for GTP. Promotes guanine nucleotide exchange on the Rho family members of small GTPases, like RHOA, RHOC, RAC1 and CDC42. Required for signal transduction pathways involved in the regulation of cytokinesis. Component of the centralspindlin complex that serves as a microtubule-dependent and Rho-mediated signaling required for the myosin contractile ring formation during the cell cycle cytokinesis. Regulates the translocation of RHOA from the central spindle to the equatorial region. Plays a role in the control of mitotic spindle assembly; regulates the activation of CDC42 in metaphase for the process of spindle fibers attachment to kinetochores before chromosome congression. Involved in the regulation of epithelial cell polarity; participates in the formation of epithelial tight junctions in a polarity complex PARD3-PARD6-protein kinase PRKCQ-dependent manner. Plays a role in the regulation of neurite outgrowth. Inhibits phenobarbital (PB)-induced NR1I3 nuclear translocation. Stimulates the activity of RAC1 through its association with the oncogenic PARD6A-PRKCI complex in cancer cells, thereby acting to coordinately drive tumor cell proliferation and invasion. Also stimulates genotoxic stress-induced RHOB activity in breast cancer cells leading to their cell death. Autoinhibited by the C-terminal PH domain which folds back and binds to the surface of the DH domain, blocking binding of RHOA to the catalytic center of the DH domain (PubMed:31888991). The 2nd BRCT domain is also involved in inhibition, probably by helping to impede RHOA binding (PubMed:31888991). Allosterically activated by binding of activated GTP-bound RHOA to the PH domain which stimulates the release of PH inhibition and promotes the binding of substrate RHOA to the catalytic center (PubMed:31888991). Binding of phosphorylated RACGAP1 to the N-terminal BRCT domain-containing region also releases autoinhibition (PubMed:25068414). Homodimer (PubMed:15545273, PubMed:14645260, PubMed:16170345). Homooligomer (PubMed:15545273). Found in the centralspindlin complex (PubMed:16236794). Interacts with NR1I3 (By similarity). Interacts (Thr-359 phosphorylated form) with PARD6A; the interaction is observed in cancer cells (PubMed:15254234, PubMed:19617897). Interacts (Thr-359 phosphorylated form) with PRKCI; the interaction is observed in cancer cells (PubMed:19617897). Interacts with PKP4; the interaction is observed at the midbody (PubMed:22814378). Interacts with RACGAP1/CYK4; the interaction is direct, occurs in a microtubule-dependent manner, occurs at anaphase and during cytokinesis, is inhibited in metaphase by phosphorylation of ECT2 on Thr-373 and is stimulated in early anaphase by dephosphorylation of ECT2 probably on Thr-373 through CDK1 activity (PubMed:16103226, PubMed:16129829, PubMed:16236794, PubMed:19468300, PubMed:19468302, PubMed:25068414). Interacts with PLK1; the interaction is stimulated upon its phosphorylation on Thr-444 (PubMed:16247472). Interacts with RHOA; the interaction results in allosteric activation of ECT2 (PubMed:31888991). Interacts with KIF23, PARD3, PARD6B and PRKCQ (PubMed:15254234, PubMed:16236794). Sequestered within the nucleus during interphase. Dispersed throughout the cytoplasm upon breakdown of the nuclear envelope during mitosis. Colocalizes with the centralspindlin complex to the mitotic spindles during anaphase/metaphase, the cleavage furrow during telophase and at the midbody at the end of cytokinesis. Colocalized with RhoA at the midbody. Its subcellular localization to tight junction is increased by calcium. Localized predominantly in the cytoplasm of numerous carcinoma cells. Expressed in lung epithelial cells (at protein level). Expressed in squamous cell carcinoma, primary non-small cell lung cancer tumors and lung adenocarcinoma. Up-regulated by calcium in cells forming cell-cell contact sites. Up-regulated by DNA damaging agents like H(2)O(2) or ionizing radiation (IR). The BRCT domains 1 and 2 are required for intramolecular interaction, but not for intermolecular oligomerization (PubMed:15545273). The BRCT domains negatively inhibit its GEF activity in interphase cells (PubMed:15545273, PubMed:31888991). The same BRCT domains may act as a positive regulatory motif for the completion of cytokinesis after the breakdown of nuclear membrane during mitosis (PubMed:15545273). Phosphorylated by PLK1 in vitro. Hyperphosphorylated during the G2 phase of the cell cycle. Phosphorylation at Thr-373 occurs during the G2/M phase, relieves its auto-inhibition status and stimulates its GEF activity. Phosphorylation at Thr-444 in G2/M phase is required for subsequent binding with PLK1 and Rho exchange activation. Dephosphorylated at the time of cytokinesis. Phosphorylation at Thr-359 is required for its transformation activity in cancer cells. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Truncated N-terminus. +Key decatenating enzyme that alters DNA topology by binding to two double-stranded DNA molecules, generating a double-stranded break in one of the strands, passing the intact strand through the broken strand, and religating the broken strand. Plays a role in B-cell differentiation. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+). Homodimer (PubMed:21778401). Interacts with KIAA1210 (By similarity). Interacts with PLSCR1 (PubMed:19690332). Expressed in the tonsil, spleen, lymph node, thymus, skin, pancreas, testis, colon, kidney, liver, brain and lung (PubMed:9155056). Also found in breast, colon and lung carcinomas, Hodgkin's disease, large-cell non-Hodgkin's lymphoma, lymphocytic lymphomas and seminomas (PubMed:9155056). Defects in TOP2B may be involved in global developmental delay with autism spectrum disorder (ASD). The disease is caused by variants affecting the gene represented in this entry. Eukaryotic topoisomerase I and II can relax both negative and positive supercoils, whereas prokaryotic enzymes relax only negative supercoils. Belongs to the type II topoisomerase family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the LeuD family. LeuD type 1 subfamily. +Specific inhibitor of cysteine proteinases. Probably involved in the regulation of endogenous processes and in defense against pests and pathogens (By similarity). Belongs to the cystatin family. Phytocystatin subfamily. Sequencing errors. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Secreted polyprotein that is packaged and proteolytically processed by prohormone convertases PCSK1 and PCSK2 in a cell-type-specific manner (PubMed:12065665, PubMed:7595538). VGF and peptides derived from its processing play many roles in neurogenesis and neuroplasticity associated with learning, memory, depression and chronic pain (By similarity). Plays a role in the control of body fluid homeostasis by regulating vasopressin release. Suppresses presynaptic glutamatergic neurons connected to vasopressin neurons. Plays a role in the control of body fluid homeostasis by regulating vasopressin release. Activates GABAergic interneurons which are inhibitory neurons of the nervous system and thereby suppresses presynaptic glutamatergic neurons (PubMed:24704271). Stimulates also feeding behavior in an orexin-dependent manner in the hypothalamus (PubMed:20551287). Functions as a positive regulator for the activation of orexin neurons resulting in elevated gastric acid secretion and gastric emptying (PubMed:28213131). Secreted multifunctional neuropeptide that binds to different cell receptors and thereby plays multiple physiological roles including modulation of energy expenditure, pain, response to stress, gastric regulation, glucose homeostasis as well as lipolysis (PubMed:28123945, PubMed:16983076). Activates the G-protein-coupled receptor C3AR1 via a folding-upon-binding mechanism leading to enhanced lipolysis in adipocytes (PubMed:23940034, PubMed:28123945). Interacts with C1QBP receptor in macrophages and microglia causing increased levels of intracellular calcium and hypersensitivity (PubMed:24106277, PubMed:19466987). Plays a role in the regulation of memory formation and depression-related behaviors potentially by influencing synaptic plasticity and neurogenesis. Induces acute and transient activation of the NTRK2/TRKB receptor and subsequent CREB phosphorylation (By similarity). Induces also insulin secretion in insulinoma cells by increasing intracellular calcium mobilization (PubMed:25917832). Interacts with HSPA8 on cell membrane (By similarity). Interacts with C3AR1 (By similarity). Interacts with C1QBP (PubMed:24106277). Stored in secretory vesicles and then secreted, NERP peptides colocalize with vasopressin in the storage granules of hypothalamus. Central and peripheral nervous systems, synthesized exclusively in neuronal and neuroendocrine cells. VGF and several of the derived peptides are present in the brain. By nerve growth factor. Multiple peptides are derived from VGF, with activities in synaptic plasticity, antidepression, penile erection, autonomic activation, and increases in energy expenditure. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +This protein is a 'fusion' protein encoding four enzymatic activities of the pyrimidine pathway (GATase, CPSase, ATCase and DHOase). 2 ATP + H2O + hydrogencarbonate + L-glutamine = 2 ADP + carbamoyl phosphate + 2 H(+) + L-glutamate + phosphate carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate (S)-dihydroorotate + H2O = H(+) + N-carbamoyl-L-aspartate Binds 3 Zn(2+) ions per subunit (for dihydroorotase activity). Binds 4 magnesium or manganese ions per subunit. Allosterically regulated and controlled by phosphorylation. 5-phosphoribose 1-diphosphate (PRPP) is an activator while UMP and UTP are inhibitors of the CPSase reaction (By similarity). Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 1/3. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 3/3. Homohexamer. Interacts with CIPC. Cytosolic and unphosphorylated in resting cells, translocates to the nucleus in response to EGF stimulation, nuclear import promotes optimal cell growth. Activated by MAP kinase (Erk1/2) phosphorylation just prior to the S phase of the cell cycle, when the demand for pyrimidine nucleotides is greatest, and down-regulated as the cells emerge from S phase by protein kinase A (PKA) phosphorylation. Phosphorylation at Ser-1859 by RPS6KB1 downstream of MTOR promotes oligomerization and stimulates dihydroorotase activity. Phosphorylation at Ser-1406 reduces sensitivity to feedback inhibition by UTP (By similarity). GATase (glutamine amidotransferase) and CPSase (carbamoyl phosphate synthase) form together the glutamine-dependent CPSase (GD-CPSase) (EC 6.3.5.5). In the central section; belongs to the metallo-dependent hydrolases superfamily. DHOase family. CAD subfamily. +Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by a SNO isoform. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-phosphate Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis. Homohexamer (By similarity). Interacts with THI11 (PubMed:12271461). By the absence of external thiamine. Belongs to the PdxS/SNZ family. +Belongs to the ABC transporter superfamily. +Avian ovomucoid consists of three homologous, tandem Kazal family inhibitory domains. +Belongs to the bacterial ribosomal protein bL35 family. +Involved in uptake of extracellular oxidized copper under copper-limiting conditions. Highly induced under copper-limiting conditions. Down-regulated by YcnK, especially under high copper concentrations. Down-regulated by CsoR. Cells lacking this gene show a growth-defective phenotype under copper deprivation as well as a reduced intracellular content of copper. In the N-terminal section; belongs to the CopC family. In the C-terminal section; belongs to the CopD family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Methylated by PrmB. Belongs to the universal ribosomal protein uL3 family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +Binds 3 Zn(2+) ions. Belongs to the AP endonuclease 2 family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Belongs to the eukaryotic ribosomal protein eS7 family. +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation. cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). Belongs to the DNA photolyase class-2 family. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +Belongs to the RNase T2 family. +Trypanothione is the parasite analog of glutathione; this enzyme is the equivalent of glutathione reductase. NADP(+) + trypanothione = H(+) + NADPH + trypanothione disulfide Binds 1 FAD per subunit. Optimum pH is 7.5-8.0. Homodimer. The N-terminus is blocked. The active site is a redox-active disulfide bond. Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. +Required for normal growth in the presence of linoleic acid hydroperoxide (LoaOOH). Present with 4530 molecules/cell in log phase SD medium. Belongs to the protein-tyrosine phosphatase family. +Involved in the final reduction of the elongation cycle of fatty acid synthesis (FAS II). Catalyzes the reduction of a carbon-carbon double bond in an enoyl moiety that is covalently linked to an acyl carrier protein (ACP). a 2,3-saturated acyl-[ACP] + NAD(+) = a (2E)-enoyl-[ACP] + H(+) + NADH Lipid metabolism; fatty acid biosynthesis. Monomer. Belongs to the TER reductase family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis. The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance. As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia. The TRiC complex plays a role in the folding of actin and tubulin. Component of the chaperonin-containing T-complex (TRiC), a heterooligomeric complex of about 850 to 900 kDa that forms two stacked rings, 12 to 16 nm in diameter. Interacts with PACRG (By similarity). Interacts with DNAAF4 (By similarity). Interacts with DLEC1 (By similarity). Belongs to the TCP-1 chaperonin family. +This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA. Binds to the 5S rRNA independently of L5 and L18. Belongs to the bacterial ribosomal protein bL25 family. CTC subfamily. +Probably required for nitrate uptake under anoxic conditions. Also possibly involved in excretion of nitrite produced by the dissimilatory reduction of nitrate (By similarity). Positively regulated by the two-component system NreB/NreC. Belongs to the major facilitator superfamily. Nitrate/nitrite porter (TC 2.A.1.8) family. +ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 2/3. Homotetramer. Belongs to the argininosuccinate synthase family. Type 1 subfamily. +Catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). The sulfur atoms are provided by the cysteine/cysteine desulfurase (IscS) system. AH2 + ATP + cytidine(32) in tRNA + S-sulfanyl-L-cysteinyl-[cysteine desulfurase] = 2-thiocytidine(32) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[cysteine desulfurase] Binds 1 [4Fe-4S] cluster per subunit. The cluster is chelated by three Cys residues, the fourth Fe has a free coordination site that may bind a sulfur atom transferred from the persulfide of IscS. tRNA modification. Homodimer. The thiolation reaction likely consists of two steps: a first activation step by ATP to form an adenylated intermediate of the target base of tRNA, and a second nucleophilic substitution step of the sulfur (S) atom supplied by the hydrosulfide attached to the Fe-S cluster. Belongs to the TtcA family. +Partially overlaps GNP1. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Constitutes, with BamD, the core component of the assembly machinery. Part of the Bam complex, which is composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. Belongs to the BamA family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase gamma chain family. +Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide. 6-carboxyhexanoyl-[ACP] + H(+) + L-alanine = (8S)-8-amino-7-oxononanoate + CO2 + holo-[ACP] Cofactor biosynthesis; biotin biosynthesis. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily. +Necessary for formate dehydrogenase activity. Belongs to the FdhE family. +Regulator of cell surface receptor signal transduction. Plays a central role in retinal vascularization by regulating norrin (NDP) signal transduction. Acts in concert with norrin (NDP) to promote FZD4 multimerization and subsequent activation of FZD4, leading to promote accumulation of beta-catenin (CTNNB1) and stimulate LEF/TCF-mediated transcriptional programs. Suprisingly, it only activate the norrin (NDP)-dependent activation of FZD4, while it does not activate the Wnt-dependent activation of FZD4, suggesting the existence of a Wnt-independent signaling that also promote accumulation the beta-catenin (CTNNB1). Acts as a regulator of membrane proteinases such as ADAM10 and MMP14/MT1-MMP. Activates ADAM10-dependent cleavage activity of amyloid precursor protein (APP). Activates MMP14/MT1-MMP-dependent cleavage activity (By similarity). Component of a complex, at least composed of TSPAN12, FZD4 and norrin (NDP) (By similarity). Interacts (when palmitoylated) with ADAM10. Interacts with MMP14/MT1-MMP (By similarity). Palmitoylated; required for interaction with ADAM10. The precise position of palmitoylated residues is unclear and occurs either on Cys-9, Cys-12 and/or Cys-83 (By similarity). Belongs to the tetraspanin (TM4SF) family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +This phospholipase A2 inhibitor neutralizes the activity of basic PLA2 myotoxins of its own and related venoms. The inhibitory profile shows specificity towards group II PLA2, either belonging to the catalytically-active (D49) or -inactive (K49) subtypes. Homotrimer; non-covalently linked. Secreted in plasma. Expressed by the liver. N-glycosylated. Belongs to the alpha-type phospholipase A2 inhibitor family. +Pore-forming subunit of a potassium efflux system that confers protection against electrophiles. Catalyzes K(+)/H(+) antiport. Interacts with the regulatory subunit KefG. Belongs to the monovalent cation:proton antiporter 2 (CPA2) transporter (TC 2.A.37) family. KefB subfamily. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Expressed in both sporophyte and gametophyte phases of the life cycle. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. ATP + L-cysteine + L-glutamate = ADP + gamma-L-glutamyl-L-cysteine + H(+) + phosphate Belongs to the glutamate--cysteine ligase type 2 family. YbdK subfamily. +May be involved in the secretion of hexose transporters from the endoplasmic reticulum. Involved in secretion of GAL2 and HXT1. Present with 21400 molecules/cell in log phase SD medium. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Belongs to the TACO1 family. +Belongs to the class I-like SAM-binding methyltransferase superfamily. Cation-dependent O-methyltransferase family. +The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination. This subunit has 5' -> 3' nuclease activity. ATP + H2O = ADP + H(+) + phosphate Heterodimer of AddA and RexB. Belongs to the helicase family. AddB/RexB type 2 subfamily. +Abundant in stationary phase (G0) cells. mRNA levels rapidly decrease upon exit from G0. +Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 magnesium ions per subunit. Monomer. Belongs to the DNA polymerase type-Y family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate. ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterodimer of GatD and GatE. Belongs to the asparaginase 1 family. GatD subfamily. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit is responsible for energy coupling to the transport system and for the release of the potassium ions to the cytoplasm. ATP + H2O + K(+)(out) = ADP + H(+) + K(+)(in) + phosphate The system is composed of three essential subunits: KdpA, KdpB and KdpC. Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IA subfamily. +ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 2/3. Homotetramer. Belongs to the argininosuccinate synthase family. Type 1 subfamily. +This b-type cytochrome is tightly associated with the reaction center of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. With its partner (PsbE) binds heme. PSII binds additional chlorophylls, carotenoids and specific lipids. Heterodimer of an alpha subunit and a beta subunit. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbE/PsbF family. +Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate. ATP + formate + N(1)-(5-phospho-beta-D-ribosyl)glycinamide = ADP + H(+) + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (formate route): step 1/1. Homodimer. Belongs to the PurK/PurT family. +Belongs to the UPF0337 (CsbD) family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 1 family. +Alpha-dioxygenase that catalyzes the primary oxygenation step of a variety of 14-20 carbon fatty acids, containing up to three unsaturated bonds, into their corresponding 2R-hydroperoxides (PubMed:9724698). Involved in the production of oxylipins that function in cell signaling, wound healing, and protection from infection (PubMed:9724698). a 1,2-saturated fatty acid + O2 = a (2R)-2-hydroperoxy fatty acid (9Z,12Z,15Z)-octadecatrienoate + O2 = (R)-2-hydroperoxy-(9Z,12Z,15Z)-octadecatrienoate (9Z,12Z)-octadecadienoate + O2 = (2R,9Z,12Z)-2-hydroperoxyoctadecadienoate Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit. Binds 1 calcium ion per subunit. Induced by the elicitor harpin (HrpN) from Erwinia amylovora and infection with E.amylovora (PubMed:9724698). Induced by infection with the bacterial pathogens Pseudomonas syringae pv syringae and Pseudomonas syringae pv tabaci (PubMed:9724698). Induced by salicylate (SA), wounding, jasmonate (JA), paraquat and 3-amino-1,2,4-triazole (3AT) (PubMed:9724698). Belongs to the peroxidase family. +Catalyzes the formation of trans cyclopropanated ketomycolate or methoxymycolate through the conversion of a double bond to a cyclopropane ring at the proximal position of an oxygenated mycolic acid via the transfer of a methylene group from S-adenosyl-L-methionine. In the absence of MmaA2, CmaA2 has a non-specific cis-cyclopropanating activity and is able to catalyze the conversion of a double bond to a cis cyclopropane ring at the distal position of an alpha mycolic acid. Cyclopropanated mycolic acids are key factors participating in cell envelope permeability, host immunomodulation and persistence. 1-acyl-2-(9Z)-enoyl-sn-glycero-3-phospholipid + S-adenosyl-L-methionine = 1-acyl-2-(9-cyclopronane)-acyl-sn-glycero-3-phospholipid + H(+) + S-adenosyl-L-homocysteine Inhibited by S-adenosyl-N-decyl-aminoethyl (SADAE) and thiacetazone (TAC). Lipid metabolism; mycolic acid biosynthesis. Homodimer. Inactivation of cmaA2 causes accumulation of unsaturated derivatives of both the methoxy- and ketomycolates. The mycolic acids of the cmaA2 mutant lack trans-cyclopropane rings but are otherwise intact with respect to cyclopropane and methyl branch content. Deletion of cmaA2 has no effect on bacterial loads during mouse infection but causes hypervirulence due to an excessive immune activation which produces more-severe granulomatous pathology than wild-type, and increases both the macrophage activation and the macrophage inflammatory response. Was identified as a high-confidence drug target. Belongs to the CFA/CMAS family. Extended N-terminus. +May be involved in multidrug export. Transmembrane domains (TMD) form a pore in the cell membrane and the ATP-binding domain (NBD) is responsible for energy generation (By similarity). Homodimer. The ATP-binding domain (NBD) and the transmembrane domain (TMD) are fused. Belongs to the ABC transporter superfamily. Extended N-terminus. +May stabilize HDL (high density lipoprotein) structure by its association with lipids, and affect the HDL metabolism. Monomer. Interacts with NAXE and NDRG1 (By similarity). Belongs to the apolipoprotein A2 family. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. In this organism, the P 'protein' is a heterodimer of two subunits. Belongs to the GcvP family. N-terminal subunit subfamily. +Mediates visceral muscle contractile activity (myotropic activity). Belongs to the periviscerokinin family. +Provides the (R)-glutamate required for cell wall biosynthesis. L-glutamate = D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the aspartate/glutamate racemases family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Ammonia produced by ureolysis increases the gastric pH thereby providing an environment permissive for colonization of the stomach. 2 H(+) + H2O + urea = CO2 + 2 NH4(+) Binds 2 nickel ions per subunit. Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterohexamer of 3 UreA (alpha) and 3 UreB (beta) subunits. Four heterohexamers assemble to form a 16 nm dodecameric complex (By similarity). Also associates with the outer membrane upon autolysis of neighboring bacteria. Carboxylation allows a single lysine to coordinate two nickel ions. The novel dodecameric structure of the enzyme may allow it to remain active at the cell surface at acidic gastric pH. Within this dodecameric structure the 12 active sites are clustered within the interior of the proteinaceous shell. This may allow a high local concentration of ammonia within the enzyme which may protect the nickel-chelating groups from protonation (By similarity). Belongs to the metallo-dependent hydrolases superfamily. Urease alpha subunit family. The orthologous protein is known as the alpha subunit (UreC) in most other bacteria. +The predicted gene has been split into 2 genes: At4g18257 and At4g18260. The predicted gene has been split into 2 genes: At4g18257 and At4g18260. +Involved in chromosome condensation, segregation and cell cycle progression. May participate in facilitating chromosome segregation by condensation DNA from both sides of a centrally located replisome during cell division. Not required for mini-F plasmid partitioning. Probably acts via its interaction with MukB and MukE. Overexpression results in anucleate cells. It has a calcium binding activity. Interacts, and probably forms a ternary complex, with MukE and MukB via its C-terminal region. The complex formation is stimulated by calcium or magnesium. It is required for an interaction between MukE and MukB. Restricted to the nucleoid region. Belongs to the MukF family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 2 subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 1 family. +Catalyzes the cyanide-resistant oxidation of ubiquinol and the reduction of molecular oxygen to water, but does not translocate protons and consequently is not linked to oxidative phosphorylation. May increase respiration when the cytochrome respiratory pathway is restricted, or in response to low temperatures (By similarity). 2 a ubiquinol + O2 = 2 a ubiquinone + 2 H2O Binds 2 iron ions per subunit. Homodimer; disulfide-linked. Mitochondrial, possibly in the inner surface of the inner mitochondrial membrane. Increased expression in developing cotyledons between days 5 and 7 but thereafter relatively constant. Belongs to the alternative oxidase family. +Belongs to the PCP4 family. +Functions as positive effectors of cell expansion through modulation of auxin transport. By auxin. Belongs to the ARG7 family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS. [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + a uridine in tRNA + ATP + H(+) + 2 reduced [2Fe-2S]-[ferredoxin] = [ThiI sulfur-carrier protein]-L-cysteine + a 4-thiouridine in tRNA + AMP + diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] [sulfur-carrier protein ThiS]-C-terminal Gly-Gly-AMP + AH2 + S-sulfanyl-L-cysteinyl-[cysteine desulfurase] = [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH + A + AMP + H(+) + L-cysteinyl-[cysteine desulfurase] Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiI family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Inhibitor of lipoprotein binding to the low density lipoprotein (LDL) receptor, LDL receptor-related protein, and very low density lipoprotein (VLDL) receptor. Associates with high density lipoproteins (HDL) and the triacylglycerol-rich lipoproteins in the plasma and makes up about 10% of the protein of the VLDL and 2% of that of HDL. Appears to interfere directly with fatty acid uptake and is also the major plasma inhibitor of cholesteryl ester transfer protein (CETP). Binds free fatty acids and reduces their intracellular esterification. Modulates the interaction of APOE with beta-migrating VLDL and inhibits binding of beta-VLDL to the LDL receptor-related protein. Belongs to the apolipoprotein C1 family. +Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents) (By similarity). 2-oxoglutarate + a methylated nucleobase within DNA + O2 = a nucleobase within DNA + CO2 + formaldehyde + succinate Binds 1 Fe(2+) ion per subunit. Belongs to the alkB family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +Catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates. Cleaves off the terminal sialic acids on the glycosylated HA during virus budding to facilitate virus release. Additionally helps virus spread through the circulation by further removing sialic acids from the cell surface. These cleavages prevent self-aggregation and ensure the efficient spread of the progeny virus from cell to cell. Otherwise, infection would be limited to one round of replication. Described as a receptor-destroying enzyme because it cleaves a terminal sialic acid from the cellular receptors. May facilitate viral invasion of the upper airways by cleaving the sialic acid moieties on the mucin of the airway epithelial cells. Likely to plays a role in the budding process through its association with lipid rafts during intracellular transport. May additionally display a raft-association independent effect on budding. Plays a role in the determination of host range restriction on replication and virulence. Sialidase activity in late endosome/lysosome traffic seems to enhance virus replication. Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates. Inhibited by the neuraminidase inhibitors zanamivir (Relenza) and oseltamivir (Tamiflu). These drugs interfere with the release of progeny virus from infected cells and are effective against all influenza strains. Resistance to neuraminidase inhibitors is quite rare. Homotetramer. Preferentially accumulates at the apical plasma membrane in infected polarized epithelial cells, which is the virus assembly site. Uses lipid rafts for cell surface transport and apical sorting. In the virion, forms a mushroom-shaped spike on the surface of the membrane. Intact N-terminus is essential for virion morphogenesis. Possesses two apical sorting signals, one in the ectodomain, which is likely to be a glycan, and the other in the transmembrane domain. The transmembrane domain also plays a role in lipid raft association. N-glycosylated. The influenza A genome consist of 8 RNA segments. Genetic variation of hemagglutinin and/or neuraminidase genes results in the emergence of new influenza strains. The mechanism of variation can be the result of point mutations or the result of genetic reassortment between segments of two different strains. Belongs to the glycosyl hydrolase 34 family. +Mediates response to the active Hedgehog (Hh) protein signal in embryos, functioning upstream or at the level of patched (ptc). Homodimer. Heterotetramer; 2 iHog chains bind 2 hh chains when facilitated by heparin, heparin is required to promote high-affinity interactions between hh and iHog (By similarity). The first fibronectin type-III domain mediates a specific interaction with Hh protein, in vitro. The second fibronectin type-III domain is additionally required for in vivo signaling activity (By similarity). Belongs to the immunoglobulin superfamily. IHOG family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +Part of a complex that catalyzes the reversible cleavage of acetyl-CoA, allowing growth on acetate as sole source of carbon and energy. Probably maintains the overall quaternary structure of the ACDS complex (By similarity). One-carbon metabolism; methanogenesis from acetate. Heterodimer of delta and gamma chains. The ACDS complex is made up of alpha, epsilon, beta, gamma and delta chains with a probable stoichiometry of (alpha(2)epsilon(2))(4)-beta(8)-(gamma(1)delta(1))(8) (Potential). Belongs to the CdhD family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a(1), b(1), b'(1) and c(9-12). Belongs to the ATPase alpha/beta chains family. +Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor. (S)-dihydroorotate + NAD(+) = H(+) + NADH + orotate Binds 1 FMN per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (NAD(+) route): step 1/1. Heterotetramer of 2 PyrK and 2 PyrD type B subunits. Belongs to the dihydroorotate dehydrogenase family. Type 1 subfamily. +Protein phosphatase that specifically mediates dephosphorylation of 'Ser-586' of Akt1, a protein that regulates the balance between cell survival and apoptosis through a cascade that primarily alters the function of transcription factors that regulate pro- and antiapoptotic genes. Dephosphorylation of 'Ser-586' of Akt1 triggers apoptosis and suppression of tumor growth. H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate +Catalyzes the reversible oxidation of malate to oxaloacetate. (S)-malate + NAD(+) = H(+) + NADH + oxaloacetate Belongs to the LDH/MDH superfamily. MDH type 2 family. +Belongs to the HflD family. +Plays an essential role in the assembly of succinate dehydrogenase (SDH), an enzyme complex (also referred to as respiratory complex II) that is a component of both the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. Required for flavinylation (covalent attachment of FAD) of the flavoprotein subunit of the SDH catalytic dimer. Interacts with the flavoprotein subunit within the SDH catalytic dimer. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the SDHAF2 family. +Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo-MPT) cofactor (Moco or molybdenum cofactor) to form Mo-molybdopterin guanine dinucleotide (Mo-MGD) cofactor. GTP + H(+) + Mo-molybdopterin = diphosphate + Mo-molybdopterin guanine dinucleotide The N-terminal domain determines nucleotide recognition and specific binding, while the C-terminal domain determines the specific binding to the target protein. Belongs to the MobA family. +Apoprotein for the two 4Fe-4S centers FA and FB of photosystem I (PSI); essential for photochemical activity. FB is the terminal electron acceptor of PSI, donating electrons to ferredoxin. The C-terminus interacts with PsaA/B/D and helps assemble the protein into the PSI complex. Required for binding of PsaD and PsaE to PSI. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. hnu + oxidized [2Fe-2S]-[ferredoxin] + reduced [plastocyanin] = oxidized [plastocyanin] + reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters. Cluster 2 is most probably the spectroscopically characterized electron acceptor FA and cluster 1 is most probably FB. The cyanobacterial PSI reaction center is composed of one copy each of PsaA,B,C,D,E,F,I,J,K,L,M and X, and forms trimeric complexes. +Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor (PubMed:12829714, PubMed:18669915). It can both act as a peptide transferase that transfers GalNAc onto unmodified peptide substrates, and as a glycopeptide transferase that requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. Prefers EA2 as substrate (PubMed:12829714). In the larval midgut, required for O-glycosylation of apical and luminal proteins within copper cells enabling proper gut acidification (PubMed:22157008). L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H(+) + UDP L-threonyl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H(+) + UDP Protein modification; protein glycosylation. Expressed during oogenesis, in the somatically derived follicle cells that surround the developing oocyte, which are involved in the maturation of the oocyte and construction of the egg shell, as well as playing a role in subsequent embryonic pattern formation. During embryonic stages 9-11, expressed in the primordium of the foregut, midgut and hindgut. Expressed in salivary glands from embryonic stage 12 onwards. During embryonic stages 12-13, expressed in the posterior midgut and hindgut. During embryonic stages 14-17, expressed in the hindgut and the posterior spiracles. Expression is also detected in the epidermis and antennomaxillary complex at embryonic stages 16-17. In third instar larvae, ubiquitously expressed in wing, eye-antennal, leg and haltere imaginal disks. Expressed throughout embryonic, larval, pupal and adult stages, with increasing levels during larval development. Transcripts are first detected during embryonic stages 9-11. There are two conserved domains in the glycosyltransferase region: the N-terminal domain (domain A, also called GT1 motif), which is probably involved in manganese coordination and substrate binding and the C-terminal domain (domain B, also called Gal/GalNAc-T motif), which is probably involved in catalytic reaction and UDP-Gal binding. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. Lethal (PubMed:22157008). RNAi-mediated knockdown in the whole body, embryonic mesoderm, respiratory system or digestive system and reproductive tract is lethal (PubMed:22157008). RNAi-mediated knockdown in the larval digestive system, results in loss of gut acidification and disruption of protein O-glycosylation in copper cells (PubMed:22157008). RNAi-mediated knockdown in hemocytes, amnioserosa, endoderm, mesoderm or nervous system causes no defect (PubMed:22157008). Belongs to the glycosyltransferase 2 family. GalNAc-T subfamily. Truncated C-terminus. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is composed of 13 subunits: eif3a, eif3b, eif3c, eif3d, eif3e, eif3f, eif3g, eif3h, eif3i, eif3j, eif3k, eif3l and eif3m. Belongs to the eIF-3 subunit L family. +Exhibits bacteriostatic activity against Gram-positive bacteria S.aureus and L.monocytogenes and Gram-negative bacterium E.coli, antifungal activity against C.neoformans and microbicidial activity against Gram-positive bacteria S.aureus and L.monocytogenes. Exhibits bacteriostatic activity against Gram-positive bacteria S.aureus and L.monocytogenes and Gram-negative bacterium E.coli, antifungal activity against C.neoformans and microbicidial activity against Gram-positive bacteria S.aureus and L.monocytogenes. Belongs to the alpha-defensin family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 1 subfamily. +Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain. acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine Binds 1 Mg(2+) ion per subunit. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; N-acetyl-alpha-D-glucosamine 1-phosphate from alpha-D-glucosamine 6-phosphate (route II): step 2/2. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; UDP-N-acetyl-alpha-D-glucosamine from N-acetyl-alpha-D-glucosamine 1-phosphate: step 1/1. Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. In the N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family. In the C-terminal section; belongs to the transferase hexapeptide repeat family. +Belongs to the UPF0301 (AlgH) family. +May act as a helicase. Belongs to the DNA2/NAM7 helicase family. +Catalytic subunit of the periplasmic nitrate reductase complex NapAB. Receives electrons from NapB and catalyzes the reduction of nitrate to nitrite. 2 Fe(II)-[cytochrome] + 2 H(+) + nitrate = 2 Fe(III)-[cytochrome] + H2O + nitrite Binds 1 [4Fe-4S] cluster. Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit. Component of the periplasmic nitrate reductase NapAB complex composed of NapA and NapB. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/NapA/NarB subfamily. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Merozoite surface antigen contain the sequence of 83 kDa, 42 kDa and 19 kDa antigens which are the major surface antigens of merozoites. The maturation take place during schizont. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +Belongs to the UPF0434 family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Shows weak antimicrobial activity against its phylogenetic relative Caulobacter crescentus. Does not show activity against other bacteria tested (E.coli, Vibrio sp, Burkhoderia thailandensis, and Salmonella newport). Unthreads upon heat treatment. Intracellular, when expressed in E.coli. The gene cluster lacks the ABC transporter usually responsible for export of the mature peptide (Probable). May be secreted in vivo (Probable). Is composed of a ring composed by 9 residues, a 5 residue-loop (SVSGQ) and a C-terminal tail (PubMed:26534965). The peptide is threaded when the C-terminal tail is inserted throught the isopeptide-bonded ring. The loop region serves as a recognition element for the isopeptidase AtxE2 (Probable). This lasso peptide is hydrolyzed to a linear form by the isopeptidase AtxE2, in vitro. The isopeptidase AtxE2 only recognizes the threaded form (but not the unthreaded form). +Belongs to the small heat shock protein (HSP20) family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Some bacteria have evolved a zinc-coordinating structure that stabilizes the LID domain. Belongs to the adenylate kinase family. +Mitochondrial tRNA N(1)-methyltransferase involved in mitochondrial tRNA maturation. Component of mitochondrial ribonuclease P, which cleaves tRNA molecules in their 5'-ends. Together with hsd17b10/mrpp2, forms a subcomplex of the mitochondrial ribonuclease P, named MRPP1-MRPP2 subcomplex, which displays functions that are independent of the ribonuclease P activity. The MRPP1-MRPP2 subcomplex catalyzes the formation of N(1)-methylguanine and N(1)-methyladenine at position 9 (m1G9 and m1A9, respectively) in tRNAs; trmt10c/mrpp1 acting as the catalytic N(1)-methyltransferase subunit. The MRPP1-MRPP2 subcomplex also acts as a tRNA maturation platform: following 5'-end cleavage by the mitochondrial ribonuclease P complex, the MRPP1-MRPP2 subcomplex enhances the efficiency of 3'-processing catalyzed by ELAC2, retains the tRNA product after elac2 processing and presents the nascent tRNA to the mitochondrial CCA tRNA nucleotidyltransferase TRNT1 enzyme. In addition to tRNA N(1)-methyltransferase activity, trmt10c/mrpp1 also acts as a mRNA N(1)-methyltransferase by mediating methylation of adenosine residues at the N(1) position of MT-ND5 mRNA. adenosine(9) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methyladenosine(9) in tRNA + S-adenosyl-L-homocysteine guanosine(9) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(9) in tRNA + S-adenosyl-L-homocysteine an adenosine in mRNA + S-adenosyl-L-methionine = an N(1)-methyladenosine in mRNA + H(+) + S-adenosyl-L-homocysteine Component of mitochondrial ribonuclease P. Interacts with HSD17B10/MRPP2. Belongs to the class IV-like SAM-binding methyltransferase superfamily. TRM10 family. +May be a regulator of cytoskeletal organization (Potential). May have a role in spermatogenesis. Interacts with WASL, and monomeric and filamentous actin. In hippocampal neurons colocalizes with WASL in the cell body, axons and the growth cone (By similarity). Localizes to the actin filaments at the Sertoli cell-spermatid junctions. Isoform 1 is expressed in brain and testis and isoform 2 is expressed only in brain (at protein level). The WH2 domain is found in a number of putative actin-binding proteins. The profilin-binding motif has been implicated in the interaction with profilin and SH3 domains. The KLKR motif is essential for G-actin binding and for actin polymerization. Mice are normal but males are sterile due to defects in spermatogenesis. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA. acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate Acetylated. Deacetylation by the SIR2-homolog deacetylase activates the enzyme. Belongs to the ATP-dependent AMP-binding enzyme family. +Initiates and terminates the replication only of its own subviral DNA molecule. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep binds a specific hairpin at the genome origin of replication. Introduces an endonucleolytic nick within the intergenic region of the genome, thereby initiating the rolling circle replication (RCR). Following cleavage, binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication. Displays origin-specific DNA cleavage, nucleotidyl transferase, ATPase and helicase activities (By similarity). ATP + H2O = ADP + H(+) + phosphate Divalent metal cations, possibly Mg(2+) or Mn(2+). Homooligomer (Potential). Rep binds to repeated DNA motifs (iterons) (By similarity). There are 3 rolling circle replication (RCR) motifs. RCR-2 is probably involved in metal coordination. RCR-3 is required for phosphodiester bond cleavage for initiation of RCR (By similarity). The genome of nanoviruses is composed of six to eight segments. In addition, some isolates contain subviral DNAs. Belongs to the nanoviridea/circoviridae replication-associated protein family. This protein is encoded by a subviral DNA that is not present in all isolates of the virus. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The NB-protein (BchN-BchB) is the catalytic component of the complex. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per heterodimer. The cluster is bound at the heterodimer interface by residues from both subunits. Porphyrin-containing compound metabolism; bacteriochlorophyll biosynthesis (light-independent). Protochlorophyllide reductase is composed of three subunits; BchL, BchN and BchB. Forms a heterotetramer of two BchB and two BchN subunits. Belongs to the ChlB/BchB/BchZ family. +Atypical and probable non DNA-binding bHLH transcription factor that integrates multiple signaling pathways to regulate cell elongation and plant development. Belongs to the bHLH protein family. +Mitogen-activated protein kinase (MAPK) which regulates abscisic acid (ABA) responses in a MAPKKK20-MKK5-MPK6 cascade involved in root growth (e.g. root cell division and elongation) and stomatal response (PubMed:27913741). Involved in oxidative stress-mediated signaling cascade (such as ozone). Involved in the innate immune MAP kinase signaling cascade (MEKK1, MKK4/MKK5 and MPK3/MPK6) downstream of bacterial flagellin receptor FLS2. May be involved in hypersensitive response (HR)-mediated signaling cascade by modulating LIP5 phosphorylation and subsequent multivesicular bodies (MVBs) trafficking. May phosphorylate regulators of WRKY transcription factors. Phosphorylates 1-aminocyclopropane-1-carboxylic acid synthases (ACS2 and ACS6) and may be involved in the regulation of bacterial elicitor flagellin-induced ethylene production. Regulates locally gene-mediated and basal resistance response to certain pathogens. May be involved in the cold and salinity stress-mediated MAP kinase signaling cascade (MEKK1, MKK1/MKK2 and MPK4/MPK6). MKK1-MPK6 module mediates abscisic acid (ABA)-dependent CAT1 expression with H(2)O(2) production and response to drought and salt stress. MKK1-MPK6 module is also involved in sugar signaling during the process of seed germination. MKK3-MPK6 module plays an important role in the jasmonate signal transduction pathway through the negative regulation of MYC2/JIN1 expression. MKK9-MPK3/MPK6 module phosphorylates and activates EIN3, leading to the promotion of EIN3-mediated transcription in ethylene signaling. MPK3/MPK6 cascade regulates camalexin synthesis through transcriptional regulation of the biosynthetic genes after pathogen infection. MKK9-MPK6 module positively regulates leaf senescence. YDA-MKK4/MKK5-MPK3/MPK6 module regulates stomatal cell fate before the guard mother cell (GMC) is specified. When activated, reinforces the feedback loop by phosphorylating BASL, and inhibits stomatal fate by phosphorylating SPCH (PubMed:25843888). This MAPK cascade also functions downstream of the ER receptor in regulating coordinated local cell proliferation, which shapes the morphology of plant organs. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by threonine and tyrosine phosphorylation. Activated by the MAP kinase kinases MKK2, MKK3, MKK4, MKK5, MKK7 and MKK9. Activated in response to touch, wounding, low temperature, low humidity, salt stress, hydrogen peroxide, ozone, ACC (an ethylene precursor), jasmonic acid (JA), mastoparan and UVC. Activated in response to elicitors: oligogalacturonides, hexameric chitin fragments, fungal xylanase, and the bacterial flagellin and harpin. Activated upon Pseudomonas syringae pv. tomato DC3000 infection. Repressed by the protein phosphatase 2C AP2C1 and the protein-tyrosine-phosphatases MKP1 and PTP1. Repressed by DSPTP1B/MKP2-mediated dephosphorylation. Activated by polarized BASL (PubMed:27746029). Triggered by MKKK20 in response to various abiotic stresses, including osmotic stress, cold and reactive oxygen species (ROS) (PubMed:21969089). Activated by MKK5 in response to abscisic acid (ABA) (PubMed:27913741). Interacts with MEKK1, MKK1 and MKK2. May form a ternary complex with MEKK1 and MKK1 or MKK2. Interacts with NDPK2, AP2C1, MKP1 and PTP1. Interacts with DSPTP1B/MKP2, especially during HR-like responses triggered by fungal elicitors. Interacts with MKK4, MKK5 and MKK6 (PubMed:12506203, PubMed:15225555, PubMed:17630279, PubMed:19513235, PubMed:19789277, PubMed:20626661, PubMed:21057191, PubMed:21575092, PubMed:27913741). Binds to LIP5 (PubMed:25010425). Interacts with VQ4 and IKU1/VQ14 (PubMed:24750137). Interacts with RACK1A, RACK1B and RACK1C (PubMed:25731164). Interacts with PTP1 (PubMed:27029354). Interacts with FLZ9 (Ref.48). Binds to BASL and YDA (PubMed:25843888). Translocated into the nucleus in response to phosphorylation (Probable). Recruited by BASL at the cell cortex in a polarized manner (PubMed:25843888). Mobility in stomatal lineage ground cells (SLGCs) is triggered by BASL, increased in response to hydrogen peroxide H(2)O(2), but repressed by U0126 (PubMed:27746029). Copolarizes with BASL, YDA and MPK3 in stomatal asymmetric cell division (ACD) cells. By Alternaria brassicae pathogen infection. The TXY motif contains the threonine and tyrosine residues whose phosphorylation activates the MAP kinases. Dually phosphorylated on Thr-221 and Tyr-223, which activates the enzyme. Dephosphorylated by DSPTP1B/MKP2. Reduced sensitivity to abscisic acid (ABA) during germination. Insensitivity to ABA in terms of root growth inhibition (e.g. root cell division and elongation) and stomatal response leading to increased water loss under dehydrated conditions (PubMed:27913741). Delayed senescence phenotype. Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. MAP kinase subfamily. +Acts as an alpha-ketoglutarate-dependent dioxygenase catalyzing hydroxylation of glutarate (GA) to L-2-hydroxyglutarate (L2HG). Functions in a L-lysine degradation pathway that proceeds via cadaverine, glutarate and L-2-hydroxyglutarate. 2-oxoglutarate + glutarate + O2 = (S)-2-hydroxyglutarate + CO2 + succinate Binds 1 Fe(2+) ion per subunit. Amino-acid degradation. Homotetramer. Belongs to the glutarate hydroxylase family. +Part of the ABC transporter complex RbsABC involved in ribose import. Responsible for energy coupling to the transport system. ATP + D-ribose(out) + H2O = ADP + D-ribose(in) + H(+) + phosphate The complex is composed of an ATP-binding protein (RbsA), two transmembrane proteins (RbsC) and a solute-binding protein (RbsB). Belongs to the ABC transporter superfamily. Ribose importer (TC 3.A.1.2.1) family. +Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate. ATP + shikimate = 3-phosphoshikimate + ADP + H(+) Binds 1 Mg(2+) ion per subunit. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 5/7. Monomer. Belongs to the shikimate kinase family. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +This b-type cytochrome is tightly associated with the reaction center of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. With its partner (PsbF) binds heme. PSII binds additional chlorophylls, carotenoids and specific lipids. Heterodimer of an alpha subunit and a beta subunit. Cyanobacterial PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins PsbO, PsbU, PsbV and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbE/PsbF family. +Plays a role as a regulator of spermatogenesis. Crucial regulator of the mitotic cell cycle and development. Required for the correct dynein-dynactin perinuclear localization important for nucleus-centrosome coupling that occur upon meiotic progression of primary spermatocytes. Crucial regulator of the mitotic cell cycle and development. Plays a role in sperm motility and fertility. May have a role in the PNG/PLU/GNU pathway (By similarity). Colocalizes with dynein-dynactin on the nuclear surface at the meiotic G2/prophase transition in primary spermatocytes. Nuclear location is required for recruitment of dynein motors to nuclear envelope at G2/M. Phosphorylated. Belongs to the asunder family. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Transfers an acetyl group from acetyl-CoA to L-homoserine, forming acetyl-L-homoserine. acetyl-CoA + L-homoserine = CoA + O-acetyl-L-homoserine Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; O-acetyl-L-homoserine from L-homoserine: step 1/1. Homodimer. Mutant cannot grow on minimal media with no added methionine. Belongs to the AB hydrolase superfamily. MetX family. +Lysis of cellular walls containing beta-1,3-glucans. Implicated in the defense against fungal pathogens (By similarity). Hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the glycosyl hydrolase 64 family. +Belongs to the major facilitator superfamily. YcaD (TC 2.A.1.26) family. +HMWC (high-molecular-weight cytochrome c), ORF2, ORF3, ORF4, ORF5 and ORF6 in the HMC operon form a transmembrane protein complex that allows electron flow from the periplasmic hydrogenase to the cytoplasmic enzymes that catalyze reduction of sulfates. Monomer. Binds 16 heme c groups per subunit. High-spin heme 15 has single axial histidine ligand and the other hemes are low-spin bis-histidinyl coordinated. +In aerobic conditions, required for intracellular iron homeostasis, thus triggering the activity of Fe(2+) prolyl hydroxylase (PHD) enzymes, and leading to HIF1A hydroxylation and subsequent proteasomal degradation. Necessary for endolysosomal acidification and lysosomal degradation (By similarity). May be involved in Golgi homeostasis (By similarity). Accessory component of the multisubunit proton-transporting vacuolar (V)-ATPase protein pump. Partial colocalization with GOLGB1. +Belongs to the RER1 family. +A stretch of 270 kb of the mitochondrial genome is duplicated within the centromere of chromosome 2 resulting in the duplication of the gene. The expression of this duplicated gene (At2g07701) is not demonstrated. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. Casein kinase I subfamily. +Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane. Required to direct preproteins in transit and direct them to the channel protein TIM23, and possibly facilitates transfer of the translocating proteins from the TOM complex to the TIM23 complex (By similarity). Component of the TIM23 complex, at least composed of tim23, tim17, tim50 and tim21. Interacts with preproteins in transit (By similarity). Belongs to the TIM50 family. +Plays an important role in protecting the acceptor side of photosystem II (PSII) against oxidative damage, especially under iron-limiting growth conditions. May also be part of a periplasmic ABC transporter complex involved in iron import. By iron limitation and to a smaller extent by manganese limitation. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the bacterial solute-binding protein 1 family. Association with the cytoplasmic side of the thylakoid membrane proposed in PubMed:9599805 is at odds with the subcellular location of orthologs in Synechocystis PCC 6803 and the presence of a signal peptide in this protein. +Involved in lignin biosynthesis. Catalyzes the final step specific for the production of lignin monomers. Catalyzes the NADPH-dependent reduction of coniferaldehyde, 5-hydroxyconiferaldehyde, sinapaldehyde, 4-coumaraldehyde and caffeyl aldehyde to their respective alcohols. (E)-cinnamyl alcohol + NADP(+) = (E)-cinnamaldehyde + H(+) + NADPH Binds 2 Zn(2+) ions per subunit. Aromatic compound metabolism; phenylpropanoid biosynthesis. Homodimer. Expressed in the differentiation and elongation zones of primary and lateral roots. Expressed in the hypocotyl, cotyledon and leaf veins, hydathodes and trichomes. In stems, expressed in the vascular cambium region. Expressed in the style, anthers, stamen filaments, vascular tissues of sepals and stigmatic regions in flowers, and abscission, style and stigmatic regions of siliques and seed testa. Belongs to the zinc-containing alcohol dehydrogenase family. +Esterase; part of the inp gene cluster that mediates the biosynthesis of fellutamide B, a mycotoxin that acts as a proteasome inhibitor (PubMed:20952652, PubMed:27294372). In the first step of fellutabmide B biosynthesis inpC activates 3-hydroxydodecanoic acid to generate 3-hydroxydodecanoyl-AMP that is then loaded onto the T0 domain of inpB (PubMed:27294372). The 3-hydroxydodecanoyl-S-phosphopantetheinyl-T0 is sequentially extended with L-Asn and L-Gln by the two CAT modules of inpB (PubMed:27294372). The linear lipodipeptide from inpB is then transferred onto inpA for the addition of the third amino acid, L-Leu (PubMed:27294372). Reductive releasing of the lipotripeptide by the TE domain of inpA produces (2S)-fellutamide B (PubMed:27294372). InpF might be involved in the release and transfer of the lipodipeptide from inpB to inpA (PubMed:27294372). The inp cluster-encoded proteasome subunit inpE confers resistance to internally produced fellutamides (PubMed:27294372). The MFS efflux transporter inpD may contribute to fellutamide resistance as well (PubMed:27294372). Secondary metabolite biosynthesis. Greatly diminishes the production of fellutamides (PubMed:27294372). Belongs to the LovG family. +Belongs to the jacalin lectin family. +Catalytic subunit of DNA primase, an RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. The small subunit contains the primase catalytic core and has DNA synthesis activity on its own. Binding to the large subunit stabilizes and modulates the activity, increasing the rate of DNA synthesis while decreasing the length of the DNA fragments, and conferring RNA synthesis capability. The DNA polymerase activity may enable DNA primase to also catalyze primer extension after primer synthesis. May also play a role in DNA repair. Heterodimer of a small subunit (PriS) and a large subunit (PriL). Belongs to the eukaryotic-type primase small subunit family. +Catalyzes the hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA), a reaction involved in phylloquinone (vitamin K1) biosynthesis. 1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA + H(+) Cofactor biosynthesis; phylloquinone biosynthesis. Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 7/7. Belongs to the 4-hydroxybenzoyl-CoA thioesterase family. DHNA-CoA hydrolase subfamily. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Oligomer. The N-terminus is blocked. Belongs to the thioester dehydratase family. FabZ subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +G-protein coupled receptor for 5-hydroxytryptamine (serotonin). Also functions as a receptor for ergot alkaloid derivatives, various anxiolytic and antidepressant drugs and other psychoactive substances. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors, such as adenylate cyclase. Signaling inhibits adenylate cyclase activity. Regulates the release of 5-hydroxytryptamine in the brain, and thereby affects neural activity. May also play a role in regulating the release of other neurotransmitters. May play a role in vasoconstriction. Homodimer. Heterodimer with HTR1B. Detected in brain neocortex and caudate nucleus (at protein level). Belongs to the G-protein coupled receptor 1 family. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Belongs to the TRIM/RBCC family. +Transports S-adenosylmethionine. Belongs to the drug/metabolite transporter (DMT) superfamily. 10 TMS drug/metabolite exporter (DME) (TC 2.A.7.3) family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Involved in the regulation of both adhesion and cell morphology and cancer progression. Functions as an anti-adhesive molecule that maintains an open filtration pathway between neighboring foot processes in the podocyte by charge repulsion. Acts as a pro-adhesive molecule, enhancing the adherence of cells to immobilized ligands, increasing the rate of migration and cell-cell contacts in an integrin-dependent manner. Induces the formation of apical actin-dependent microvilli. Involved in the formation of a preapical plasma membrane subdomain to set up initial epithelial polarization and the apical lumen formation during renal tubulogenesis. Plays a role in cancer development and aggressiveness by inducing cell migration and invasion through its interaction with the actin-binding protein EZR. Affects EZR-dependent signaling events, leading to increased activities of the MAPK and PI3K pathways in cancer cells. Found in a complex with EZR, PODXL and SLC9A3R2. Associates with the actin cytoskeleton through complex formation with EZR and SLC9A3R2. Interacts (via the C-terminal PDZ-binding motif DTHL) with SLC9A3R1 (via the PDZ domains); interaction is not detected in glomerular epithelium cells. Interacts (via the C-terminal PDZ-binding motif DTHL) with SLC9A3R2 (via the PDZ 1 domain); interaction is detected in glomerular epithelium cells. Interacts with EZR (By similarity). Monomer; when associated with the membrane raft. Oligomer; when integrated in the apical membrane. Interacts with SLC9A3R2. Interacts (via the C-terminal PDZ-binding motif DTHL) with SLC9A3R1 (via the PDZ domains); the interaction take place early in the secretory pathway and is necessary for its apical membrane sorting. Forms granular, punctuated pattern, forming patches, preferentially adopting a polar distribution, located on the migrating poles of the cell or forming clusters along the terminal ends of filipodia establishing contact with the endothelial cells. Colocalizes with the submembrane actin of lamellipodia, particularly associated with ruffles. Colocalizes with vinculin at protrusions of cells. Colocalizes with ITGB1. Colocalizes with actin filaments, ezrin and SLC9A3R1 in a punctate pattern at the apical cell surface where microvilli form. Colocalizes with EZR and SLC9A3R2 at the apical cell membrane of glomerular epithelium cells (By similarity). In single attached epithelial cells is restricted to a preapical pole on the free plasma membrane whereas other apical and basolateral proteins are not yet polarized. Colocalizes with SLC9A3R2 at the apical plasma membrane during epithelial polarization. Colocalizes with SLC9A3R1 at the trans-Golgi network (transiently) and at the apical plasma membrane. Its association with the membrane raft is transient. Colocalizes with PARD3, PRKCI, EXOC5, OCLN, RAB11A and RAB8A in apical membrane initiation sites (AMIS) during the generation of apical surface and luminogenesis (By similarity). Expressed in glomerular and tubular epithelial cells and peritubular capillaries of the kidney (at protein level). Expressed in heart, lung, renal cortex and medulla, kidney and muscle. The large highly anionic extracellular domain allows to maintain open filtration pathways between neighboring podocyte foot processes. The cytoplasmic C-terminus PDZ-binding motif (DTHL) is essential for interaction with SLC9A3R1 and for targeting SLC9A3R1 to the apical cell membrane. The extracellular domain is necessary for microvillus formation (By similarity). Both the O-glycan-rich domain of the extracellular domain and the C-terminus PDZ-binding motif (DTHL) in the cytoplasmic tail harbor an apical sorting signal. The cytoplasmic domain is necessary for the apical membrane targeting and renal tubulogenesis. N- and O-linked glycosylated. Sialoglycoprotein. Belongs to the podocalyxin family. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Subunit of mTORC2, which regulates cell growth and survival in response to hormonal signals. mTORC2 is activated by growth factors, but, in contrast to mTORC1, seems to be nutrient-insensitive. mTORC2 seems to function upstream of Rho GTPases to regulate the actin cytoskeleton, probably by activating one or more Rho-type guanine nucleotide exchange factors. mTORC2 promotes the serum-induced formation of stress-fibers or F-actin. mTORC2 plays a critical role in AKT1 'Ser-473' phosphorylation, which may facilitate the phosphorylation of the activation loop of AKT1 on 'Thr-308' by PDK1 which is a prerequisite for full activation. mTORC2 regulates the phosphorylation of SGK1 at 'Ser-422'. mTORC2 also modulates the phosphorylation of PRKCA on 'Ser-657'. Within mTORC2, MAPKAP1 is required for complex formation and mTORC2 kinase activity. MAPKAP1 inhibits MAP3K2 by preventing its dimerization and autophosphorylation. Inhibits HRAS and KRAS signaling. Enhances osmotic stress-induced phosphorylation of ATF2 and ATF2-mediated transcription. Involved in ciliogenesis, regulates cilia length through its interaction with CCDC28B independently of mTORC2 complex. All isoforms except isoform 4 can be incorporated into the mammalian target of rapamycin complex 2 (mTORC2) which contains MTOR, MLST8, PRR5, RICTOR, MAPKAP1 and DEPTOR (PubMed:16962653, PubMed:16919458, PubMed:33378666). Contrary to mTORC1, mTORC2 does not bind to and is not sensitive to FKBP12-rapamycin. Interacts with ATF2, MAP3K2 and MAPK8. Interacts with GTP-bound HRAS and KRAS. Interacts with IFNAR2 and SGK1. Isoform 2 interacts with NBN. Isoform 1 interacts with CCDC28B. Ubiquitously expressed, with highest levels in heart and skeletal muscle. Not involved in a TORC2 complex. Belongs to the SIN1 family. +Plays a role in virus cell tropism, and may be required for efficient virus replication in macrophages. Belongs to the asfivirus MGF 360 family. +Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known. Homodimer. Binds 1 heme group per subunit. +Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) Binds 1 zinc ion per subunit. Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. Belongs to the class-II aminoacyl-tRNA synthetase family. +Required for resistance to DNA-damaging agents. Homodimer. Unlike MJ0577, UspA shows no evidence of ATP binding activity. Belongs to the universal stress protein A family. +Transfers a succinyl group from succinyl-CoA to L-homoserine, forming succinyl-L-homoserine. L-homoserine + succinyl-CoA = CoA + O-succinyl-L-homoserine Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; O-succinyl-L-homoserine from L-homoserine: step 1/1. Homodimer. Belongs to the MetA family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. Binds 1 heme group covalently. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, petD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer (By similarity). Belongs to the cytochrome f family. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 1 subfamily. +Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors. [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H(+) Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 51 family. +RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit. Belongs to the RnpA family. +Involved in rRNA processing. Belongs to the EFG1 family. +Catalyzes the conversion of 5-oxopentanoate (glutarate semialdehyde) to glutarate. Involved in L-lysine degradation. 5-oxopentanoate + H2O + NADP(+) = glutarate + 2 H(+) + NADPH Amino-acid degradation. Belongs to the aldehyde dehydrogenase family. +Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin-protein ligase complex that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C is thought to confer substrate specificity and, in the presence of ubiquitin-conjugating E2 enzymes, it catalyzes the formation of protein-ubiquitin conjugates that are subsequently degraded by the 26S proteasome. Appears to play a role in spore wall formation. The APC/C is composed of at least 13 subunits: apc1, apc2, nuc2, apc4, apc5, cut9, apc8, apc10, apc11, hcn1, apc13, apc14 and apc15. Abnormal spore wall formation (PubMed:12786945). Abnormal spore wall polysaccharide composition during sporulation (PubMed:12786945). Irregular spore wall thickness (PubMed:12786945). +Transports acetate. Belongs to the sodium:solute symporter (SSF) (TC 2.A.21) family. +To K.pneumoniae SorE. +Centriole-enriched microtubule-binding protein involved in centriole biogenesis. In collaboration with CEP295 and POC1B, is required for the centriole-to-centrosome conversion by ensuring the formation of bona fide centriole wall. Functions as a linker component that maintains centrosome cohesion. Associates with CROCC and regulates its stability and localization to the centrosome. Interacts with CROCC. Interacts with POC1B; the interaction is direct and recruits POC1B to centriolar microtubules. Binds to centriolar microtubules. Localizes to the proximal end of mother and daughter centrioles. +Catalyzes the reduction of the double bond of an array of alpha,beta-unsaturated aldehydes and ketones. It also reduces the nitro group of nitroester and nitroaromatic compounds. It could have a role in detoxification processes. A + H(+) + NADPH = AH2 + NADP(+) Homotetramer. Belongs to the NADH:flavin oxidoreductase/NADH oxidase family. NamA subfamily. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Reversibly catalyzes the transfer of phosphate between ATP and various phosphogens (e.g. creatine phosphate). Creatine kinase isoenzymes play a central role in energy transduction in tissues with large, fluctuating energy demands, such as skeletal muscle, heart, brain and spermatozoa. ATP + creatine = ADP + H(+) + N-phosphocreatine Exists as an octamer composed of four MTCK homodimers. Mitochondrial creatine kinase binds cardiolipin. Belongs to the ATP:guanido phosphotransferase family. +Belongs to the bacterial ribosomal protein bL36 family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids (By similarity). Belongs to the DnaA family. +Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetE route): step 1/1. Belongs to the vitamin-B12 independent methionine synthase family. +Cytokine that in its homotrimeric form binds to TNFRSF1A/TNFR1, TNFRSF1B/TNFBR and TNFRSF14/HVEM (By similarity). In its heterotrimeric form with LTB binds to TNFRSF3/LTBR. Lymphotoxin is produced by lymphocytes and is cytotoxic for a wide range of tumor cells in vitro and in vivo. Homotrimer, and heterotrimer of either two LTB and one LTA subunits or (less prevalent) two LTA and one LTB subunits. Interacts with TNFRSF14. The homotrimer is secreted. The heterotrimer is membrane-associated. Belongs to the tumor necrosis factor family. +Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + UDP-N-acetyl-alpha-D-glucosamine = a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + holo-[ACP] Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 1/6. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxA subfamily. +Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell. Belongs to the MinE family. +Extended N-terminus. Extended N-terminus. Extended N-terminus. +Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP). 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP Binds 1 divalent metal cation per subunit. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 4/6. Homotrimer. Belongs to the IspF family. +Polycomb group (PcG) protein. Component of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' and 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. Also recognizes 'Lys-26' trimethylated histone H1 with the effect of inhibiting PRC2 complex methyltransferase activity on nucleosomal histone H3 'Lys-27', whereas H3 'Lys-27' recognition has the opposite effect, enabling the propagation of this repressive mark (By similarity). The PRC2/EED-EZH2 complex may also serve as a recruiting platform for DNA methyltransferases, thereby linking two epigenetic repression systems (By similarity). Genes repressed by the PRC2/EED-EZH2 complex include HOXA7, HOXB6 and HOXC8. Plays a role in X chromosome inactivation (XCI), in which one of the two X chromosomes in female mammals is transcriptionally silenced to equalize X-linked gene dosage with XY males. Required for stable maintenance of XCI in both embryonic and extraembryonic tissues. May prevent transcriptional activation of facultative heterochromatin during differentiation. Required for development of secondary trophoblast giant cells during placental development. May regulate hippocampal synaptic plasticity in the developing brain. Component of the PRC2/EED-EZH2 complex, which includes EED, EZH2, SUZ12, RBBP4 and RBBP7 and possibly AEBP2 (By similarity). The minimum components required for methyltransferase activity of the PRC2/EED-EZH2 complex are EED, EZH2 and SUZ12 (By similarity). Component of the PRC2/EED-EZH1 complex, which includes EED, EZH1, SUZ12, RBBP4 and AEBP2. The PRC2 complex may also interact with DNMT1, DNMT3A, DNMT3B and PHF1 via the EZH2 subunit and with SIRT1 via the SUZ12 subunit (By similarity). Interacts with HDAC, HDAC2, histone H1 and YY1 (By similarity). May interact with ITGA4, ITGAE and ITGB7 (By similarity). Interacts with CDYL (By similarity). Interacts with EZH2. Interacts with KMT2A/MLL1 in adult brain. Interacts with ARNTL/BMAL1. Localizes to the inactive X chromosome in cells of the early embryo and in stem cells of the extraembryonic trophectoderm lineage. Recruitment to the inactive X-chromosome requires XIST. Additional isoforms may be produced by alternative initiation from other non-canonical start codons but their precise positions have not been unambiguously determined. Expressed in brain, heart, kidney, liver, lung, muscle, ovary, spleen and testis. Expressed throughout the brain. Maternally expressed. Expressed from 5.5 dpc, and expression remains high throughout development. Expression decreases during differentiation of embryonic stem cells (ES cells). Expression increases in prostate during prostate tumor development. Induced in embryonic stem cells (ES cells) by STAT3 and POU5F1. The WD repeat domain mediates recognition of trimethylated histone peptides at the consensus sequence Ala-Arg-Lys-Ser. This is achieved through an aromatic cage encircling the methyllysine, and involving Phe-97, Tyr-148 and Tyr-365 (By similarity). Methylated. Binding to histone H1 'Lys-26' promotes mono-, di-, and trimethylation of internal lysines (By similarity). Mice homozygous for a null allele of this protein (Pro-196) exhibit disrupted anterior posterior patterning of the primitive streak during gastrulation and reduced numbers of trophoblast giant cells. Mice homozygous for a hypomorphic allele of this protein (Asn-193) exhibit posterior transformations along the axial skeleton and altered patterns of Hox gene expression. Translation initiates from a non-canonical start codon (GUG). Belongs to the WD repeat ESC family. Was originally thought (PubMed:9234727) to interact with HNRNPK. This apparent interaction may be mediated by the translated product of the 5'-UTR sequence of the 2-hybrid clone. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. +Belongs to the bacterial ribosomal protein bL27 family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Cell wall formation. NADP(+) + UDP-N-acetyl-alpha-D-muramate = H(+) + NADPH + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurB family. +Involved in the phenylpropanoid metabolism by mediating the activation of a number of hydroxycinnamates for the biosynthesis of monolignols and other phenolic secondary metabolites (PubMed:21807887, PubMed:23246835). Catalyzes the formation of CoA esters of cinnamate, 4-coumarate, caffeate and ferulate (PubMed:21807887, PubMed:23246835). Is more efficient with substrates in the following order: ferulate > 4-coumarate > cinnamate > caffeate (PubMed:21807887). Cannot convert sinapate to its corresponding CoA ester (PubMed:21807887, PubMed:23246835). (E)-4-coumarate + ATP + CoA = (E)-4-coumaroyl-CoA + AMP + diphosphate kcat is 0.37 min(-1) with cinnamate as substrate (PubMed:21807887). kcat is 0.49 min(-1) with 4-coumarate as substrate (PubMed:21807887). kcat is 0.52 min(-1) with caffeate as substrate (PubMed:21807887). kcat is 0.41 min(-1) with ferulate as substrate (PubMed:21807887). Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene biosynthesis; 3,4',5-trihydroxystilbene from trans-4-coumarate: step 1/2. Expressed in roots, stems, leaf blades and leaf sheaths. Induced by fungal elicitor and UV irradiation. Down-regulated by wounding and UV irradiation (PubMed:23246835). Both substrate-binding domains (SBD1 and SBD2) are involved in the substrate recognition, and are sufficient to confer the substrate specificity. Belongs to the ATP-dependent AMP-binding enzyme family. +Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. BUB1 subfamily. In contrast to other species, in which it plays an essential role as component of the mitotic checkpoint, bub1 is predicted to be inactive in D.discoideum. Its function is therefore highly unsure. +Belongs to the UPF0306 family. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +Putative nucleotidyltransferase required for several aspects of embryonic development including normal development of the eye (By similarity). It is unclear whether it displays nucleotidyltransferase activity in vivo. Binds single-stranded RNA (ssRNA) (By similarity). Monomer. Homodecamer; composed of 2 back to back homopentamers. The protein may exist as monomer in solution and oiligomerizes upon ligand binding. Belongs to the mab-21 family. +Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. 2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2 The D1/D2 heterodimer binds P680, chlorophylls that are the primary electron donor of PSII, and subsequent electron acceptors. It shares a non-heme iron and each subunit binds pheophytin, quinone, additional chlorophylls, carotenoids and lipids. D1 provides most of the ligands for the Mn4-Ca-O5 cluster of the oxygen-evolving complex (OEC). There is also a Cl(-1) ion associated with D1 and D2, which is required for oxygen evolution. The PSII complex binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Tyr-161 forms a radical intermediate that is referred to as redox-active TyrZ, YZ or Y-Z. C-terminally processed by CTPA; processing is essential to allow assembly of the oxygen-evolving complex and thus photosynthetic growth. 2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water. Herbicides such as atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer. Belongs to the reaction center PufL/M/PsbA/D family. +Early structural protein. Belongs to the asfivirus envelope protein p22 family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Involved in oxygen transport from the lung to the various peripheral tissues. Heterotetramer of two alpha chains and two beta chains. Red blood cells. Belongs to the globin family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Mediates high-affinity intracellular uptake of the rare oligo-element molybdenum. Belongs to the major facilitator superfamily. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +Involved in the biosynthesis of the spirotetramate antibiotics pyrroindomycins. Catalyzes the intramolecular cyclization forming the spiro-conjugate moiety in pyrroindomycins, via an exo-selective [4+2] cycloaddition reaction. 4-[(1R,2R,4aS,5S,8aR)-2-[(2R,3R,5E,7E)-3-ethyl-2-hydroxy-5,7-dimethylnona-5,7-dien-1-yl]-5-hydroxy-1-methyl-1,2,4a,5,6,7,8,8a-octahydronaphthalene-1-carbonyl]-2-methylidene-5-oxo-2,5-dihydro-1H-pyrrol-3-olate = (1S,3R,6R,8R,9R,11R,14S,15S,19R,20R)-8-ethyl-9,15-dihydroxy-3,4,6,20-tetramethyl-21,23-dioxo-24-azapentacyclo[20.2.1.0(1,6).0(11,20).0(14,19)]pentacosa-4,12,22(25)-trien-25-olate kcat is 342.6 min(-1). Antibiotic biosynthesis. Homodimer. The N-terminal 10-AA residues are absolutely required for enzymatic activity. Cells lacking this gene lose the ability to produce pyrroindomycins. Reaction occurs via a unique trapping mechanism whereby the lid-like action of the N-terminal tail imposes conformational constraints on the beta-barrel catalytic core, which enhances the proximity and polarization effects of reactive groups (1,3-diene and alkene) to drive cyclization in a regio- and stereo-specific manner. Truncated N-terminus. +RNA-directed RNA polymerase that is involved in transcription and genome replication. Following infection, it catalyzes the synthesis of fully conservative plus strands. After core assembly, which consists in recruitment of one capped plus-strand for each genomic segments and polymerase complexes, the polymerase switches mode and catalyzes the synthesis of complementary minus-strands (By similarity). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Belongs to the reoviridae RNA-directed RNA polymerase family. +Uptake of L-rhamnose across the cytoplasmic membrane with the concomitant transport of protons into the cell (symport system). H(+)(in) + L-rhamnopyranose(in) = H(+)(out) + L-rhamnopyranose(out) Belongs to the L-rhamnose transporter (TC 2.A.7.6) family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. Probable anchoring protein which tethers the nucleus to the cytoskeleton by binding PLEC which can associate with the intermediate filament system. Plays a role in the regulation of aortic epithelial cell morphology, and is required for flow-induced centrosome polarization and directional migration in aortic endothelial cells (By similarity). Core component of LINC complexes which are composed of inner nuclear membrane SUN domain-containing proteins coupled to outer nuclear membrane KASH domain-containing nesprins. SUN and KASH domain-containing proteins seem to bind each other promiscuously; however, differentially expression of LINC complex constituents can give rise to specific assemblies. Interacts with SUN1 and SUN2; probably forming respective LINC complexes. Interacts with PLEC (via actin-binding domain). Interacts with DST. Interacts with SYNE1. Interacts (via KASH domain) with TOR1A (ATP-bound); the interaction is required for SYNE3 nuclear envelope localization. Ubiquitous. The KASH domain is involved in the binding to SUN1 and SUN2 through recognition of their SUN domains. The disulfid bond with SUN1 or SUN2 is required for stability of the respective LINC complex under tensile forces. Belongs to the nesprin family. +Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins. Binds 1 zinc ion per subunit. Homohexamer. Not essential for growth. A number of proteins can be seen to be more stable in the disruption mutants, suggesting some of them may be substrates for the protease. In the central section; belongs to the AAA ATPase family. In the C-terminal section; belongs to the peptidase M41 family. Extended N-terminus. +NDH-1 shuttles electrons from an unknown electron donor, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) Binds 1 [4Fe-4S] cluster. NDH-1 can be composed of about 15 different subunits; different subcomplexes with different compositions have been identified which probably have different functions. Belongs to the complex I 20 kDa subunit family. +Belongs to the Speedy/Ringo family. +Plays a critical role in virus induced T-cell transformation. Binds to T-cell-specific tyrosine kinase LCK SH2 and SH3 domains, thereby activating its kinase activity. Once phosphorylated by host LCK, forms a complex with at least STAT 1 and 3, resulting on the phosphorylation of STAT3 and presumably STAT1, and their migration into the nucleus to induce transcription of target genes. Stimulates host ILF3/NF-AT-90 activity. Association with host NXF1/TAP transduces the signal up-regulating surface expression of adhesion molecules as well as activating NF-kappa-B activity. Acts synergistically with StpC to stimulate NF-kappa-B activity and interleukin-2 gene expression. Activation of NF-kappa-B protects lymphocytes from apoptosis, thereby facilitating viral induced cell transformation. May cause down-regulation of host LCK and cell apoptosis when stably overexpressed ex vivo. Interaction with WDR48 induce degradation of T-cell receptor in a lysosome-dependent fashion, when both proteins are overexpressed. The biological effect of this interaction remains controversial since no T-cell receptor degradation is observed in infected cells (By similarity). Binds host LCK, human WDR48 and human NXF1/TAP. Forms a complex with activated LCK and STAT1 and STAT3 (By similarity). The SH3B/LBD1 (SH3-binding) region binds LCK SH3 domain and CSKH (C-terminal Src-related kinase homology) region binds the kinase domains of LCK. Both motif are required to activate LCK (By similarity). Phosphorylation on Tyr-123 acts as a docking site for the recruitment of STATs 1 and 3. Used in cell biology research to transform T-cell lymphocytes. Saimiriine herpesvirus 2 transforms T-cell lymphocytes, including human, to continuous growth in vitro. 2 viral proteins, Tip and StpC, are essential for this function. In its host, LCK protein is inactivated, preventing T-cell transformation activity. +Binds 2 Zn(2+) ions per subunit. Belongs to the peptidase M28 family. M28B subfamily. +Participates in both the initiation and recycling phases of transcription. In the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling. RNAP is composed of a core of 2 alpha, a beta and a beta' subunits. The core is associated with a delta subunit and one of several sigma factors. Belongs to the RpoE family. +Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. a plastoquinol + 2 H(+)(in) + 2 oxidized [plastocyanin] = a plastoquinone + 4 H(+)(out) + 2 reduced [plastocyanin] Binds 1 [2Fe-2S] cluster per subunit. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. The transmembrane helix obliquely spans the membrane in one monomer, and its extrinsic C-terminal domain is part of the other monomer. The Rieske iron-sulfur protein is a high potential 2Fe-2S protein. Belongs to the Rieske iron-sulfur protein family. +Belongs to the LOB domain-containing protein family. +Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL. ATP + H2O + L-glutamine + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide = 2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ADP + H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole from N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide: step 1/2. Part of the FGAM synthase complex composed of 1 PurL, 1 PurQ and 2 PurS subunits. +Belongs to the FTH family. +Possesses calcium-dependent ppGpp (guanosine 3'-diphosphate 5'-diphosphate) synthetase activity in vitro and is able to functionally complement E.coli relA mutants. May be involved in a rapid plant ppGpp-mediated response to pathogens and other stresses. ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate Activated by calcium. Expressed in shoots. The calcium-binding sites of the 2 EF-hand domains are required for enzyme activity. Belongs to the RelA/SpoT family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the 50S ribosomal subunit. Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Forms a heptameric L10(L12)2(L12)2(L12)2 complex, where L10 forms an elongated spine to which the L12 dimers bind in a sequential fashion. Belongs to the universal ribosomal protein uL10 family. +Catalyzes the transfer of a formyl group from 10-formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and tetrahydrofolate. (6S)-10-formyltetrahydrofolate + N(1)-(5-phospho-beta-D-ribosyl)glycinamide = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide Purine metabolism; IMP biosynthesis via de novo pathway; N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (10-formyl THF route): step 1/1. Belongs to the GART family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Snake prothrombin activator that attacks the hemostatic system of prey. This non-catalytic subunit is functionally similar to blood coagulation factor V (PubMed:12362232, PubMed:23869089). It serves as a critical cofactor for the prothrombinase activity of the catalytic subunit, which is similar to the blood coagulation factor X (PubMed:12362232, PubMed:23869089). The complex converts prothrombin to thrombin by sequential cleavage at two positions, Arg-320 followed by Arg-271 (PubMed:23869089). Cleavage at Arg-320 produces an active intermediate known as meizothrombin (PubMed:23869089). Meizothrombin is the 'second' substrate for prothrombinase, and it docks in an altered manner to present the second cleavage site (271) (PubMed:23869089). Cleavage at Arg-271 releases active thrombin from its pro-fragment (PubMed:23869089). This order of events is reversed if the protease component of prothrombinase is used on its own, suggesting that the 271 site is inherently more accessible to proteolysis (PubMed:23869089). The complex converts prothrombin to thrombin in presence but also in the absence of membrane (PubMed:23869089). Heterodimer of a light and a heavy chains; non-disulfide-linked. The interaction between the two chains is calcium-dependent (By similarity). Found in its active form associated with pseutarin-C catalytic subunit (AC Q56VR3). Expressed by the venom gland. In physiological conditions, blood coagulation factor V and factor Va are inactivated by activated protein C (APC) through proteolytic degradation of the heavy chain. However, pseutarin-C non-catalytic subunit (factor V-like protein) retains its full activity even at high concentration of APC. This has two explanations: this protein has only one of the three cleavage sites present in factor V that are targeted by the APC for inactivation, and the binding with the catalytic subunit protect the cleavage site from inactivation. Is under preclinical trial by the Australian biopharmaceutical company QRxPharma Ltd, its subsidiary Venomics Pty Ltd (VPL) and the University of Queensland (UQ) under the name CoVase (V0801). Tested as a procoagulant cofactor that may have application as a systemic anti-bleeding agent in the treatment of internal bleeding and non-compressible hemorrhage. In contrast to blood coagulation factors that circulate as inactive zymogen in plasma, venom prothrombin activators are always found in the active form in the venom. Hence, catalytic and non-catalytic subunits are found naturally in venom as stable complexes. Belongs to the multicopper oxidase family. +Belongs to the UPF0397 family. +Plays an important role in amino acid transport by acting as binding partner of amino acid transporters SLC6A18 and SLC6A19, regulating their trafficking on the cell surface and their activity (By similarity). May also play a role in trafficking of amino acid transporters SLC3A1 and SLC7A9 to the renal cortical cell membrane (By similarity). Regulator of SNARE complex function (By similarity). Stimulator of beta cell replication (By similarity). Monomer. Homodimer; dimerization prevents CLTRN cleavage by BACE2 (By similarity). Interacts with SLC6A18; this interaction regulates the trafficking of SLC6A18 to the cell membrane and its amino acid transporter activity. Interacts with SLC6A19; this interaction regulates the trafficking of SLC6A19 to the cell membrane and its amino acid transporter activity (By similarity). Interacts with SNAPIN (By similarity). Localizes to the brush border membranes of cells in the proximal tubules of kidney. Colocalized with SLC6A19 in the early proximal S1 tubule. The cleavage site containing the double Phe-Phe motif acts as negative regulator of shedding by BACE2. Glycosylated. Glycosylation is required for plasma membrane localization and for its cleavage by BACE2. Proteolytically processed in pancreatic beta cells by BACE2 leading to the generation and extracellular release of soluble CLTRN, and a corresponding cell-associated C-terminal fragment which is later cleaved by gamma-secretase. This shedding process inactivates CLTRN (By similarity). Three cleavage sites have been identified for BACE2, two clustered sites after Phe-116 and Leu-118 and a more membrane proximal site at Phe-125; the preferred BACE2 cleavage site seems to be between Phe-125 and Leu-126, Phe-116 and Leu-118 act as alternative sites (By similarity). Belongs to the CLTRN family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Some bacteria have evolved a zinc-coordinating structure that stabilizes the LID domain. Belongs to the adenylate kinase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Involved in the synthesis of diacylglycerol galactolipids that are specifically found in thylakoid membranes. Specific for alpha-glycosidic linkages. a 1,2-diacyl-3-O-(beta-D-galactosyl)-sn-glycerol + UDP-alpha-D-galactose = 1,2-diacyl-3-O-[alpha-D-galactosyl-(1->6)-beta-D-galactosyl]-sn-glycerol + H(+) + UDP High expression in nodules infected cells, but low in nodule inner cortex and root central cylinder. Belongs to the glycosyltransferase group 1 family. Glycosyltransferase 4 subfamily. +Involved in the degradation of certain denaturated proteins, including DnaA, during heat shock stress. Belongs to the HspQ family. +Removes 5-oxoproline from various penultimate amino acid residues except L-proline. Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro. Homotetramer. Belongs to the peptidase C15 family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetE route): step 1/1. Belongs to the vitamin-B12 independent methionine synthase family. +Actins are highly conserved proteins that are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells. Multiple isoforms are involved in various cellular functions such as cytoskeleton structure, cell mobility, chromosome movement and muscle contraction. Oxidation of Met-45 to form methionine sulfoxide promotes actin filament depolymerization. Methionine sulfoxide is produced stereospecifically, but it is not known whether the (S)-S-oxide or the (R)-S-oxide is produced (By similarity). There are at least 4 actin isoforms expressed during artemia development. Belongs to the actin family. +a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) Belongs to the complex I subunit 4 family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Belongs to the universal ribosomal protein uS4 family. +Catalyzes the formation of sulfite from adenosine 5'-phosphosulfate (APS) using thioredoxin as an electron donor. [thioredoxin]-disulfide + AMP + 2 H(+) + sulfite = [thioredoxin]-dithiol + adenosine 5'-phosphosulfate Binds 1 [4Fe-4S] cluster per subunit. Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate. Belongs to the PAPS reductase family. CysH subfamily. +Belongs to the bile acid:sodium symporter (BASS) (TC 2.A.28) family. +Binds specifically to H3K4me3 regions of target genes (e.g. WUS and WOX5) promoters to repress their transcription via chromatin remodeling. Required for the shoot apical meristem (SAM) organization and maintenance, by confining WUS expression to the organizing center, and for the quiescent center (QC) development in the root apical meristem (RAM), by repressing WOX5 expression in the root proximal meristem (PubMed:18591352, PubMed:25631790). Plays a role in DNA repair and in cell-cycle control. Required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR) (PubMed:16957774). Component of a DNA-protein complex on WUS and WOX5 promoters (PubMed:25631790, PubMed:18591352). Interacts with SYD (PubMed:18591352). Forms heterodimer with BRCA1 (PubMed:16957774). Additional isoforms seem to exist. Expressed in the shoot apical meristem (SAM), roots, flowers, embryos and seedlings (PubMed:18591352). Mostly expressed in flowers and siliques, and, to a lower extent, in roots, rosette leaves, inflorescence and young cauline leaves (PubMed:16957774). Expressed specifically in the apical domains of the shoot apical meristem (SAM), inflorescences, ovules, anthers and embryos. In young seedlings, localized mainly in the outermost three to four cell layers of the main shoot apex and in developing leaf primordia and young leaves. Also present in the meristem zone of primary roots and in the initiation site of lateral roots. Up-regulated by the transcription factor ERF114. Enhanced sensitivity to genotoxic stresses (e.g. bleomycin and mitomycin C (MMC)) due to reduced intrachromosomal homologous recombination (HR) (PubMed:16957774). Meristem defects associated with ectopic WUSCHEL expression at high levels (e.g. 238 fold higher than controls) mainly in the outermost cell layers instead of the organizing center (PubMed:18591352). Abnormal quiescent center (QC) in the root apical meristem (RAM) and defects in cell differentiation leading to short roots and loss of gravitropic response, probably due to defect in columella cell differentiation. Ectopic expression of WOX5 in RAM cells that normally express ROW1 (PubMed:25631790). +Utilization of purines as secondary nitrogen sources, when primary sources are limiting. allantoate + H2O = (S)-ureidoglycolate + urea Nitrogen metabolism; (S)-allantoin degradation; (S)-ureidoglycolate from allantoate (aminidohydrolase route): step 1/1. Repressed by nitrogen. Belongs to the allantoicase family. +Belongs to the universal ribosomal protein uL29 family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Alpha-conotoxins bind to the nicotinic acetylcholine receptors (nAChR) and inhibit them. A synthetic amidated version of this toxin potently and preferentially antagonizes neuronal rat alpha-3-beta-2 (IC(50)=55.7 nM) and alpha-6/alpha-3-beta-4 (IC(50)=90.69 nM) nAChRs. Expressed by the venom duct. The cysteine framework is I (CC-C-C). Alpha4/7 pattern. Shows no or weak inhibitory activity on a range of nAChRs subtypes, including human and rat alpha-9-alpha-10, mouse alpha-1-beta-1-delta-epsilon, rat alpha-7, rat alpha-6/alpha-3-beta-2-beta-3, rat alpha-3-beta-4, rat alpha-4-beta-2, and rat alpha-9-alpha-10. Belongs to the conotoxin A superfamily. +Probable transcription regulator that functions in the development of the carpel margin meristem similarly to SEUSS (SEU). In association with SEU, supports organ development from meristematic regions by facilitating auxin response and thus organ initiation, and by sustaining meristematic potential through the maintenance of PHABULOSA expression (PubMed:20007451). DNA-binding adapter subunit of the SEU-SLK1 transcriptional corepressor of abiotic stress (e.g. salt and osmotic stress) response genes (PubMed:24564815). Forms corepressor complexes with LUH; LUH is the transcription repressor subunit and SLK1 the specific DNA-binding adapters. Expressed in young flower meristems, ovules and the carpel margin meristem. No visible phenotype under normal growth conditions, but the double mutants seu and slk1 are short in stature, sterile and display strong disruptions of floral development and high frequency of female gametophyte disruption (PubMed:20007451). Enhanced tolerance to salt and osmotic stress conditions (PubMed:24564815). Belongs to the adn1/SEU family. +Expressed by the venom gland. +May act as a scaffolding protein within caveolar membranes. Forms a stable heterooligomeric complex with CAV2 that targets to lipid rafts and drives caveolae formation. Mediates the recruitment of CAVIN proteins (CAVIN1/2/3/4) to the caveolae (By similarity). Interacts directly with G-protein alpha subunits and can functionally regulate their activity (By similarity). Involved in the costimulatory signal essential for T-cell receptor (TCR)-mediated T-cell activation. Its binding to DPP4 induces T-cell proliferation and NF-kappa-B activation in a T-cell receptor/CD3-dependent manner (By similarity). Recruits CTNNB1 to caveolar membranes and may regulate CTNNB1-mediated signaling through the Wnt pathway (By similarity). Negatively regulates TGFB1-mediated activation of SMAD2/3 by mediating the internalization of TGFBR1 from membrane rafts leading to its subsequent degradation (By similarity). Homooligomer. Interacts (via the N-terminus) with DPP4; the interaction is direct. Forms a stable heterooligomeric complex with CAV2 that targets to lipid rafts and drives caveolae formation. Interacts with PACSIN2; this interaction induces membrane tubulation (By similarity). Interacts with BMX, BTK, CTNNB1, CDH1, GLIPR2, JUP, NOSTRIN, SNAP25 and STX1A. Interacts with SLC7A9. Interacts with TGFBR1. Interacts with CAVIN3 (via leucine-zipper domain) in a cholesterol-sensitive manner. Interacts with CAVIN1. Interacts with EHD2 in a cholesterol-dependent manner. Forms a ternary complex with UBXN6 and VCP; mediates CAV1 targeting to lysosomes for degradation. Interacts with ABCG1; this interaction regulates ABCG1-mediated cholesterol efflux (By similarity). Interacts with NEU3; this interaction enhances NEU3 sialidase activity within caveola. Interacts (via C-terminus) with SPRY1, SPRY2 (via C-terminus), SPRY3, and SPRY4 (By similarity). Colocalized with DPP4 in membrane rafts. Potential hairpin-like structure in the membrane. Membrane protein of caveolae (By similarity). Phosphorylated at Tyr-14 by ABL1 in response to oxidative stress. Ubiquitinated. Undergo monoubiquitination and multi- and/or polyubiquitination. Monoubiquitination of N-terminal lysines promotes integration in a ternary complex with UBXN6 and VCP which promotes oligomeric CAV1 targeting to lysosomes for degradation. Belongs to the caveolin family. +H(+)-stimulated, divalent metal cation uptake system. Belongs to the NRAMP family. Truncated N-terminus. Truncated N-terminus. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homotetramer; dimer of dimers. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiC family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Cytochrome b subunit of the cytochrome bc1 complex, an essential component of the respiratory electron transport chain required for ATP synthesis. The bc1 complex catalyzes the oxidation of ubiquinol and the reduction of cytochrome c in the respiratory chain. The bc1 complex operates through a Q-cycle mechanism that couples electron transfer to generation of the proton gradient that drives ATP synthesis. The cytochrome b subunit contains two ubiquinol reactive sites: the oxidation (QP) site and the reduction (QN) site. a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)-[cytochrome c](out) + 2 H(+)(out) Binds 2 heme groups non-covalently per subunit. The cytochrome bc1 complex is composed of a cytochrome b (QcrB), the Rieske iron-sulfur protein (QcrA) and a diheme cytochrome c (QcrC) subunit. Belongs to the cytochrome b family. +Required for anaerobic carnitine reduction. May bring reductant to CaiA. Amine and polyamine metabolism; carnitine metabolism. Heterodimer of FixA and FixB. Belongs to the ETF beta-subunit/FixA family. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +glucuronate acceptor + UDP-alpha-D-glucuronate = acceptor beta-D-glucuronoside + H(+) + UDP Belongs to the UDP-glycosyltransferase family. +E2-like enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy and nucleophagy. Acts as an E2-like enzyme that catalyzes the conjugation of ATG12 to ATG5. ATG12 conjugation to ATG5 is required for proper localization of ATG8 to the preautophagosomal structure (PAS). Likely serves as an ATG5-recognition molecule. Forms homooligomers. Interacts with ATG7 and ATG12. Belongs to the ATG10 family. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Cell wall formation. ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) + phosphate Binds 2 magnesium or manganese ions per subunit. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the D-alanine--D-alanine ligase family. +Synthesizes alpha-1,4-glucan chains using ADP-glucose. [(1->4)-alpha-D-glucosyl](n) + ADP-alpha-D-glucose = [(1->4)-alpha-D-glucosyl](n+1) + ADP + H(+) Glycan biosynthesis; glycogen biosynthesis. Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily. +Promotes, when overexpressed, the influx of extracellular Ca2+, leading to membrane permeability and host cell necrosis. Belongs to the chordopoxvirinae A38 protein family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +3'-to-5' exoribonuclease specific for small oligoribonucleotides. Belongs to the oligoribonuclease family. +Expressed in the early phase of the viral replicative cycle. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. D2 is needed for assembly of a stable PSII complex. 2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2 The D1/D2 heterodimer binds P680, chlorophylls that are the primary electron donor of PSII, and subsequent electron acceptors. It shares a non-heme iron and each subunit binds pheophytin, quinone, additional chlorophylls, carotenoids and lipids. There is also a Cl(-1) ion associated with D1 and D2, which is required for oxygen evolution. The PSII complex binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. 2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water. Belongs to the reaction center PufL/M/PsbA/D family. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +In presence of calcium ions, it binds to surfactant phospholipids and contributes to lower the surface tension at the air-liquid interface in the alveoli of the mammalian lung and is essential for normal respiration. Enhances the expression of MYO18A/SP-R210 on alveolar macrophages. Oligomeric complex of 6 set of homotrimers. Pulmonary surfactant consists of 90% lipid and 10% protein. There are 4 surfactant-associated proteins: 2 collagenous, carbohydrate-binding glycoproteins (SP-A and SP-D) and 2 small hydrophobic proteins (SP-B and SP-C). Belongs to the SFTPA family. +Preferentially hydrolyzes pNP-GlcNAc, hydrolyzes pNP-GalNAc to a lesser extent. Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. Activity is decreased by HgCl(2) and maltose. Activity is stimulated by Na(2)SeO(4), BaCl(2), MgCl(2), chondroitin 6-sulfate and phenylmethylsulfonyl fluoride. Optimum pH is 5.0. Active over a broad range of pH values. Has maximum activity at 45 to 60 degrees Celsius. Inactive at temperatures of 70 degrees Celsius and above. Belongs to the glycosyl hydrolase 18 family. Chitinase class II subfamily. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. Belongs to the radical SAM superfamily. Lipoyl synthase family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +Metallothioneins have a high content of cysteine residues that bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids. Monomer. Expressed in reticulocytes. Class I metallothioneins contain 2 metal-binding domains: four divalent ions are chelated within cluster A of the alpha domain and are coordinated via cysteinyl thiolate bridges to 11 cysteine ligands. Cluster B, the corresponding region within the beta domain, can ligate three divalent ions to 9 cysteines. Belongs to the metallothionein superfamily. Type 1 family. +Seems to be a coreceptor in inhibin signaling, but seems not to be a high-affinity inhibin receptor. Antagonizes activin A signaling in the presence or absence of inhibin B. Necessary to mediate a specific antagonistic effect of inhibin B on activin-stimulated transcription (By similarity). Interacts with INHA; the interaction is not confirmed by standard receptor binding assays (By similarity). Interacts with ACVR1B; the interaction appears to be ligand-dependent as it is diminished by inhibin B and activin A. Interacts with ACVR2A, ACVR2B, ACVRL1 and BMPR1B (By similarity). Interacts with HECTD1 (By similarity). Expressed at embryonic day (E) 12.5 in embryo. Mice are viable and fertile and show no alterations in FSH synthesis or secretion or in ovarian and testicular function. According to PubMed:23143598 male mice show diminished pituitary and serum thyroid-stimulating hormone (TSH) concentrations, reduced pituitary thyrotropin-releasing hormone (TRH) receptor expression, decreased triiodothyronine concentrations and increased body mass. Produced by alternative promoter usage. Produced by alternative splicing of isoform 1. Produced by alternative splicing of isoform 1. Produced by alternative splicing of isoform 1. Produced by alternative promoter usage. It is uncertain whether Met-1 or Met-2 is the initiator. Extended N-terminus. +Serine/threonine-protein acetyltransferase translocated into infected cells, which inhibits the host immune response and induces cell death by mediating acetylation of target proteins (PubMed:9535085, PubMed:22520462). Inhibits the MAPK and NF-kappa-B signaling pathways by acetylating protein-kinases such as MAP2K1, MAP2K6, MAP3K7/TAK1 and I-kappa-B kinase (CHUK/IKKA and IKBKB) on serine and threonine residues critical for their activation by phosphorylation, thereby preventing protein-kinase activation (By similarity). Promotes pyroptosis, a programmed cell death, in host cells by mediating acetylation of MAP3K7/TAK1: MAP3K7/TAK1 inactivation triggers activation of caspase-8 (CASP8), followed by CASP8-dependent cleavage of gasdermin-D (GSDMD) and induction of pyroptosis (By similarity). Also able to induce intestinal barrier dysfunction by acetylating and inhibiting host protein-kinases RIPK2/RICK and MAP3K7/TAK1, thereby promoting cell death (PubMed:22520462). acetyl-CoA + L-threonyl-[protein] = CoA + O-acetyl-L-threonyl-[protein] acetyl-CoA + L-seryl-[protein] = CoA + O-acetyl-L-seryl-[protein] 1D-myo-inositol hexakisphosphate activates protein-acetyltransferase activity via an allosteric mechanism: 1D-myo-inositol hexakisphosphate-binding induces a conformational rearrangement that stimulates the interaction with acetyl-CoA. Secreted via type III secretion system (TTSS). At 37 degrees Celsius in the absence of calcium. Belongs to the acetyltransferase YopJ family. +Involved in the biosynthesis of ADP-glucose, a building block required for the elongation reactions to produce glycogen. Catalyzes the reaction between ATP and alpha-D-glucose 1-phosphate (G1P) to produce pyrophosphate and ADP-Glc. alpha-D-glucose 1-phosphate + ATP + H(+) = ADP-alpha-D-glucose + diphosphate Glycan biosynthesis; glycogen biosynthesis. Homotetramer. Belongs to the bacterial/plant glucose-1-phosphate adenylyltransferase family. +Homodimer and heterodimers. Belongs to the Casparian strip membrane proteins (CASP) family. +Extracellular aminopeptidase that allows assimilation of proteinaceous substrates. Binds 2 Zn(2+) ions per subunit. Monomer. Belongs to the peptidase M28 family. M28E subfamily. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate. Plays a role in recovery after DNA ADP-ribosylation. Forms a heterotetramer with UvrB during the search for lesions. Significantly reduced survival of cells expressing DNA ADP-ribosyl transferase (darT) mutant G49D. Belongs to the ABC transporter superfamily. UvrA family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +Plays a role in endosomal protein trafficking and in targeting proteins for lysosomal degradation. May also contribute to the regulation of gene expression in the nucleus. Binds DNA (in vitro) and may play a synergistic role in the nucleus in regulating the expression of numerous cytokines. Associated with membranes of lysosomes, early and late endosomes. Can translocate from the cytoplasm into the nucleus (By similarity). Detected at Schmidt-Lanterman incisures and in nodal regions of myelinating Schwann cells (By similarity). The LITAF domain is stabilized by a bound zinc ion. The LITAF domain contains an amphipathic helix that mediates interaction with lipid membranes. Belongs to the CDIP1/LITAF family. +FAD-linked oxidoreductase; part of the gene cluster that mediates the biosynthesis of azaphilones, a class of fungal metabolites characterized by a highly oxygenated pyrano-quinone bicyclic core and exhibiting a broad range of bioactivities (PubMed:22921072). In the first step, the non-reducing polyketide synthase azaA forms the hexaketide precursor from successive condensations of five malonyl-CoA units, presumably with a simple acetyl-CoA starter unit (PubMed:22921072). The reactive polyketide chain then undergoes a PT-mediated C2-C7 cyclization to afford the aromatic ring and is eventually released as an aldehyde through the R-domain (PubMed:22921072). The putative ketoreductase azaE is proposed to catalyze the reduction of the terminal ketone resulting in the early culture product FK17-P2a (PubMed:22921072). The monooxygenase azaH was demonstrated to be the only enzyme required to convert FK17-P2a to azanigerone E (PubMed:22921072). AzaH first hydroxylates the benzaldehyde intermediate FK17-P2a at C4, which triggers the formation of the pyran-ring to afford azanigerone E (PubMed:22921072). In parallel, the 2,4-dimethylhexanoyl chain is synthesized by the HR-PKS azaB and is proposed to be transferred to the C4-hydroxyl of azanigerone E by the acyltransferase azaD directly from the ACP domain of azaB (PubMed:22921072). Alternatively, the 2,4-dimethyl-hexanoyl chain may be offloaded from the HR-PKS as a carboxylic acid and converted to an acyl-CoA by azaF (PubMed:22921072). The resulting acyl-CoA molecule could then be taken up as a substrate by AzaD to form azanigerone B (PubMed:22921072). To yield the carboxylic acid substituent in azanigerone A, the hydroxypropyl side chain of azanigerone B would need to undergo a C-C oxidative cleavage catalyzed by cytochrome P450 AzaI (PubMed:22921072). AzaI is proposed to act on a vicinal diol that leads to a C-C bond scission either through an alkoxyradical intermediate or a peroxy complex (PubMed:22921072). In the biosynthesis of azanigerone A, azanigerone B first undergoes hydroxylation at C10, possibly catalyzed by one of the two FAD-dependent monooxygenases encoded in the cluster, azaG or azaL, resulting in the vicinal diol azanigerone C (PubMed:22921072). Oxidative cleavage of azanigerone C by azaI would yield the corresponding aldehyde derivative of azanigerone A (PubMed:22921072). Finally, the dehydrogenase azaJ is proposed to convert the aldehyde functional group into the carboxylic acid, completing the conversion from azanigerone B to azanigerone A (PubMed:22921072). Alternatively, the oxidation of aldehyde to carboxylic acid may be catalyzed by the same P450 enzyme azaI via consecutive oxidation or by endogenous alcohol dehydrogenase (PubMed:22921072). Secondary metabolite biosynthesis. Expression is under the control of the azaphilone cluster-specific transcription factor azaR (PubMed:22921072). Belongs to the oxygen-dependent FAD-linked oxidoreductase family. +One of the components of the core complex of photosystem II (PSII), required for its stability and/or assembly. May regulate electron transport between the quinone binding sites of the reaction center (PubMed:7626631, Ref.6). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. Cyanobacterial PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins PsbO, PsbU, PsbV and a large number of cofactors. It forms dimeric complexes. A monocistronic transcript that is strongly expressed. Phosphorylated in vitro in the presence or absence of light; phosphorylation is inhibited by oxidizing conditions, DCMU and zinc ions. Reduced growth under photoautotrophic conditions and increased photosensitivity; approximately normal amounts of PSII accumulate but electron flow from QA to QB is impaired (Ref.6). Increased photodamage to D1 but it is degraded slower (PubMed:7626631). Belongs to the PsbH family. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. Truncated N-terminus. +Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. NUP120 is involved in nuclear poly(A)+ RNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organization. Component of the nuclear pore complex (NPC). NPC constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. Due to its 8-fold rotational symmetry, all subunits are present with 8 copies or multiples thereof. NUP120 is part of the heptameric 0.5 MDa autoassembling NUP84 NPC subcomplex (NUP84, NUP85, NUP120, NUP133, NUP145C, SEC13 and SEH1). Symmetric distribution. +DEAD-box RNA helicase involved in RNA degradation. Has RNA-dependent ATPase activity and unwinds double-stranded RNA. ATP + H2O = ADP + H(+) + phosphate Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Belongs to the DEAD box helicase family. RhlB subfamily. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Protein modification; protein ubiquitination. The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module in different E3 ubiquitin ligase complexes. Belongs to the small GTPase superfamily. Rab family. +Belongs to the SfsA family. +Belongs to the TACO1 family. YeeN subfamily. +Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate. (S)-dihydroorotate + H2O = H(+) + N-carbamoyl-L-aspartate Binds 2 Zn(2+) ions per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 3/3. Belongs to the metallo-dependent hydrolases superfamily. DHOase family. Class I DHOase subfamily. +Belongs to the ABC transporter superfamily. ABCI family. +Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. [sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Monomer. Belongs to the methylthiotransferase family. MiaB subfamily. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +H(+) + NADP(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADPH + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Homodimer. Belongs to the ferredoxin--NADP reductase type 2 family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +Component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins. Belongs to the bacterial ribosomal protein bL36 family. +Transforms N(2)-succinylglutamate into succinate and glutamate. H2O + N-succinyl-L-glutamate = L-glutamate + succinate Binds 1 zinc ion per subunit. Amino-acid degradation; L-arginine degradation via AST pathway; L-glutamate and succinate from L-arginine: step 5/5. Belongs to the AspA/AstE family. Succinylglutamate desuccinylase subfamily. +Component of the coenzyme Q biosynthetic pathway. May play a role in organizing a multi-subunit COQ enzyme complex required for coenzyme Q biosynthesis. Required for steady-state levels of other COQ polypeptides. Cofactor biosynthesis; ubiquinone biosynthesis. Component of a multi-subunit COQ enzyme complex, composed of at least coq3, coq4, coq5, coq6, coq7 and coq9. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the COQ4 family. +Involved in retinal laminar formation. Expressed in the retinal ganglion cell layer. Expression starts at stage 32. Belongs to the FAM3 family. +Plays a role in cell-cell adhesion and neuron guidance via its interactions with FLRT2 and FLRT3 that are expressed at the surface of adjacent cells (PubMed:22405201, PubMed:25728924, PubMed:26235031). Plays a role in the development of glutamatergic synapses in the cortex (PubMed:22405201, PubMed:24739570). Important in determining the connectivity rates between the principal neurons in the cortex (PubMed:24739570). Interacts (via olfactomedin-like domain) with FLRT3 (via extracellular domain); the interaction is direct(PubMed:22405201, PubMed:24739570, PubMed:26235031). Identified in a complex with FLRT3 and UNC5B; does not interact with UNC5B by itself. Identified in a complex with FLRT3 and UNC5D; does not interact with UNC5D by itself (By similarity). Interacts (via olfactomedin-like domain) with FLRT1 (via extracellular domain) (PubMed:22405201). Interacts (via olfactomedin-like domain) with FLRT2 (via extracellular domain) (PubMed:22405201, PubMed:25728924). Interacts (via extracellular domain) with TENM1 (PubMed:24739570). Interacts (via extracellular domain) with TENM3 (PubMed:22405201). The Olfactomedin-like domain is required for the synapse-promoting function and the interaction with FLRT3. The Olfactomedin-like and the SUEL-type lectin domains are required for the interaction with TENM1. Proteolytically cleaved into 2 subunits, an extracellular subunit and a seven-transmembrane subunit. O-glycosylated (major) and N-glycosylated. Mutant mice are viable and present no obvious physical phenotype. Compared to wild-type, mutants are hyperactive, and their dorsal striatum contains higher levels of the neurotransmitters dopamine and serotonin. Cocaine treatment causes a higher increase in locomotor activity than in wild-type. Belongs to the G-protein coupled receptor 2 family. LN-TM7 subfamily. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. Belongs to the FlgH family. +May be involved in transcriptional regulation. May play a role in spermatogenesis (By similarity). Belongs to the krueppel C2H2-type zinc-finger protein family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Plays a major role in decreasing resistance to glycopeptide antibiotics. Belongs to the TcaA family. +Proteolytically removes the C-terminal three residues of farnesylated and geranylated proteins. Belongs to the peptidase U48 family. +Catalyzes both oxygenative decarboxylation and oxidative deamination, depending on the substrate used. Has high activity for L-Phe and L-Tyr, but relatively low activities for L-Met and L-Trp. L-Phe is mainly oxygenated and L-Met is mainly oxidized. L-phenylalanine + O2 = 2-phenylacetamide + CO2 + H2O Binds 2 FAD per tetramer. Optimum pH is 6-9 for the oxygenation reaction and 10.5 for the oxidation reaction. Optimum temperature is 45 degrees Celsius for the oxygenation reaction and 65 degrees Celsius for the oxygenation reaction. Stable up to 70 degrees Celsius. Heterotetramer composed of 2 alpha and 2 beta subunits. Proteolytically cleaved to yield the active enzyme. Cleavage of the linkage between the 2 subunits causes reshaping of the oxygen channel and the hydrophobic environment around the flavin ring. Removal of the prosequence causes opening of the amino acid channel. Belongs to the phenylalanine 2-monooxygenase family. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +Known to stabilize the outer membrane. Belongs to the outer membrane OOP (TC 1.B.6) superfamily. +Belongs to the CbrB family. +Plasma membrane osmosensor that activates the high osmolarity glycerol (HOG) MAPK signaling pathway in response to high osmolarity. Forms homooligomers. Belongs to the SHO1 family. +Transfers a succinyl group from succinyl-CoA to L-homoserine, forming succinyl-L-homoserine. L-homoserine + succinyl-CoA = CoA + O-succinyl-L-homoserine Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; O-succinyl-L-homoserine from L-homoserine: step 1/1. Homodimer. Belongs to the MetA family. +Necessary for the introduction of cis unsaturation into fatty acids. Catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to E-(2)-decenoyl-ACP and then its isomerization to Z-(3)-decenoyl-ACP. Can catalyze the dehydratase reaction for beta-hydroxyacyl-ACPs with saturated chain lengths up to 16:0, being most active on intermediate chain length. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O (3R)-hydroxydecanoyl-[ACP] = (2E)-decenoyl-[ACP] + H2O (2E)-decenoyl-[ACP] = (3Z)-decenoyl-[ACP] Lipid metabolism; fatty acid biosynthesis. Homodimer. Belongs to the thioester dehydratase family. FabA subfamily. +carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family. +Catalyzes the formation of 5-methyl-uridine at position 747 (m5U747) in 23S rRNA. S-adenosyl-L-methionine + uridine(747) in 23S rRNA = 5-methyluridine(747) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmC subfamily. +Essential for viral replication in vivo (By similarity). Plays a role in the association of the matrix protein with the nucleocapsid, which initiates assembly and budding (By similarity). Homotetramer. The homotetramer interacts with RNA. Interacts with the phosphoprotein (P); this interaction is required for protein M2-1 function, localization in host inclusion bodies. Interacts with the nucleoprotein (N). Interacts with the matrix protein (M); this interaction directs M localization to cytoplasmic inclusions comprising viral proteins L, N, P, and M2-1 and mediates M association with the nucleocapsid. Localizes in cytoplasmic inclusion bodies substructures called inclusion bodies associated granules (IBAGs). Forms a layer between the matrix and nucleocapsid. Contains a zinc-finger domain on its N-terminus essential for its function (By similarity). Contains an oligomerization domain. The central globular core is responsible for binding to RNA and phosphoprotein (By similarity). Phosphorylated by host in infected cells. Phosphorylation is not essential for zinc binding activity and oligomerization, but zinc binding activity is necessary for the phosphorylation and oligomerization. Phosphorylation up-regulates viral RNA synthesis, replication, and pathogenesis in vivo. Belongs to the pneumoviridae M2-1 protein family. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Required for efficient assembly of cytochrome c oxidase in the mitochondrial inner membrane. Involved in a step that couples MSS51-COX14-dependent regulation of COX1 translation to early steps of cytochrome c oxidase assembly. Interacts with COA1, COX14 and MSS51. Present with 623 molecules/cell in log phase SD medium. Belongs to the SURF1 family. +One of 2 TIR-like protein components of antiviral defense system Thoeris, composed of ThsA, TIR1 (thsB1) and TIR2 (thsB2). Phage infection activates this protein; by 70 minutes post-infection with phage SPO1, TIR1 generates a signal molecule that activates the NAD(+) hydrolase activity of ThsA (tested with B.cereus). The signal is similar to cyclic ADP-D-ribose, but how it differs is unknown. Expression of Thoeris in B.subtilis (strain BEST7003) confers resistance to phages phi29, phi3T, SPBeta, SBSphi11, SBSphi13, SBSphiJ, SPO1 and SPR but not SBSphiC. The TIR paralogs confer resistance to different phages; this subunit confers resistance to phi29, SBSphi11, SBSphi13, SBSphiJ, SPO1 and SPR but not phi3T, SBSphiC or SPBeta. There is overlap in the phage range for this system, both TIR1 and TIR2 are activated by SBSphi13, SBSphiJ, SPO1 and SPR. Activated upon phage infection. Belongs to the Thoeris B TIR-like family. +Involved in defensive oleoresin formation in conifers in response to insect attack or other injury (By similarity). Involved in diterpene (C20) olefins biosynthesis. Bifunctional enzyme that catalyzes two sequential cyclizations of geranylgeranyl diphosphate (GGPP) to levopimaradiene. Levopimaradiene is the major products of the enzyme followed by abietadiene, neoabietadiene and palustradiene. (2E,6E,10E)-geranylgeranyl diphosphate = (+)-copalyl diphosphate (+)-copalyl diphosphate = abieta-8(14),12-diene + diphosphate Binds 3 Mg(2+) ions per subunit. Terpene metabolism; oleoresin biosynthesis. The Asp-Xaa-Asp-Asp (DXDD) motif is important for the catalytic activity in the class II active site relevant for the cyclization of GGPP. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity in the class I active site, presumably through binding to Mg(2+). Belongs to the terpene synthase family. Tpsd subfamily. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +Stimulates the release of gastrin and other gastrointestinal hormones (By similarity). Contributes to the perception of prurient stimuli and to the transmission of itch signals in the spinal cord that promote scratching behavior (By similarity). Contributes primarily to nonhistaminergic itch sensation (By similarity). In one study, shown to act in the amygdala as part of an inhibitory network which inhibits memory specifically related to learned fear (By similarity). In another study, shown to act on vasoactive intestinal peptide (VIP)-expressing cells in the auditory cortex, most likely via extrasynaptic diffusion from local and long-range sources, to mediate disinhibition of glutamatergic cells via VIP cell-specific GRPR signaling which leads to enhanced auditory fear memories (By similarity). Contributes to the regulation of food intake (By similarity). Inhibits voltage-gated sodium channels but enhances voltage-gated potassium channels in hippocampal neurons (By similarity). Induces sighing by acting directly on the pre-Botzinger complex, a cluster of several thousand neurons in the ventrolateral medulla responsible for inspiration during respiratory activity (By similarity). Induces an itch response through activation of receptors present on mast cells, triggering mast cell degranulation. In neurons of the retrotrapezoid nucleus/parafacial respiratory group, expressed on neuron projections which project into the pre-Botzinger complex. Detected in adrenal medulla (at protein level). Belongs to the bombesin/neuromedin-B/ranatensin family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity). a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [2Fe-2S] cluster per subunit. Binds 2 [4Fe-4S] clusters per subunit. Belongs to the complex I 75 kDa subunit family. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Belongs to the UPF0262 family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. Belongs to the phosphatidylserine decarboxylase family. PSD-A subfamily. +Protects actin filaments from depolymerization. Interacts with FLNC and VASP (By similarity). Interacts with F-actin and CTNNB1. Colocalizes with actin stress fibers. Expressed in heart and skeletal muscle. In heart, present in intercalated disks (at protein level). At 8 dpc, expression is restricted to cardiogenic cells. At 10 dpc, expressed in heart and rostral somites. At 13.5 dpc, expressed in heart and skeletal muscle (at protein level). Xin repeats bind F-actin. Mice are predisposed to hypertrophic cardiomyopathy, and display abnormal cardiac electrophysiological characteristics, including defects in atrial depolarization and ventricular repolarization. Belongs to the Xin family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +Probable transcription factor involved in plant development. Expressed in seedlings, roots, cotyledons, leaves and flowers. Belongs to the GRAS family. +Carboxylic ester hydrolase that may be involved in ulvan degradation (Probable). Ulvan is the main polysaccharide component of the Ulvales (green seaweed) cell wall. It is composed of disaccharide building blocks comprising 3-sulfated rhamnose (Rha3S) linked to D-glucuronic acid (GlcA), L-iduronic acid (IduA), or D-xylose (Xyl) (Probable). Catalyzes the hydrolysis of 6-phosphogluconolactone to 6-phosphogluconate (By similarity). 6-phospho-D-glucono-1,5-lactone + H2O = 6-phospho-D-gluconate + H(+) Carbohydrate degradation; pentose phosphate pathway; D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 2/3. By ulvan and rhamnose. Belongs to the cycloisomerase 2 family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules unsing 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix (By similarity). NDUFA4 is required for complex IV maintenance (By similarity). Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I1 (or COX4I2), COX5A, COX5B, COX6A2 (or COX6A1), COX6B1 (or COX6B2), COX6C, COX7A1 (or COX7A2), COX7B, COX7C, COX8B and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Interacts with RAB5IF (By similarity). Belongs to the complex IV NDUFA4 subunit family. Was initially believed to be a subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (complex I). However, was not present in all complex I preparations and presence correlated with contamination by COX6B1 (PubMed:12837546). +May act as a calcium-activated chloride channel. Belongs to the anoctamin (TC 1.A.17) family. +Probably plays a role in anchoring the complex to other cellular components. EF-1 is composed of four subunits: alpha, beta, delta, and gamma. +Type IV dipeptidyl-peptidase which removes N-terminal dipeptides sequentially from polypeptides having unsubstituted N-termini provided that the penultimate residue is proline. Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, from a polypeptide, preferentially when Yaa is Pro, provided Zaa is neither Pro nor hydroxyproline. Lysosome-like vacuoles. Belongs to the peptidase S9B family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization (By similarity). During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA (By similarity). Was shown to bind heme, but the precise role of heme is unclear. Belongs to the glutamyl-tRNA reductase family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Catalyzes the formation of N(4)-acetylcytidine (ac(4)C) at the wobble position of elongator tRNA(Met), using acetate and ATP as substrates. First activates an acetate ion to form acetyladenylate (Ac-AMP) and then transfers the acetyl group to tRNA to form ac(4)C34. acetate + ATP + cytidine(34) in elongator tRNA(Met) = AMP + diphosphate + N(4)-acetylcytidine(34) in elongator tRNA(Met) Belongs to the TmcAL family. +May be involved in transcriptional regulation. +Ribonucleoside-diphosphate reductase holoenzyme provides the precursors necessary for viral DNA synthesis. Allows virus growth in non-dividing cells. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity). [thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-diphosphate Binds 2 iron ions per subunit. Genetic information processing; DNA replication. Heterodimer of a large and a small chain. Belongs to the ribonucleoside diphosphate reductase small chain family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Enzyme involved in the catabolism of H(2)CO(3) but that does not mediates the reversible hydration of carbon dioxide. Mediates complex I assembly in mitochondria and respiration (By similarity). Homotrimer. Component of the mitochondrial oxidoreductase respiratory chain complex I; element of the extra matrix-exposed domain, which is attached to the membrane arm of this complex (Probable). Probably integral to the membrane. A number of isoforms are produced. According to EST sequences. Belongs to the gamma-class carbonic anhydrase family. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +A methylase that recognizes the double-stranded sequence 5'-GCNGC-3', methylates C-? on both strands, and protects the DNA from cleavage by the Bsp6I endonuclease. a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family. +Belongs to the universal ribosomal protein uS9 family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene). 5-methylsulfanyl-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 3/6. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 4/6. Monomer. Belongs to the HAD-like hydrolase superfamily. MasA/MtnC family. +Binds interleukin-1 and possibly interleukin-6. Could prevent these cytokines reaching their natural receptors. In consequence the inflammatory response would be diminished and virus replication enhanced. Or secretory glycoprotein. Belongs to the interleukin-1 receptor family. +Involved in the catabolism of homogentisate (2,5-dihydroxyphenylacetate or 2,5-OH-PhAc), a central intermediate in the degradation of phenylalanine and tyrosine. Catalyzes the oxidative ring cleavage of the aromatic ring of homogentisate to yield maleylacetoacetate. homogentisate + O2 = 4-maleylacetoacetate + H(+) Amino-acid degradation; L-phenylalanine degradation; acetoacetate and fumarate from L-phenylalanine: step 4/6. Hexamer; dimer of trimers. Belongs to the homogentisate dioxygenase family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Involved in host translation shutoff without degradating host RNA. By suppressing host gene expression, facilitates the evasion from host type I interferon immune response. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Belongs to the PsaL family. Extended N-terminus. +Decarboxylates L-threonine-O-3-phosphate to yield (R)-1-amino-2-propanol O-2-phosphate, the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin. H(+) + O-phospho-L-threonine = (R)-1-aminopropan-2-yl phosphate + CO2 Cofactor biosynthesis; adenosylcobalamin biosynthesis. Homodimer. With pyridoxal phosphate. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. +Catalyzes the phosphorolysis of diverse nucleosides, yielding D-ribose 1-phosphate and the respective free bases. Can use uridine, adenosine, guanosine, cytidine, thymidine, inosine and xanthosine as substrates. Also catalyzes the reverse reactions. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha-D-ribose 1-phosphate adenosine + phosphate = adenine + alpha-D-ribose 1-phosphate cytidine + phosphate = alpha-D-ribose 1-phosphate + cytosine guanosine + phosphate = alpha-D-ribose 1-phosphate + guanine inosine + phosphate = alpha-D-ribose 1-phosphate + hypoxanthine phosphate + thymidine = 2-deoxy-alpha-D-ribose 1-phosphate + thymine phosphate + uridine = alpha-D-ribose 1-phosphate + uracil phosphate + xanthosine = alpha-D-ribose 1-phosphate + xanthine Belongs to the nucleoside phosphorylase PpnP family. +DEAD-box RNA helicase-like protein required for pre-18S rRNA processing, specifically at sites A0, A1, and A2. Component of the ribosomal small subunit (SSU) processome composed of at least 40 protein subunits and snoRNA U3. Belongs to the UTP25 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Catalyzes the NAD-dependent reduction of succinylglutamate semialdehyde into succinylglutamate. H2O + N-succinyl-L-glutamate 5-semialdehyde + NAD(+) = 2 H(+) + N-succinyl-L-glutamate + NADH Amino-acid degradation; L-arginine degradation via AST pathway; L-glutamate and succinate from L-arginine: step 4/5. Belongs to the aldehyde dehydrogenase family. AstD subfamily. +Catalyzes the transfer of a methyl group from dimethylamine to the corrinoid cofactor of MtbC. Co(I)-[dimethylamine-specific corrinoid protein] + dimethylamine + H(+) = methyl-Co(III)-[dimethylamine-specific corrinoid protein] + methylamine One-carbon metabolism; methanogenesis from dimethylamine. Belongs to the dimethylamine methyltransferase family. +One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA. Homotetramer, a dimer of dimers. One homotetramer interacts with 1 SecA dimer. Belongs to the SecB family. +Belongs to the potassium channel KCNE family. Product of a dubious gene prediction. The corresponding gene is on a region of chromosome 21 that is known to be an artifactual duplication of another chromosome 21 region in the GRCh38 assembly. This entry may represent an artifactual copy of AC P15382. +Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source. D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate Homodimer. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +May be involved in transcriptional regulation. Belongs to the krueppel C2H2-type zinc-finger protein family. +Catalyzes the hydroxylation of 2-nonaprenyl-3-methyl-6-methoxy-1,4-benzoquinol during ubiquinone biosynthesis. a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + AH2 + O2 = A + a 3-demethylubiquinol + H2O Binds 2 iron ions per subunit. Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the COQ7 family. +Transcriptional activator which binds specifically to the MEF2 element, 5'-YTA[AT](4)TAR-3', found in numerous muscle-specific genes. Also involved in the activation of numerous growth factor- and stress-induced genes. Mediates cellular functions not only in skeletal and cardiac muscle development, but also in neuronal differentiation and survival. Plays diverse roles in the control of cell growth, survival and apoptosis via p38 MAPK signaling in muscle-specific and/or growth factor-related transcription. In cerebellar granule neurons, phosphorylated and sumoylated MEF2A represses transcription of NUR77 promoting synaptic differentiation. Associates with chromatin to the ZNF16 promoter (By similarity). Binds DNA as a homo- or heterodimer. Dimerizes with MEF2D. Interacts with HDAC7. Interacts with PIAS1; the interaction enhances sumoylation. Interacts with HDAC4, HDAC9 and SLC2A4RG. Interacts (via the N-terminal) with MAPK7; the interaction results in the phosphorylation and transcriptional activity of MEF2A (By similarity). Widely expressed though mainly restricted to skeletal and cardiac muscle, brain, neurons and lymphocytes. Differentially expressed depending on if isoforms contain the beta domain or not, with the total expression of the beta domain-lacking isoforms vastly exceding that of the beta domain-containing isoforms. Isoforms containing the beta domain are expressed primarily in skeletal and cardiac muscle and in brain. Also present in lung and testis. Splicing to include the beta domain is induced in differentiating myocytes. Isoforms lacking the beta domain are expressed less abundantly in skeletal muscle, brain and lymphocytes, and are uniquely found in ovary, liver, spleen and kidney. In embryos, the beta domain-containing and beta domain-lacking isoforms are equally expressed. Also expressed cerebellar granule neurons and other regions of the CNS. Highest levels in the olfactory bulb, cortex, hippocampus, thalamus and cerebellum. In the developing cerebellum, increasing levels after birth. The majority of this increase occurs around postnataL day 9 reaching a peak at postnatal day 15-18 which is maintained in adults. The beta domain, missing in a number of isoforms, is required for enhancement of transcriptional activity. Constitutive phosphorylation on Ser-406 promotes Lys-401 sumoylation thus preventing acetylation at this site. Dephosphorylation on Ser-406 by PPP3CA upon neuron depolarization promotes a switch from sumoylation to acetylation on residue Lys-403 leading to inhibition of dendrite claw differentiation. Phosphorylation on Thr-312 and Thr-319 are the main sites involved in p38 MAPK signaling and activate transcription. Phosphorylated on these sites by MAPK14/p38alpha and MAPK11/p38beta, but not by MAPK13/p38delta nor by MAPK12/p38gamma. Phosphorylation on Ser-408 by CDK5 induced by neurotoxicity inhibits MEF2A transcriptional activation leading to apoptosis of cortical neurons. Phosphorylation on Thr-312, Thr-319 and Ser-355 can be induced by EGF (By similarity). Isoform 3 is phosphorylated on Ser-98 and Thr-108. Sumoylation on Lys-401 is enhanced by PIAS1 and represses transcriptional activity. Phosphorylation on Ser-406 is required for sumoylation. Has no effect on nuclear location nor on DNA binding. Sumoylated with SUMO1 and, to a lesser extent with SUMO2 and SUMO3. PIASx facilitates sumoylation in postsynaptic dendrites in the cerebellar cortex and promotes their morphogenesis (By similarity). Acetylation on Lys-401 activates transcriptional activity. Acetylated by p300 on several sites in diffentiating myocytes. Acetylation on Lys-4 increases DNA binding and transactivation. Hyperacetylation by p300 leads to enhanced cardiac myocyte growth and heart failure (By similarity). Proteolytically cleaved in cerebellar granule neurons on several sites by caspase 3 and caspase 7 following neurotoxicity. Preferentially cleaves the CDK5-mediated hyperphosphorylated form which leads to neuron apoptosis and transcriptional inactivation (By similarity). Belongs to the MEF2 family. +(S)-lactate + NAD(+) = H(+) + NADH + pyruvate Fermentation; pyruvate fermentation to lactate; (S)-lactate from pyruvate: step 1/1. Homotetramer. Belongs to the LDH/MDH superfamily. LDH family. +Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily. +Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetE route): step 1/1. Belongs to the vitamin-B12 independent methionine synthase family. +Plays a critical role in induction and maintenance of immune tolerance to self (PubMed:11015443, PubMed:28813417, PubMed:28813410). As a ligand for the inhibitory receptor PDCD1/PD-1, modulates the activation threshold of T-cells and limits T-cell effector response (PubMed:11015443, PubMed:28813417, PubMed:28813410). Through a yet unknown activating receptor, may costimulate T-cell subsets that predominantly produce interleukin-10 (IL10) (PubMed:10581077). The PDCD1-mediated inhibitory pathway is exploited by tumors to attenuate anti-tumor immunity and escape destruction by the immune system, thereby facilitating tumor survival (PubMed:28813417, PubMed:28813410). The interaction with PDCD1/PD-1 inhibits cytotoxic T lymphocytes (CTLs) effector function (By similarity). The blockage of the PDCD1-mediated pathway results in the reversal of the exhausted T-cell phenotype and the normalization of the anti-tumor response, providing a rationale for cancer immunotherapy (By similarity). Interacts with PDCD1 (PubMed:11015443, PubMed:18287011, PubMed:26602187). Interacts (via transmembrane domain) with CMTM4 and CMTM6 (PubMed:28813417, PubMed:28813410). Associates with CMTM6 at recycling endosomes, where it is protected from being targeted for lysosomal degradation. Highly expressed in the heart, skeletal muscle, placenta and lung. Weakly expressed in the thymus, spleen, kidney and liver. Expressed on activated T- and B-cells, dendritic cells, keratinocytes and monocytes. Up-regulated on T- and B-cells, dendritic cells, keratinocytes and monocytes after LPS and IFNG activation. Up-regulated in B-cells activated by surface Ig cross-linking. Ubiquitinated; STUB1 likely mediates polyubiquitination of PD-L1/CD274 triggering its degradation. Truncation of the 3'-untranslated (3'-UTR) region of CD274 transcripts leads to elevated expression of CD274 in multiple cancers including T-cell leukemia, diffuse large B-cell lymphoma and stomach adenocarcinoma (PubMed:27281199). Disruption of 3'-UTR region is caused by structural variants that stabilize CD274 transcripts, leading to overexpression (PubMed:27281199). Increased expression in tumors promotes immune evasion and tumor cell growth by allowing malignant cells to escape destruction by the immune system (PubMed:27281199). May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the immunoglobulin superfamily. BTN/MOG family. Truncated N-terminus. +Provides the (R)-glutamate required for cell wall biosynthesis. L-glutamate = D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the aspartate/glutamate racemases family. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homotetramer; dimer of dimers. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the insertion of ferrous iron into coproporphyrin III to form Fe-coproporphyrin III. Fe-coproporphyrin III + 2 H(+) = coproporphyrin III + Fe(2+) Porphyrin-containing compound metabolism; protoheme biosynthesis. Belongs to the ferrochelatase family. +In elementary bodies (EBs, the infectious stage, which is able to survive outside the host cell) provides the structural integrity of the outer envelope through disulfide cross-links with the small cysteine-rich protein and the large cysteine-rich periplasmic protein. It has been described in publications as the Sarkosyl-insoluble COMC (Chlamydia outer membrane complex), and serves as the functional equivalent of peptidoglycan (By similarity). Permits diffusion of specific solutes through the outer membrane. Part of a disulfide cross-linked outer membrane complex (COMC) composed of the major outer membrane porin (MOMP), the small cysteine-rich protein (OmcA) and the large cysteine-rich periplasmic protein (OmcB). It is present but some of the disulfide bonds are reduced in reticulate bodies (RBs). Belongs to the chlamydial porin (CP) (TC 1.B.2) family. +Bifunctional serine/threonine kinase and phosphorylase involved in the regulation of the pyruvate, phosphate dikinase (PPDK) by catalyzing its phosphorylation/dephosphorylation. ADP + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] = AMP + H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] + phosphate = diphosphate + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] Belongs to the pyruvate, phosphate/water dikinase regulatory protein family. PDRP subfamily. +Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Forms a DNA-binding heterodimer with transcription factor PBX1. Belongs to the Antp homeobox family. +Catalyzes the oxidative deamination of positively charged L-amino acids L-Lys and L-Arg but not of amino acids L-His, L-Asp or L-Glu. Has antibacterial activity against the Gram-positive bacterium S.aureus (MIC=15 ug/ml). This antibacterial activity is bacteriostatic in the absence of amino acids L-Lys or L-Arg but bactericidal in their presence. The antibacterial effect is largely dependent on H(2)O(2) produced in the oxidative deamination of substrates. Has hemagglutinating activity towards rabbit erythrocytes. Hemagglutinating activity is inhibited by the glycoprotein fetuin, but not by glucose, mannose, galactose, N-acetylglucosamine, N-acetylgalactosamine or sialic acid. an L-alpha-amino acid + H2O + O2 = a 2-oxocarboxylate + H2O2 + NH4(+) Optimum pH is 8. More than 50% activity is retained between pH 3 and 12. Inactive at pH 2. Activity remains stable after 30 min at 55 degrees Celsius. Monomer. Expressed by the ink gland. Not glycosylated. Belongs to the flavin monoamine oxidase family. +Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Heterohexamer, formed by a dimer of trimers. The hexameric TusBCD complex contains 2 copies each of TusB, TusC and TusD. The TusBCD complex interacts with TusE. Belongs to the DsrF/TusC family. +Transport protein involved in the redistribution of lysosomes to the peri-Golgi region (By similarity). Plays a role in the maturation of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis. Plays a role in the fusion of phagosomes with lysosomes (By similarity). Acts also as a positive regulator of hedgehog signaling and regulates ciliary function (By similarity). Interacts with RILP. Recruited to phagosomes containing S.aureus or Mycobacterium. Belongs to the small GTPase superfamily. Rab family. +A methylase, recognizes the double-stranded sequence 5'-CYCGRG-3', methylates C-1 on both strands, and protects the DNA from cleavage by the AquI endonuclease. a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + H(+) + S-adenosyl-L-homocysteine Heterodimer of an alpha and a beta subunit. Corresponds to the C-terminal half of the enzymatic domain. Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +This peptide both inhibits the activity of the angiotensin-converting enzyme (ACE) and enhances the action of bradykinin by inhibiting the peptidases that inactivate it. It acts as an indirect hypotensive agent (By similarity). Expressed by the venom gland. Belongs to the bradykinin-potentiating peptide family. +The PAF1 complex is a multifunctional complex. Involved in transcription initiation via genetic interactions with TATA-binding proteins. Involved in elongation. It regulates 3'-end formation of snR47 by modulating the recruitment or stable association of NRD1 and NAB3 with RNA polymerase II. Also has a role in transcription-coupled histone modification. Required for activation of RAD6 ubiquitin conjugate and the BRE1 ubiquitin ligase which ubiquitinate 'Lys-126' histone H2B. Activates the SET1 histone methyltransferase complex for methylation of 'Lys-4' of histone H3 and for methylation of 'Lys-73' of histone H3 by DOT1 and 'Lys-36' of histone H3 by SET2. Important for TATA site selection by TBP. Directly or indirectly regulates the DNA-binding properties of SPT15, the TATA box-binding protein, and the relative activities of different TATA elements. Component of the PAF1 complex which consists of at least CDC73, CTR9, LEO1, PAF1 and RTF1. Present with 6510 molecules/cell in log phase SD medium. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Involved in the export of arginine. Important to control the intracellular level of arginine and the correct balance between arginine and lysine. L-arginine(in) = L-arginine(out) Belongs to the LysE/ArgO transporter (TC 2.A.75) family. +During the asexual blood stage, participates in initial cleavage of native host hemoglobin (Hb) resulting in Hb denaturation (PubMed:8844673, PubMed:11782538, PubMed:15574427). May cleave preferentially denatured hemoglobin that has been cleaved by PMI (PubMed:8844673). Digestion of host Hb is an essential step which provides the parasite with amino acids for protein synthesis, and regulates osmolarity (Probable). Hydrolysis of the bonds linking certain hydrophobic residues in hemoglobin or globin. Also cleaves small molecules substrates such as Ala-Leu-Glu-Arg-Thr-Phe-|-Phe(NO2)-Ser-Phe-Pro-Thr. Inhibited by pepstatin A. Component of the hemozoin formation complex (HFC) composed of falcipain 2, plasmepsins PMII, PMIII/HAP and PMIV, heme detoxifying protein HDP and falcilysin FLN. The HFC complex is involved in hemoglobin degradation and detoxification of heme in the food vacuole during the asexual blood stage. At the beginning of the asexual blood stage, the transmembrane zymogen is transported to the cytostome, an endocytic structure spanning the parasite cell membrane and the parasitophorous vacuole membrane where host proteins such as hemoglobin are endocytosed (PubMed:9169469). Following endocytosis, localizes to the cytostome vacuole membrane to be then delivered to the digestive (or food) vacuole where it is cleaved into the soluble and active enzyme (PubMed:9169469). In trophozoites, localizes to the digestive vacuole, an acidic vacuole where host hemoglobin is digested (PubMed:9169469, PubMed:11782538). Expressed during the asexual blood stage; expression begins in late rings, increases in trophozoites and continues in schizonts (at protein level). Not N-glycosylated. Proteolytically cleaved into the soluble active mature form in the digestive vacuole by cysteine protease falcipains; the process begins at the early ring stage (PubMed:9169469). Proteolysis requires an acidic environment (By similarity). In absence of falcipains, autoprocessing may serve as an alternate activation system (By similarity). Belongs to the peptidase A1 family. +Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides. Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low. Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids. Binds 2 manganese ions per subunit. Belongs to the peptidase M17 family. +Belongs to the UPF0597 family. +This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA. Binds to the 5S rRNA independently of L5 and L18. Belongs to the bacterial ribosomal protein bL25 family. CTC subfamily. +Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + H(+) + holo-[ACP] Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxD subfamily. +Acts partially redundantly with other irx members in neural patterning. Required for formation of the posterior forebrain, midbrain, hindbrain, and to a lesser extent, spinal cord. Both up-regulates and down-regulates gene expression during neural development. Acts early in neural plate development to induce proneural gene expression and specify a neural precursor state. Also up-regulates repressors that prevent neuronal differentiation. Required during at least two stages of pronephros kidney development; during neurula stages, maintains transcription of key renal genes to define the size and identity of the pronephric anlage, probably in part through regulation of bmp-signaling. Subsequently required for proper formation of the intermediate tubule segment of the pronephros. Primarily expressed in the developing central nervous system (CNS). At gastrula stage, expressed in both the superficial and deep layers of the presumptive neural plate with expression spreading to the prospective hindbrain, spinal cord and midbrain-hindbrain junction as neurulation proceeds. Not expressed in the anterior neural plate and CNS expression in the tadpole excludes the forebrain. Outside of the CNS, expressed around the closing blastopore at early gastrula stages and as gastrulation proceeds, expression switches to the anterior lateral plate mesoderm. In tadpoles, expressed in the ectodermal layer of the branchial arches, and in the otic vesicle. Also expressed in specific and overlapping dynamic patterns with irx1 and irx2 during pronephric kidney development. Renal expression begins before segment-specific terminal differentiation in the pronephric anlage at mid-neurula stage, and is later found in proximal tubule PT3 as well as intermediate tubule segments IT1 and IT2, with expression in the kidney being maintained through to the tadpole stage. By a combination of a neural inducing signal (nog/noggin) and a posteriorizing signal (bFGF). Inhibited in the neural plate by foxd5. The anterior limit of expression at the future border between the prethalamus and thalamus is defined by mutual repression with the anterior repressor fezf2, and also by arx. Induced by retinoic acid (RA) during kidney development. Belongs to the TALE/IRO homeobox family. +Molecular chaperone; binds unfolded polypeptides in vitro, and has a weak ATPase activity. Forms a Heterooligomeric complex of two stacked eight-membered rings. Belongs to the TCP-1 chaperonin family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Present with 184 molecules/cell in log phase SD medium. Truncated C-terminus. +Binds 2 magnesium or manganese ions per subunit. Belongs to the RimK family. +Troponin I is the inhibitory subunit of troponin, the thin filament regulatory complex which confers calcium-sensitivity to striated muscle actomyosin ATPase activity. Binds to actin and tropomyosin. In the muscle sample, approximately 25% of the chains were blocked. Pro-1 is probably acetylated. The N-terminus is blocked. Belongs to the troponin I family. +Transcription factor which regulates nonfermentable carbon utilization. Activator of gluconeogenetic genes (By similarity). Belongs to the ERT1/acuK family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Methylates ribosomal protein L11. L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. PrmA family. +Belongs to the DEFL family. Could be the product of a pseudogene. Lacks 2 of the 4 disulfide bonds, which are conserved features of the family. +P22 kil is essential for lytic growth in the absence of abc. Expression of P22 kil causes filamentation and cell death. +RNA-dependent RNA polymerase, which is responsible for the replication and transcription of the viral RNA genome using antigenomic RNA as an intermediate (By similarity). During transcription, synthesizes subgenomic RNAs and assures their capping by a cap-snatching mechanism, which involves the endonuclease activity cleaving the host capped pre-mRNAs (By similarity). These short capped RNAs are then used as primers for viral transcription. The 3'-end of subgenomic mRNAs molecules are not polyadenylated. During replication, the polymerase binds the 5' and 3' vRNA extremities at distinct sites (By similarity). In turn, significant conformational changes occur in the polymerase and in vRNA to initiate active RNA synthesis (By similarity). As a consequence of the use of the same enzyme for both transcription and replication, these mechanisms need to be well coordinated (By similarity). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) For endonuclease activity. Binds 2 Mn(2+) ions in the active site (By similarity). The divalent metal ions are crucial for catalytic activity (PubMed:31948728). For polymerase activity. Initiation activity is stronger in the presence of Mn(2+) than in the presence of Mg(2+). Homomultimer (By similarity). Interacts with the glycoprotein N; this interaction allows efficient polymerase packaging into virus particles (By similarity). Interacts with nucleoprotein N (By similarity). The N-terminus contains the endonuclease activity (endoN) (By similarity). The central region contains the RdRp activity (By similarity). The C-terminus contains the cap-binding region (By similarity). Classified as His(+) endonuclease since it has a histidine upstream of the active site that coordinates the first cation. Belongs to the Bunyavirales RNA polymerase family. +The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. This system is involved in glucose transport. D-glucose(out) + N(pros)-phospho-L-histidyl-[protein] = D-glucose 6-phosphate(in) + L-histidyl-[protein] The EIIC domain forms the PTS system translocation channel and contains the specific substrate-binding site. The EIIB domain is phosphorylated by phospho-EIIA on a cysteinyl or histidyl residue, depending on the transported sugar. Then, it transfers the phosphoryl group to the sugar substrate concomitantly with the sugar uptake processed by the EIIC domain. The EIIA domain is phosphorylated by phospho-HPr on a histidyl residue. Then, it transfers the phosphoryl group to the EIIB domain. +Metalloprotease that participate in microfibrils assembly. Microfibrils are extracellular matrix components occurring independently or along with elastin in the formation of elastic tissues (By similarity). Binds 1 zinc ion per subunit. Interacts with FBN1; this interaction promotes microfibrils assembly. Widely expressed in adult tissues. Widely expressed throughout embryo development. Widespread expression in embryo until 12.5 days of gestation, after which it is then expressed in a more restricted fashion, with especially strong expression in developing lung, bone, and craniofacial region. The spacer domain and the TSP type-1 domains are important for a tight interaction with the extracellular matrix. Glycosylated. Can be O-fucosylated by POFUT2 on a serine or a threonine residue found within the consensus sequence C1-X(2)-(S/T)-C2-G of the TSP type-1 repeat domains where C1 and C2 are the first and second cysteine residue of the repeat, respectively. Fucosylated repeats can then be further glycosylated by the addition of a beta-1,3-glucose residue by the glucosyltransferase, B3GALTL. Fucosylation mediates the efficient secretion of ADAMTS family members. Can also be C-glycosylated with one or two mannose molecules on tryptophan residues within the consensus sequence W-X-X-W of the TPRs, and N-glycosylated. These other glycosylations can also facilitate secretion (By similarity). May be due to intron retention. Truncated N-terminus. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 4 family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvP family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate. (2R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (2S)-2-acetolactate + H(+) + NADPH (2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP(+) = (S)-2-ethyl-2-hydroxy-3-oxobutanoate + H(+) + NADPH Binds 2 magnesium ions per subunit. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 2/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 2/4. Belongs to the ketol-acid reductoisomerase family. +Galactose and N-acetyllactosamine specific lectin. Homodimer. Binds one manganese ion and one calcium ion. Belongs to the leguminous lectin family. ECA +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively. Also cleaves 5'-deoxyadenosine, a toxic by-product of radical S-adenosylmethionine (SAM) enzymes, into 5-deoxyribose and adenine. Thus, is required for in vivo function of the radical SAM enzymes biotin synthase and lipoic acid synthase, that are inhibited by 5'-deoxyadenosine accumulation. H2O + S-adenosyl-L-homocysteine = adenine + S-(5-deoxy-D-ribos-5-yl)-L-homocysteine H2O + S-methyl-5'-thioadenosine = 5-(methylsulfanyl)-D-ribose + adenine 5'-deoxyadenosine + H2O = 5-deoxy-D-ribose + adenine Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; S-methyl-5-thio-alpha-D-ribose 1-phosphate from S-methyl-5'-thioadenosine (hydrolase route): step 1/2. Homodimer. Belongs to the PNP/UDP phosphorylase family. MtnN subfamily. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. Extended N-terminus. +Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Expressed both maternally and zygotically, from ova through to 48 hours post-fertilization. Belongs to the Abd-B homeobox family. +A core subunit of photosystem II (PSII). Belongs to the Ycf12 family. +Required for organization of the cellular microtubule array and microtubule anchoring at the centrosome. May regulate microtubule organization at least in part by targeting the microtubule severing protein KATNA1 to the centrosome. Also positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus ends. Required for several dynein- and microtubule-dependent processes such as the maintenance of Golgi integrity, the centripetal motion of secretory vesicles and the coupling of the nucleus and centrosome. Also required during brain development for the migration of newly formed neurons from the ventricular/subventricular zone toward the cortical plate. Plays a role, together with DISC1, in the regulation of neurite outgrowth. Required for mitosis in some cell types but appears to be dispensible for mitosis in cortical neuronal progenitors, which instead requires NDE1. Facilitates the polymerization of neurofilaments from the individual subunits NEFH and NEFL. Positively regulates lysosome peripheral distribution and ruffled border formation in osteoclasts (By similarity). Self-associates. Interacts with DISC1, dynein, dynactin, tubulin gamma, KATNA1, KATNB1, microtubules, PAFAH1B1, PCM1, PCNT, and YWHAE. Interacts directly with NEFL and indirectly with NEFH. Interacts (via C-terminus) with CENPF. Interacts with ZNF365. Interacts with PLEKHM1 (via N- and C-terminus). Localizes to the interphase centrosome and the mitotic spindle. Localizes to the cell body of the motor neurons and colocalizes with assembled neurofilaments within axonal processes. Localizes to the microtubules of the manchette in elongated spermatids. Colocalizes with DISC1 in the perinuclear region, including the centrosome. Localizes to the kinetochore in a CENPF-dependent manner (By similarity). Expressed at low levels in heart, hypothalamus, liver, lung, spleen and stomach. Expressed at higher levels in testis and brain. Within the brain, expressed in cerebellum, cerebral stem, cortex and striatum. Phosphorylated in mitosis. Can be phosphorylated by CDK1, CDK5 and MAPK1. Phosphorylation by CDK5 promotes interaction with KATNA1 and YWHAE (By similarity). Palmitoylation at Cys-273 reduces affinity for dynein. Belongs to the nudE family. Was originally thought to function as an oligopeptidase (NUDEL-oligopeptidase or endooligopeptidase A) which could regulate peptide levels relevant to brain function. +Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NAD(+) (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADPH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NADP(+) Homodimer. Belongs to the MnmG family. TrmFO subfamily. +Catalytic subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as an RNA ligase with broad substrate specificity, and may function toward other RNAs. a 3'-end 3'-phospho-ribonucleotide-RNA + a 5'-end dephospho-ribonucleoside-RNA + GTP = a ribonucleotidyl-ribonucleotide-RNA + diphosphate + GMP a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + a 5'-end dephospho-ribonucleoside-RNA + GTP + H2O = a ribonucleotidyl-ribonucleotide-RNA + diphosphate + GMP + H(+) Binds 2 manganese ions per subunit. Catalytic component of the tRNA-splicing ligase complex. Ligation probably proceeds through 3 nucleotidyl transfer steps, with 2',3'-cyclic phosphate termini being hydrolyzed to 3'-P termini in a step that precedes 3'-P activation with GMP. In the first nucleotidyl transfer step, RTCB reacts with GTP to form a covalent RTCB-histidine-GMP intermediate with release of PPi; in the second step, the GMP moiety is transferred to the RNA 3'-P; in the third step, the 5'-OH from the opposite RNA strand attacks the activated 3'-P to form a 3',5'-phosphodiester bond and release GMP. Belongs to the RtcB family. +Bifunctional terpene synthase; part of the gene cluster that mediates the biosynthesis of aspergiltriene A, aspergildienes A-D and aspergilols A-D (PubMed:33480256). The bifunctional terpene synthase AuAS converts isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) into sesterterpenes (PubMed:33480256). The C-terminal prenyltransferase (PT) domain of AuAS catalyzes formation of GFPP, whereas the N-terminal terpene cyclase (TC) domain catalyzes the cyclization of GFPP into 5 distinct sesterterpenes: aspergiltriene A, aspergildiene A, aspergildiene B, aspergildiene C and aspergildiene D (PubMed:33480256). The cytochrome P450 monooxygenase AP450 then hydroxylates the aspergildienes A, B, C and D to yield the corresponding sesterterpene alcohols, aspergilols A-D (PubMed:33480256). (2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = (2E,6E,10E)-geranylgeranyl diphosphate + diphosphate (2E,6E,10E)-geranylgeranyl diphosphate + isopentenyl diphosphate = (2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate Secondary metabolite biosynthesis; terpenoid biosynthesis. Hexamer. The conserved DDXXD motifs as well as the NSE/DTE motif are important for the catalytic activity, presumably through binding to Mg(2+). Aspergilol A shows a weak cytotoxicity toward MCF-7, MDA-MB231, and HepG2 cancer cells lines, with an IC(50) value ranging from 21.21 to 48.76 uM; whereas aspergilol B only shows a weak cytotoxicity against MCF-7 cells, with an IC(50) value of 27.41 uM (PubMed:33480256). None of the aspergilols have antifungal or antibacterial activities (PubMed:33480256). In the N-terminal section; belongs to the terpene synthase family. In the C-terminal section; belongs to the FPP/GGPP synthase family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Acts as a transcriptional activator that mediates the calcium- and neuron-selective induction of BDNF exon III transcription. Binds to the consensus calcium-response element CaRE1 5'-CTATTTCGAG-3' sequence. The N-terminus is necessary for DNA-binding. The C-terminus is necessary for transcriptional activation (PubMed:11832226). Truncated N-terminus. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress. These functions might be dependent on each isozyme/isoform in each plant tissue. 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O Binds 2 calcium ions per subunit. Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit. On the 2D-gel the determined pI of this protein is: 6.5, its MW is: 33 kDa. Belongs to the peroxidase family. Classical plant (class III) peroxidase subfamily. +Part of the UhpABC signaling cascade that controls the expression of the hexose phosphate transporter UhpT. UhpB functions as a membrane-associated protein kinase that autophosphorylates in response to interaction with UhpC, and subsequently transfers its phosphate group to the response regulator UhpA. Can also dephosphorylate UhpA. ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. Autophosphorylated. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +Belongs to the UPF0434 family. +Catalyzes the reversible oxidation of malate to oxaloacetate. (S)-malate + NAD(+) = H(+) + NADH + oxaloacetate Belongs to the LDH/MDH superfamily. MDH type 2 family. +Belongs to the universal ribosomal protein uS9 family. +Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine. [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(S)-S-oxide-[protein] [thioredoxin]-disulfide + H2O + L-methionine = [thioredoxin]-dithiol + L-methionine (S)-S-oxide Belongs to the MsrA Met sulfoxide reductase family. +Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates. It is required to regulate sister chromatid segregation and to limit DNA crossover. Essential for the stability, localization, and function of BLM, TOP3A, and complexes containing BLM. In the RMI complex, it is required to target BLM to chromatin and stress-induced nuclear foci and mitotic phosphorylation of BLM. Component of the RMI complex, containing at least TOP3A, RMI1 and RMI2. The RMI complex interacts with BLM (By similarity). Colocalizes with BLM at nuclear DNA repair foci. Phosphorylated during mitosis. Belongs to the RMI2 family. +Surface protein antigen implicated in dental caries. A short internal peptide (residues 452-470) has been used as a miniprotein to examine protein folding and stability. Detected as a 185 kDa cell surface protein, but also as 2 proteins in S.mutans culture supernatants of about 150 kDa (antigen I) and 50 kDa (antigen II); antigen II is only seen after proteolysis. Antigen I and II have the same N-terminus but different C-termini. Belongs to the antigen I/II family. +Catalyzes both the uptake and excretion of putrescine. The uptake of putrescine is dependent on the membrane potential and the excretion involves putrescine-ornithine antiporter activity. H(+)(in) + putrescine(in) = H(+)(out) + putrescine(out) L-ornithine(out) + putrescine(in) = L-ornithine(in) + putrescine(out) Uptake activity, but not antiporter activity, is inhibited by CCCP and N-ethylmaleimide (NEM). Uptake of putrescine is inhibited by high concentrations of ornithine. Optimum pH is 6.5 for uptake activity. Optimum pH is 9.2 for antiporter activity. Monomer. Induced at low environmental pH. Part of the speFL-speF-potE operon. Belongs to the amino acid-polyamine-organocation (APC) superfamily. Basic amino acid/polyamine antiporter (APA) (TC 2.A.3.2) family. +Catalyzes a trans-dehydration via an enolate intermediate. 3-dehydroquinate = 3-dehydroshikimate + H2O Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 3/7. Homododecamer. Belongs to the type-II 3-dehydroquinase family. +Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetE route): step 1/1. Belongs to the vitamin-B12 independent methionine synthase family. +Involved in DNA repair and RecF pathway recombination. Belongs to the RecO family. +K(+)/H(+) antiporter that extrudes potassium in exchange for external protons and maintains the internal concentration of potassium under toxic levels. H(+)(out) + K(+)(in) = H(+)(in) + K(+)(out) Belongs to the monovalent cation:proton antiporter 1 (CPA1) transporter (TC 2.A.36) family. NhaP2 subfamily. +Belongs to the bacterial ribosomal protein bL28 family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Binds to the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the eukaryotic ribosomal protein eL43 family. Putative zinc-binding subfamily. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +May play a role in cortex development as part of the Notch signaling pathway. Downstream of Notch may repress the expression of proneural genes and inhibit neuronal differentiation thereby maintaining neural progenitors. May also play a role in preimplentation embryo development. The disease may be caused by variants affecting the gene represented in this entry. Belongs to the nepro family. Extended N-terminus. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +May be involved in neuron regeneration. Belongs to the Nav/unc-53 family. +Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate. 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = H(+) + 2 H2O + phosphate + pyridoxine 5'-phosphate Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. Homooctamer; tetramer of dimers. Belongs to the PNP synthase family. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Belongs to the UPF0352 family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL30 family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +Tyrosine-protein phosphatase which dephosphorylates CTNNB1. Regulates CTNNB1 function both in cell adhesion and signaling. May function in cell proliferation and migration and play a role in the maintenance of epithelial integrity. May play a role in megakaryocytopoiesis (By similarity). H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate Forms homooligomeric complexes which mediate cell homotypic adhesion (Probable). Interacts (via the cytoplasmic juxtamembrane domain) with CTNNB1; may mediate interaction with the cadherin/catenin adhesion complex. Interacts with KIT (By similarity). May interact with AP3B1 (By similarity). Transcripts of different sizes are differentially expressed in a subset of tissues. Detected in brain, lung, skeletal muscle, heart, kidney and placenta. In brain; expressed in olfactory bulb, cerebral cortex, hippocampus and cerebellum. Expressed throughout embryonic development. First detected at 7 dpc. The extracellular domain is proteolytically processed through cleavage within the fibronectin type-III 4 domain. In addition to the 190 kDa full-length protein, proteolytic products of 100 kDa, 80 kDa and 73 kDa are observed (By similarity). N-glycosylated. Phosphorylated on tyrosine residues upon activation of KIT with stem cell factor (SCF). The 73 kDa proteolytic product is not phosphorylated (By similarity). Belongs to the protein-tyrosine phosphatase family. Receptor class 2B subfamily. Truncated C-terminus. Contaminating sequence. Potential poly-A sequence. Intron retention. +Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Binds vitamin B12 and delivers it to the periplasmic surface of BtuC. The complex is composed of two ATP-binding proteins (BtuD), two transmembrane proteins (BtuC) and a solute-binding protein (BtuF). Belongs to the BtuF family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Tetramer of two alpha and two beta subunits. Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 2 subfamily. +Catalyzes the rearrangement of 1-deoxy-D-xylulose 5-phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S. 1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + [sulfur-carrier protein ThiS]-C-terminal Gly-Gly + 2 H(+) + 2 H2O Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homotetramer. Forms heterodimers with either ThiH or ThiS. Belongs to the ThiG family. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +May modulate splice site selection during alternative splicing of pre-mRNAs. Regulates transcription and acts as corepressor. Recruits repressors to the histone deacetylase complex (HDAC) (By similarity). +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Reduces trimethylamine-N-oxide (TMAO) into trimethylamine; an anaerobic reaction coupled to energy-yielding reactions. Can also reduce other N- and S-oxide compounds such as 4-methylmorpholine-N-oxide and biotin sulfoxide (BSO), but with a lower catalytic efficiency (By similarity). 2 Fe(III)-[cytochrome c] + H2O + trimethylamine = 2 Fe(II)-[cytochrome c] + 3 H(+) + trimethylamine N-oxide Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Expression of torYZ allows E.coli to grow anaerobically on a wider range of substrates than does expression of torCAD. Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. +Involved in the biosynthesis of osmoregulated periplasmic glucans (OPGs). Glycan metabolism; osmoregulated periplasmic glucan (OPG) biosynthesis. Belongs to the glycosyltransferase 2 family. OpgH subfamily. +Activates transcription. Positively regulates PcrtB promoter upstream of the crtB operon in a cAMP-independent manner. Regulated genes include genes encoding DNA photolyase, phytoene synthase and cytochrome P450 monooxygenase, which are involved in carotenoid biosynthesis. Positively regulates the light-inducible gene cluster in the megaplasmid in a cAMP-independent manner. Homodimer. +Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate + tRNA(n) Homohexameric ring arranged as a trimer of dimers. Belongs to the RNase PH family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Potent suppressor of cytokine production that acts as a regulator of innate immune signaling and inflammation. Acts as a key negative regulator of select cytokine and chemokine responses elicited by TRIF-independent Toll-like receptors (TLRs), thereby limiting inflammatory cytokine responses to minor insults. In response to more threatening pathogens, cleaved by CASP8 downstream of TLR3 or TLR4, leading to its inactivation, thereby allowing production of inflammatory cytokines (By similarity). Acts as a restriction factor against some viruses, such as HIV-1: restricts HIV-1 replication by binding to HIV-1 mRNAs and mediating their degradation via its ribonuclease activity (PubMed:31133753). Also acts as an inhibitor of the E3 ubiquitin-protein ligase ITCH: acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates (By similarity). Proteolytic cleavage by CASP8 or MALT1 leads to its inactivation. Interacts with NEDD4. Interacts with ITCH (via WW domain 2). Primarily localizes to the nucleolus. Also localizes to the PML nuclear bodies, when desumoylated. Detected in heart, lung, brain, liver, skeletal muscle, pancreas, kidney, spleen, testis and ovary. Up-regulated in response to interferon alpha (IFN-alpha) stimulation (at protein level). The CoCUN region mediates binding to ubiquitin (PubMed:31319543). Does not interact with NEDD8 (PubMed:31319543). Proteolytically cleaved by CASP8 downstream of TLR3 or TLR4, leading to its inactivation. Mainly cleaved at Asp-490 by CASP8 (By similarity). Cleaved by caspase-like protein MALT1 in T-cells following TCR-mediated activation, leading to its inactivation and subsequent viral reactivation during HIV-1 infection (PubMed:31133753). Mono- and polyubiquitinated on the CoCUN region (PubMed:31319543). Monoubiquitinated by NEDD4 (By similarity). Polyubiquitinated, leading to its degradation by the proteasome (By similarity). Sumoylated with SUMO1, abrogating polyubiquitination and subsequent degradation (By similarity). Desumoylated by SENP1, leading to accumulation in PML nuclear bodies (By similarity). Belongs to the N4BP1 family. Extended N-terminus. +Outward rectifying potassium channel. Produces rapidly activating outward rectifier K(+) currents. Activated by high intracellular sodium and chloride levels (PubMed:14684870, PubMed:29069600). Channel activity is inhibited by ATP and by inhalation anesthetics, such as isoflurane (PubMed:17699666). Inhibited upon stimulation of G-protein coupled receptors, such as CHRM1 and GRM1 (By similarity). Detected in brain, and at low levels in heart. Detected in brainstem, including auditory neurons such as the medial nucleus of the trapezoid body. Detected in the olfactory bulb, red nucleus, facial nucleus, pontine nucleus, oculomotor nucleus, substantia nigra, deep cerebellar nuclei, vestibular nucleus, and the thalamus. Detected in hippocampal CA1, CA2, and CA3 regions, the dentate gyrus, supraoptic nucleus, hypothalamus, dorsal root ganglion, and cortical layers II, III, and V. Detected in striatum cholinergic interneurons. Phosphorylated by protein kinase C. Phosphorylation inhibits channel activity (By similarity). Belongs to the potassium channel family. Calcium-activated (TC 1.A.1.3) subfamily. KCa4.2/KCNT2 sub-subfamily. +The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins (By similarity). Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits. The coatomer is cytoplasmic or polymerized on the cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it. Belongs to the adaptor complexes medium subunit family. Delta-COP subfamily. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit. Belongs to the RnpA family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 2 family. +Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain. acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine Binds 1 Mg(2+) ion per subunit. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; N-acetyl-alpha-D-glucosamine 1-phosphate from alpha-D-glucosamine 6-phosphate (route II): step 2/2. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; UDP-N-acetyl-alpha-D-glucosamine from N-acetyl-alpha-D-glucosamine 1-phosphate: step 1/1. Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. In the N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family. In the C-terminal section; belongs to the transferase hexapeptide repeat family. +Catalyzes the conversion of urocanate to 4-imidazolone-5-propionate. 4-imidazolone-5-propanoate = H2O + trans-urocanate Binds 1 NAD(+) per subunit. Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 2/3. Belongs to the urocanase family. +Belongs to the SufE family. +Belongs to the UPF0234 family. +Catalyzes the phosphorylation of thiamine to thiamine phosphate. ATP + thiamine = ADP + H(+) + thiamine phosphate Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from thiamine: step 1/1. Belongs to the thiamine kinase family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Involved in oxygen transport from the lung to the various peripheral tissues. Heterotetramer of two alpha chains and two beta chains. Red blood cells. Belongs to the globin family. +Catalyzes the final step of fatty acid oxidation in which acetyl-CoA is released and the CoA ester of a fatty acid two carbons shorter is formed. acetyl-CoA + an acyl-CoA = a 3-oxoacyl-CoA + CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadJ) and two beta chains (FadI). Belongs to the thiolase-like superfamily. Thiolase family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Homodimer. Belongs to the DXR family. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +May be involved in protein transport from Golgi to cell surface. The ZDHHC9-GOLGA7 complex is a palmitoyltransferase specific for HRAS and NRAS. Interacts with GOLGA3. Interacts with ZDHHC9. Expressed in all tissues except colon and thymus. Palmitoylated on Cys-69 and Cys-72; which is required for Golgi localization and interaction with GOLGA3. Belongs to the ERF4 family. +Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. (2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 4/5. Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface. Belongs to the enolase family. +Purine salvage pathway enzyme that catalyzes the transfer of the ribosyl-5-phosphate group from 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to the N9 position of the 6-oxopurines guanine and xanthine to form the corresponding ribonucleotides GMP (guanosine 5'-monophosphate) and XMP (xanthosine 5'-monophosphate), with the release of PPi. To a lesser extent, also acts on hypoxanthine. diphosphate + GMP = 5-phospho-alpha-D-ribose 1-diphosphate + guanine diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine diphosphate + IMP = 5-phospho-alpha-D-ribose 1-diphosphate + hypoxanthine Purine metabolism; GMP biosynthesis via salvage pathway; GMP from guanine: step 1/1. Purine metabolism; XMP biosynthesis via salvage pathway; XMP from xanthine: step 1/1. Homotetramer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. XGPT subfamily. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +Contributes to invasiveness in malignant prostate cancer. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Two specific sites, Thr-718 (activation loop of the kinase domain) and Thr-860 (turn motif), need to be phosphorylated for its full activation. Nuclear and perinuclear Golgi region. Expressed in prostate tumors and various cancer cell lines. Not expressed in adult tissues. The C1 domain does not bind the diacylglycerol (DAG). Autophosphorylated. Belongs to the protein kinase superfamily. AGC Ser/Thr protein kinase family. PKC subfamily. +Catalyzes the transfer of sialic acid from a CMP-linked sialic acid donor onto the terminal sialic acid of an acceptor through alpha-2,8-linkages. Is active with alpha-2,3-linked, alpha-2,6-linked and alpha-2,8-linked sialic acid of N-linked oligosaccharides of glycoproteins and glycolipids. Displays preference for substrates with alpha-2,3-linked terminal sialic acid. It can form polysialic acid in vitro directly on alpha-2,3-, alpha-2,6-, or alpha-2,8-linked sialic acid. Protein modification; protein glycosylation. Homodimer. Expressed in brain and testes. Expressed first in 20 dpc fetal brain and decreases thereafter during development. Belongs to the glycosyltransferase 29 family. ST8Sia III +Pair-rule protein that regulates embryonic segmentation and adult bristle patterning. Transcriptional repressor of genes that require a bHLH protein for their transcription (e.g. ftz). Transcription repression requires formation of a complex with a corepressor protein (Groucho). Interacts with gro (via WPRW motif) and Topors. Has a particular type of basic domain (presence of a helix-interrupting proline) that binds to the N-box (CACNAG), rather than the canonical E-box (CANNTG). The C-terminal WRPW motif is a transcriptional repression domain necessary for the interaction with Groucho, a transcriptional corepressor recruited to specific target DNA by Hairy-related proteins. Ubiquitinated by Topors. +DNA-binding protein that specifically binds heat shock promoter elements (HSE) and activates transcription. Homotrimer. Exhibits temperature-dependent phosphorylation. Belongs to the HSF family. +Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate. D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+) Binds 2 divalent metal cations per subunit. Magnesium or manganese. Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. Homodimer. Belongs to the DHBP synthase family. +Required for FRI-mediated up-regulation of FLC transcripts, but not redundant with FRI and only partially redundant with FRL2. Required for the stabilization of the FRI-C complex. Component of the transcription activator complex FRI-C composed of FRI, FRL1, SUF4, FLX and FES1. Interacts with FRI and SUF4. Expressed during seed development and in dry seed. Preferentially expressed in the chalazal endosperm during early stages of seed development. Reduced levels of FLC expression and early flowering, but not redundant with FRI. Frl1 and frl2 double mutants flower earlier than frl1 single mutant, due to a partial redundancy. In cv. Columbia and cv. Landsberg erecta, either FRL1 or FRL2, but not both, is functional and required for FRI-mediated up-regulation of FLC (PubMed:17056759). Belongs to the Frigida family. In cv. Landsberg erecta, FRL1 (AC P0DKC9) is not functional due to a naturally occurring premature stop codon at position 279. +Component of the soft endocuticle of desert locust. +The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpA family. +Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP). 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP Binds 1 divalent metal cation per subunit. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 4/6. Homotrimer. Belongs to the IspF family. +Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsin, covalently linked to cis-retinal. Phosphorylated on some or all of the serine and threonine residues present in the C-terminal region. Each Drosophila eye is composed of 800 facets or ommatidia. Each ommatidium contains 8 photoreceptor cells (R1-R8), the R1 to R6 cells are outer cells, while R7 and R8 are inner cells. Opsin Rh4 is sensitive to UV light. Belongs to the G-protein coupled receptor 1 family. Opsin subfamily. +Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. Involved in gene silencing by neighboring heterochromatin, blockage of the silencing spreading along the chromosome, and required for cell cycle progression through G2/M (By similarity). Component of the NuA4 histone acetyltransferase complex. Belongs to the enhancer of polycomb family. +Chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Has a low intrinsic ATPase activity which is markedly stimulated by HscB. Belongs to the heat shock protein 70 family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Belongs to the imidazoleglycerol-phosphate dehydratase family. +DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms part of the jaw domain. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Part of the RNA polymerase complex. This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation. Belongs to the RNA polymerase beta' chain family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +(6S)-5,6,7,8-tetrahydrofolate + ATP + formate = (6S)-10-formyltetrahydrofolate + ADP + phosphate One-carbon metabolism; tetrahydrofolate interconversion. Belongs to the formate--tetrahydrofolate ligase family. +ATP-binding RNA helicase involved in translation initiation. Part of the 43S pre-initiation complex that is required for efficient initiation on mRNAs of higher eukaryotes with structured 5'-UTRs by promoting efficient NTPase-dependent 48S complex formation. Specifically binds to the 40S ribosome near the mRNA entrance. Does not possess a processive helicase activity. ATP + H2O = ADP + H(+) + phosphate Part of the 43S pre-initiation complex (PIC) that contains at least Met-tRNA, EIF1, EIF1A (EIF1AX or EIF1AY), EIF2S1, EIF2S2, EIF2S3, EIF3A, EIF3B, EIF3C, EIF3D, EIF3E, EIF3F, EIF3G, EIF3H, EIF3I, EIF3J, EIF3K, EIF3L, EIF3M, DHX29 and the 40S ribosomal subunit. Belongs to the DEAD box helicase family. DEAH subfamily. +Accessory component of the DNA polymerase epsilon complex (By similarity). Participates in DNA repair and in chromosomal DNA replication (By similarity). Forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1 (By similarity). Does not enhance nucleosome sliding activity of the ACF-5 ISWI chromatin remodeling complex (By similarity). Component of the DNA polymerase epsilon complex consisting of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. Interaction with POLE4 is a prerequisite for further binding with POLE and POLE2. Heterodimer with CHRAC1; binds to DNA (By similarity). Component of the CHRAC ISWI chromatin remodeling complex at least composed of SMARCA5/SNF2H, BAZ1A/ACF1, CHRAC1 and POLE3; the complex preferentially binds DNA through the CHRAC1-POLE3 heterodimer and possesses ATP-dependent nucleosome-remodeling activity (By similarity). Within the complex, the heterodimer with CHRAC1 interacts with SMARCA5/SNF2H; the interaction is direct and enhances nucleosome sliding activity by the SMARCA5/SNF2H and BAZ1A/ACF1 interaction (By similarity). Within the complex, the heterodimer with CHRAC1 interacts with BAZ1A/ACF1; the interactions are direct (By similarity). +Plays an important role in stimulating the translation of viral mRNAs. These mRNAs are capped but not polyadenylated, instead terminating in a conserved sequence 'GACC' at the 3' that is recognized by NSP3, which competes with host PABPC1 for EIF4G1 binding. The interaction between NSP3 and host EIF4G1 stabilizes the EIF4E-EIF4G1 interaction, thereby facilitating the initiation of capped mRNA translation. Homodimer. Interacts (via the coiled-coil region) with host ZC3H7B (via LD motif). Interacts with host EIF4G1. Belongs to the rotavirus NSP3 family. +Component of the 90S pre-ribosome involved in the maturation of rRNAs. Required for early cleavages of the pre-RNAs in the 40S ribosomal subunit maturation pathway (By similarity). Associates with 90S and pre-40S pre-ribosomal particles. Belongs to the RRP36 family. +The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently. Component of the Sec protein translocase complex. Heterotrimer consisting of alpha (SecY), beta (SecG) and gamma (SecE) subunits. The heterotrimers can form oligomers, although 1 heterotrimer is thought to be able to translocate proteins. Interacts with the ribosome. May interact with SecDF, and other proteins may be involved. Belongs to the SecY/SEC61-alpha family. +Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (PubMed:31104841). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (PubMed:31104841). Capsid protein VP1 mainly forms the vertices of the capsid (PubMed:31104841). Capsid protein VP1 interacts with host cell receptor to provide virion attachment to target host cells (By similarity). This attachment induces virion internalization (By similarity). Tyrosine kinases are probably involved in the entry process (By similarity). After binding to its receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP1 N-terminus (that contains an amphipathic alpha-helix) and capsid protein VP4 are externalized (By similarity). Together, they shape a pore in the host membrane through which viral genome is translocated to host cell cytoplasm (By similarity). Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (PubMed:31104841). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (PubMed:31104841). Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (PubMed:31104841). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (PubMed:31104841). Lies on the inner surface of the capsid shell (PubMed:31104841). After binding to the host receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP4 is released, Capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm (By similarity). Component of immature procapsids, which is cleaved into capsid proteins VP4 and VP2 after maturation (By similarity). Allows the capsid to remain inactive before the maturation step (By similarity). Cysteine protease that cleaves viral polyprotein and specific host proteins (By similarity). It is responsible for the autocatalytic cleavage between the P1 and P2 regions, which is the first cleavage occurring in the polyprotein (By similarity). Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation (By similarity). Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores (By similarity). Counteracts stress granule formation probably by antagonizing its assembly or promoting its dissassembly (By similarity). Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host reticulum endoplasmic and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cytoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication. Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3. Localizes the viral replication complex to the surface of membranous vesicles. Together with protein 3CD binds the Cis-Active RNA Element (CRE) which is involved in RNA synthesis initiation. Acts as a cofactor to stimulate the activity of 3D polymerase, maybe through a nucleid acid chaperone activity. Localizes the viral replication complex to the surface of membranous vesicles (By similarity). It inhibits host cell endoplasmic reticulum-to-Golgi apparatus transport and causes the disassembly of the Golgi complex, possibly through GBF1 interaction (By similarity). This would result in depletion of MHC, trail receptors and IFN receptors at the host cell surface (By similarity). Plays an essential role in viral RNA replication by recruiting ACBD3 and PI4KB at the viral replication sites, thereby allowing the formation of the rearranged membranous structures where viral replication takes place (By similarity). Acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU (By similarity). The oriI viral genomic sequence may act as a template for this. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome (By similarity). Following genome release from the infecting virion in the cytoplasm, the VPg-RNA linkage is probably removed by host TDP2 (By similarity). During the late stage of the replication cycle, host TDP2 is excluded from sites of viral RNA synthesis and encapsidation, allowing for the generation of progeny virions (By similarity). Involved in the viral replication complex and viral polypeptide maturation. It exhibits protease activity with a specificity and catalytic efficiency that is different from protease 3C. Protein 3CD binds to the 5'UTR of the viral genome. Replicates the viral genomic RNA on the surface of intracellular membranes. May form linear arrays of subunits that propagate along a strong head-to-tail interaction called interface-I. Covalently attaches UMP to a tyrosine of VPg, which is used to prime RNA synthesis. The positive stranded RNA genome is first replicated at virus induced membranous vesicles, creating a dsRNA genomic replication form. This dsRNA is then used as template to synthesize positive stranded RNA genomes. ss(+)RNA genomes are either translated, replicated or encapsidated. Major viral protease that mediates proteolytic processing of the polyprotein (By similarity). Cleaves host EIF5B, contributing to host translation shutoff (By similarity). Cleaves also host PABPC1, contributing to host translation shutoff (By similarity). Cleaves host NLRP1, triggers host N-glycine-mediated degradation of the autoinhibitory NLRP1 N-terminal fragment (By similarity). a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. Binds 2 magnesium ions that constitute a dinuclear catalytic metal center (By similarity). The magnesium ions are not prebound but only present for catalysis (By similarity). Requires the presence of 3CDpro or 3CPro (By similarity). Replication or transcription is subject to high level of random mutations by the nucleotide analog ribavirin. Interacts with capsid protein VP1 and capsid protein VP3 to form heterotrimeric protomers. Interacts with capsid protein VP0, and capsid protein VP3 to form heterotrimeric protomers (By similarity). Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid (By similarity). Interacts with capsid protein VP2, capsid protein VP3 and capsid protein VP4 following cleavage of capsid protein VP0 (PubMed:31104841). Interacts with host CD55 and FCGRT; these interactions promote virus attachment to the host cell and subsequent internalization (PubMed:31104841). Interacts with capsid protein VP1 and capsid protein VP3 in the mature capsid (PubMed:31104841). Interacts with host CD55 and FCGRT; these interactions promote virus attachment to the host cell and subsequent internalization (PubMed:31104841). Interacts with capsid protein VP0 and capsid protein VP1 to form heterotrimeric protomers (By similarity). Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid (By similarity). Interacts with capsid protein VP4 in the mature capsid (PubMed:31104841). Interacts with protein 2C; this interaction may be important for virion morphogenesis (By similarity). Interacts with host FCGRT; this interaction promotes virus attachment to the host cell and subsequent internalization (PubMed:31104841). Interacts with capsid protein VP1 and capsid protein VP3. Homodimer. Homohexamer; forms a hexameric ring structure with 6-fold symmetry characteristic of AAA+ ATPases (By similarity). Interacts (via N-terminus) with host RTN3 (via reticulon domain); this interaction is important for viral replication (By similarity). Interacts with capsid protein VP3; this interaction may be important for virion morphogenesis (By similarity). Interacts with protein 3CD. Homodimer (By similarity). Interacts with host GBF1 (By similarity). Interacts (via GOLD domain) with host ACBD3 (via GOLD domain); this interaction allows the formation of a viral protein 3A/ACBD3 heterotetramer with a 2:2 stoichiometry, which will stimulate the recruitment of host PI4KB in order to synthesize PI4P at the viral RNA replication sites (By similarity). Interacts with RNA-directed RNA polymerase. Interacts with protein 3AB and with RNA-directed RNA polymerase. Interacts with Viral protein genome-linked and with protein 3CD. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. The N-terminus has membrane-binding (By similarity). The N-terminus also displays RNA-binding properties (By similarity). The N-terminus is involved in oligomerization (By similarity). The central part contains an ATPase domain and a degenerate C4-type zinc-finger with only 3 cysteines (By similarity). The C-terminus is involved in RNA-binding (By similarity). The extreme C-terminus contains a region involved in oligomerization (By similarity). Specific enzymatic cleavages in vivo by the viral proteases yield processing intermediates and the mature proteins. Myristoylation is required for the formation of pentamers during virus assembly. Further assembly of 12 pentamers and a molecule of genomic RNA generates the provirion. During virion maturation, immature virions are rendered infectious following cleavage of VP0 into VP4 and VP2. This maturation seems to be an autocatalytic event triggered by the presence of RNA in the capsid and it is followed by a conformational change infectious virion. Myristoylation is required during RNA encapsidation and formation of the mature virus particle. VPg is uridylylated by the polymerase into VPg-pUpU. This acts as a nucleotide-peptide primer for the genomic RNA replication. Belongs to the picornaviruses polyprotein family. +Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin. Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin. Inhibited by SERPINA5. Found in high and low molecular mass forms. Each consists of two chains, A and B. The high molecular mass form contains a long chain A which is cleaved to yield a short chain A. Forms heterodimer with SERPINA5. Binds LRP1B; binding is followed by internalization and degradation. Interacts with MRC2. Interacts with PLAUR. In complex with SERPINE1, interacts with PLAUR/uPAR. Interacts with SORL1 and LRP1, either alone or in complex with SERPINE1; these interactions are abolished in the presence of LRPAP1/RAP. The ternary complex composed of PLAUR-PLAU-PAI1 also interacts with SORLA. Phosphorylation of Ser-157 and Ser-325 abolishes proadhesive ability but does not interfere with receptor binding. Produced as an inactive single-chain protein (pro-uPA or sc-uPA), is processed into the active disulfide-linked two-chain form of PLAU/uPA by a proteolytic event mediated, at least, by TMPRSS4. Belongs to the peptidase S1 family. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Heterodimer composed of a glutamine amidotransferase subunit (A) and a GMP-binding subunit (B). +Highly reducing polyketide synthase; part of the gene cluster that mediates the biosynthesis of the selective antifungal agent ascochitine, an o-quinone methide that plays a possible protective role against other microbial competitors in nature and is considered to be important for pathogenicity of legume-associated Didymella species (PubMed:31554725). The pathway probably begins with the synthesis of a keto-aldehyde intermediate by the ascochitine non-reducing polyketide synthase pksAC from successive condensations of 4 malonyl-CoA units, presumably with a simple acetyl-CoA starter unit (Probable). Release of the keto-aldehyde intermediate is consistent with the presence of the C-terminal reductive release domain (Probable). The HR-PKS (orf7) probably makes a diketide starter unit which is passed to the non-reducing polyketide synthase pksAC for further extension, producing ascochital and ascochitine (Probable). The aldehyde dehydrogenase (orf1), the 2-oxoglutarate-dependent dioxygenase (orf3) and the dehydrogenase (orf9) are probably involved in subsequent oxidations of methyl groups to the carboxylic acid of the heterocyclic ring (Probable). The ascochitine gene cluster also includes a gene encoding a short peptide with a cupin domain (orf2) that is often found in secondary metabolite gene clusters and which function has still to be determined (Probable). Mycotoxin biosynthesis. Multidomain protein; including a ketosynthase (KS) that catalyzes repeated decarboxylative condensation to elongate the polyketide backbone; a malonyl-CoA:ACP transacylase (MAT) that selects and transfers the extender unit malonyl-CoA; a dehydratase (DH) domain that reduces hydroxyl groups to enoyl groups; an enoylreductase (ER) domain that reduces enoyl groups to alkyl groups; a ketoreductase (KR) domain that catalyzes beta-ketoreduction steps; and an acyl-carrier protein (ACP) that serves as the tether of the growing and completed polyketide via its phosphopantetheinyl arm. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Mono-, di- and trimethylated to form H3K4me1/2/3. H3K4me activates gene expression by regulating transcription elongation and plays a role in telomere length maintenance. H3K4me enrichment correlates with transcription levels, and occurs in a 5' to 3' gradient with H3K4me3 enrichment at the 5'-end of genes, shifting to H3K4me2 and then H3K4me1 (By similarity). Acetylation of histone H3 leads to transcriptional activation. Belongs to the histone H3 family. To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H3K4me1/2/3 = mono-, di- and trimethylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me1 = monomethylated Lys-10; H3K14ac = acetylated Lys-15; H3K14me2 = dimethylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me1 = monomethylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me1 = monomethylated Lys-24; H3K56ac = acetylated Lys-56; H3K64ac = acetylated Lys-64. +Cell division inhibitor that blocks the formation of polar Z ring septums. Rapidly oscillates between the poles of the cell to destabilize FtsZ filaments that have formed before they mature into polar Z rings. Prevents FtsZ polymerization. Interacts with MinD and FtsZ. Belongs to the MinC family. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +A cytochrome P450 monooxygenase that catalyzes omega and omega-1 hydroxylation of saturated fatty acids. Exhibits preferential omega versus omega-1 regioselectivity and (R) versus (S) stereoselectivity for hydroxylation of dodecanoic (lauric) acid. Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (CPR; NADPH-ferrihemoprotein reductase). an omega-methyl-long-chain fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy-long-chain fatty acid + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] dodecanoate + O2 + reduced [NADPH--hemoprotein reductase] = (11R)-hydroxydodecanoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] dodecanoate + O2 + reduced [NADPH--hemoprotein reductase] = 12-hydroxydodecanoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] O2 + reduced [NADPH--hemoprotein reductase] + tetradecanoate = 14-hydroxytetradecanoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Lipid metabolism; fatty acid metabolism. By clofibrate. Belongs to the cytochrome P450 family. +Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source. ATP + deamido-NAD(+) + NH4(+) = AMP + diphosphate + H(+) + NAD(+) Cofactor biosynthesis; NAD(+) biosynthesis; NAD(+) from deamido-NAD(+) (ammonia route): step 1/1. Homodimer. Belongs to the NAD synthetase family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. RnhC subfamily. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Complex I is composed of 37 different subunits. Belongs to the complex I subunit 4 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase epsilon chain family. +Belongs to the FAM102 family. +Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate. AH2 + GTP + S-adenosyl-L-methionine = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + A + H(+) + L-methionine Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate. Cofactor biosynthesis; molybdopterin biosynthesis. Belongs to the radical SAM superfamily. MoaA family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Belongs to the UPF0387 family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +May be involved in the storage of translationally inactive mRNAs and protect them from degradation (By similarity). Plays a role in control of mRNA translation (By similarity). Component of a ribonucleoprotein (RNP) complex, at least composed of cpeb1, lsm14b/rap55b, ddx6/Xp54, ybx2/frgy2, pat1/P100, eif4enif1/4E-T and eif4e1b. Different translationally-repressed mRNP complexes probably exist that contain either lsm14a/rap55a or lsm14b/rap55b depending on the developmental stage (By similarity). Component of a ribonucleoprotein (RNP) complex, composed at least of elavl1/elrA and/or elavl2/elrB, igf2bp3/vg1RBP, ddx6/Xp54, ybx2/frgy2, lsm14b/rap55b and, in a subset of RNP complexes, stau1/staufen. Belongs to the LSM14 family. +Globally modulates RNA abundance by binding to RNase E (Rne) and regulating its endonucleolytic activity. Can modulate Rne action in a substrate-dependent manner by altering the composition of the degradosome. Modulates RNA-binding and helicase activities of the degradosome. Homotrimer. Binds to both RNA-binding sites in the C-terminal region of Rne and to RhlB. Belongs to the RraA family. +Mediates the nuclear export of encapsidated genomic RNAs (ribonucleoproteins, RNPs). Acts as an adapter between viral RNPs complexes and the nuclear export machinery of the cell. Possesses no intrinsic RNA-binding activity, but includes a C-terminal M1-binding domain. This domain is believed to allow recognition of RNPs bound to the protein M1. Since protein M1 is not available in large quantities before late stages of infection, such an indirect recognition mechanism probably ensures that genomic RNPs are not exported from the host nucleus until sufficient quantities of viral mRNA and progeny genomic RNA have been synthesized. Furthermore, the RNPs enter the host cytoplasm only when associated with the M1 protein that is necessary to guide them to the plasma membrane. May down-regulate viral RNA synthesis when overproduced. Interacts with protein M1. May interact with host nucleoporin RAB/HRB and exportin XPO1/CRM1. Average number present in a viral particle is estimated to be 130-200 molecules. Belongs to the influenza viruses NEP family. +Belongs to the bacterial ribosomal protein bL33 family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system. The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. Belongs to the TatA/E family. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +acetyl-CoA + H2O + oxaloacetate = citrate + CoA + H(+) Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate from oxaloacetate: step 1/2. Citrate synthase is found in nearly all cells capable of oxidative metabolism. Belongs to the citrate synthase family. +Probable transmembrane reductase that may use ascorbate as an electron donor and transfer electrons across membranes to reduce monodehydro-L-ascorbate radical and iron cations Fe(3+) in another cellular compartment. L-ascorbate(in) + monodehydro-L-ascorbate radical(out) = L-ascorbate(out) + monodehydro-L-ascorbate radical(in) Fe(3+)(out) + L-ascorbate(in) = Fe(2+)(out) + H(+) + monodehydro-L-ascorbate radical(in) Binds 2 heme b groups non-covalently. +Regulatory subunit of the DNA primase complex and component of the DNA polymerase alpha complex (also known as the alpha DNA polymerase-primase complex) which play an essential role in the initiation of DNA synthesis (PubMed:9705292, PubMed:17893144, PubMed:25550159, PubMed:26975377). During the S phase of the cell cycle, the DNA polymerase alpha complex (composed of a catalytic subunit POLA1, an accessory subunit POLA2 and two primase subunits, the catalytic subunit PRIM1 and the regulatory subunit PRIM2) is recruited to DNA at the replicative forks via direct interactions with MCM10 and WDHD1 (By similarity). The primase subunit of the polymerase alpha complex initiates DNA synthesis by oligomerising short RNA primers on both leading and lagging strands (PubMed:17893144). These primers are initially extended by the polymerase alpha catalytic subunit and subsequently transferred to polymerase delta and polymerase epsilon for processive synthesis on the lagging and leading strand, respectively (By similarity). In the primase complex, both subunits are necessary for the initial di-nucleotide formation, but the extension of the primer depends only on the catalytic subunit (PubMed:17893144, PubMed:25550159). Binds RNA:DNA duplex and coordinates the catalytic activities of PRIM1 and POLA2 during primase-to-polymerase switch. Binds 1 [4Fe-4S] cluster. Heterodimer of a catalytic subunit PRIM1 and a regulatory subunit PRIM2, also known as the DNA primase complex (PubMed:9705292, PubMed:17893144). Interacts via (C-terminus) with PRIM1 (PubMed:17893144). Component of the alpha DNA polymerase complex (also known as the alpha DNA polymerase-primase complex) consisting of four subunits: the catalytic subunit POLA1, the regulatory subunit POLA2, and the primase complex subunits PRIM1 and PRIM2 respectively (PubMed:9705292, PubMed:26975377). Within the complex, POLA1 directly interacts with PRIM2. The RNA:DNA duplex-binding domain interacts with the template phosphates at positions -2, -1, 1, and 2 positioning its bases -1, 1, and 2 for duplex formation. Interacts only with the beta- and gamma-phosphates of triphosphate moiety of initiating NTP of the primer. The side chain of His-303 mimics a RNA base that would be paired with the template nucleotide at position -1 via a hydrogen bond, thereby facilitating the stacking of the initiating NTP. In the initiating primosome a 'mini RNA:DNA' duplex is formed comprising three template nucleotides at positions -1, 1, and 2 on one strand and His-303, initiating NTP, and incoming NTP on the other strand. The interdomain linker provides flexibility in movement relative to primosome platform composed of PRIM1, the N-terminus of PRIM2, the C-terminus of POLA1 and POLA2. Together with POLA1 interdomain linker, allows for large-scale conformational changes of primosome and coordinated autoregulation of catalytic centers of PRIM1 and POLA1. It is proposed to move the C-terminus of PRIM2 close to PRIM1 during initiation, then move it away with the 5'-end of the nascent primer during elongation. The steric hindrance between the N- and C-terminus of PRIM2 as the RNA primer is elongated limits its length to 9 nucleotides. Ultimately a large rotation of the C-terminus of PRIM2 transfers the primer to POLA1 active site for DNA synthesis. Belongs to the eukaryotic-type primase large subunit family. +A non-essential component of RNA polymerase (RNAP) (Probable). Has a similar structure to bacteriophage T7 protein Gp2 (AC P03704), which is known to bind to RNAP in the DNA binding-cleft. Unlike Gp2 however, this protein does not inhibit transcription inititation (PubMed:25092033). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Monomer (PubMed:25092033). RNAP is composed of a core of 2 alpha, a beta and a beta' subunit. The core is associated with a delta subunit, and at least one of epsilon or omega. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription (By similarity). Belongs to the RNA polymerase subunit epsilon family. +Guanine nucleotide-binding proteins (G proteins) are involved as a modulator or transducer in various transmembrane signaling systems. The beta and gamma chains are required for the GTPase activity, for replacement of GDP by GTP, and for G protein-effector interaction. In the early embryo, controls the magnitude of the forces acting on centrosomes but is not required for generating asymmetric forces (PubMed:14534135). G proteins are composed of 3 units, alpha, beta and gamma (By similarity). Interacts with G protein gamma subunits gpc-1 and gpc-2 and with egl-10 and eat-16 (PubMed:11333232). Interacts with goa-1 (in GDP-bound form) (PubMed:12730122). RNAi-mediated knockdown in one-cell embryo results in hyperactive nuclear and spindle movements from early prophase to metaphase characterized by vigorous rocking of nuclear/centrosome complex and its failure to center properly. Normal centrosome alignment during metaphase. Belongs to the WD repeat G protein beta family. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the trans-Golgi network (TGN) and endosomes. The AP complexes mediate the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. Adaptor protein complex 1 (AP-1) is a heterotetramer composed of two large adaptins (gamma-type subunit AP1G1 and beta-type subunit AP1B1), a medium adaptin (mu-type subunit AP1M1 or AP1M2) and a small adaptin (sigma-type subunit AP1S1 or AP1S2 or AP1S3). Interacts with MARCHF11 (By similarity). Associates with the AP1(MU)-Nef-MHC-I complex; this complex is required for MHC-I internalization. (Microbial infection) Interacts with HIV-1 Nef. Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi complex. Phosphorylation of membrane-bound AP1M1/AP1M2 increases its affinity for sorting signals. Belongs to the adaptor complexes medium subunit family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Binds with high affinity to muscular (alpha-1/CHRNA1) and neuronal (alpha-7/CHRNA7) nicotinic acetylcholine receptor (nAChR) and inhibits acetylcholine from binding to the receptor, thereby impairing neuromuscular and neuronal transmission. Expressed by the venom gland. Belongs to the snake three-finger toxin family. Long-chain subfamily. Type II alpha-neurotoxin sub-subfamily. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +Potassium-selective channel essential in the virus replication cycle. May be involved in preventing multiple infections (Potential). Belongs to the two pore domain potassium channel (TC 1.A.1.12) family. +Plays important roles in the innate immune response as effector of glucocorticoid-mediated responses and regulator of the inflammatory process. Has anti-inflammatory activity. Plays a role in glucocorticoid-mediated down-regulation of the early phase of the inflammatory response. Contributes to the adaptive immune response by enhancing signaling cascades that are triggered by T-cell activation, regulates differentiation and proliferation of activated T-cells. Promotes the differentiation of T-cells into Th1 cells and negatively regulates differentiation into Th2 cells (By similarity). Has no effect on unstimulated T-cells. Negatively regulates hormone exocytosis via activation of the formyl peptide receptors and reorganization of the actin cytoskeleton (By similarity). Has high affinity for Ca(2+) and can bind up to eight Ca(2+) ions (By similarity). Displays Ca(2+)-dependent binding to phospholipid membranes (By similarity). Plays a role in the formation of phagocytic cups and phagosomes. Plays a role in phagocytosis by mediating the Ca(2+)-dependent interaction between phagosomes and the actin cytoskeleton (By similarity). Functions at least in part by activating the formyl peptide receptors and downstream signaling cascades. Promotes chemotaxis of granulocytes and monocytes via activation of the formyl peptide receptors. Promotes rearrangement of the actin cytoskeleton, cell polarization and cell migration. Promotes resolution of inflammation and wound healing. Acts via neutrophil N-formyl peptide receptors to enhance the release of CXCL2. Homodimer; non-covalently linked (By similarity). Homodimer; linked by transglutamylation. Homodimers linked by transglutamylation are observed in placenta, but not in other tissues. Interacts with S100A11. Heterotetramer, formed by two molecules each of S100A11 and ANXA1 (By similarity). Interacts with DYSF (By similarity). Interacts with EGFR (By similarity). Colocalizes with actin fibers at phagocytic cups. Secreted, at least in part via exosomes and other secretory vesicles. Detected in exosomes and other extracellular vesicles. Secretion is increased in response to wounding and inflammation (By similarity). Alternatively, the secretion is dependent on protein unfolding and facilitated by the cargo receptor TMED10; it results in the protein translocation from the cytoplasm into ERGIC (endoplasmic reticulum-Golgi intermediate compartment) followed by vesicle entry and secretion (By similarity). Detected in gelatinase granules in resting neutrophils. Neutrophil adhesion to endothelial cells stimulates secretion via gelatinase granules, but foreign particle phagocytosis has no effect. Displays calcium-dependent binding to phospholipid membranes (By similarity). The full-length protein can bind eight Ca(2+) ions via the annexin repeats. Calcium binding causes a major conformation change that modifies dimer contacts and leads to surface exposure of the N-terminal phosphorylation sites; in the absence of Ca(2+), these sites are buried in the interior of the protein core. The N-terminal region becomes disordered in response to calcium-binding. Phosphorylated by protein kinase C, EGFR and TRPM7. Phosphorylated in response to EGF treatment. Sumoylated. Proteolytically cleaved by cathepsin CTSG to release the active N-terminal peptide Ac2-26. Was originally identified as calcium and phospholipid binding protein that displays Ca(2+)-dependent binding to phospholipid membranes and can promote membrane aggregation in vitro. Was initially identified as inhibitor of phospholipase A2 activity (in vitro). Inhibition of phospholipase activity is mediated via its phospholipid binding activity that limits the access of phospholipase to its substrates. Belongs to the annexin family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate from the periplasm across the membrane. Belongs to the dicarboxylate/amino acid:cation symporter (DAACS) (TC 2.A.23) family. +Expressed exclusively in embryos before or up to the 8-cell stage. Belongs to the TRIM/RBCC family. +Belongs to the DsrB family. +Involved in the catabolism of L-rhamnose (6-deoxy-L-mannose). Catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose to yield L-rhamnulose 1-phosphate. ATP + L-rhamnulose = ADP + H(+) + L-rhamnulose 1-phosphate Carbohydrate degradation; L-rhamnose degradation; glycerone phosphate from L-rhamnose: step 2/3. Belongs to the rhamnulokinase family. +Catalyzes the oxidative decarboxylation of (S)-malate in the presence of NADP(+) and divalent metal ions, and decarboxylation of oxaloacetate. (S)-malate + NADP(+) = CO2 + NADPH + pyruvate H(+) + oxaloacetate = CO2 + pyruvate Divalent metal cations. Prefers magnesium or manganese. Optimum pH is 7.8-8.1. Homotetramer. Expressed in all tissues tested including liver, placenta and white adipose tissue. Belongs to the malic enzymes family. +Catalyzes the transfer of CoA to carnitine, generating the initial carnitinyl-CoA needed for the CaiB reaction cycle. Also has activity toward crotonobetaine and gamma-butyrobetaine. 4-(trimethylamino)butanoate + ATP + CoA = AMP + diphosphate + gamma-butyrobetainyl-CoA ATP + CoA + crotonobetaine = AMP + crotonobetainyl-CoA + diphosphate (R)-carnitine + ATP + CoA = (R)-carnitinyl-CoA + AMP + diphosphate Amine and polyamine metabolism; carnitine metabolism. Belongs to the ATP-dependent AMP-binding enzyme family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes a trans-dehydration via an enolate intermediate. 3-dehydroquinate = 3-dehydroshikimate + H2O Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 3/7. Homododecamer. Belongs to the type-II 3-dehydroquinase family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The L component serves as a unique electron donor to the NB-component of the complex, and binds Mg-ATP. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per dimer. Porphyrin-containing compound metabolism; bacteriochlorophyll biosynthesis (light-independent). Homodimer. Protochlorophyllide reductase is composed of three subunits; BchL, BchN and BchB. Belongs to the NifH/BchL/ChlL family. +Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA and the activity is stimulated by poly(A)-binding protein pab1. PAN deadenylation is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping and subsequent 5'-3' exonucleolytic degradation by xrn1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails. Exonucleolytic cleavage of poly(A) to 5'-AMP. Binds 2 metal cations per subunit in the catalytic exonuclease domain. Positively regulated by the regulatory subunit pan3. Forms a heterotrimer with an asymmetric homodimer of the regulatory subunit pan3 to form the poly(A)-nuclease (PAN) deadenylation complex. Contains a pseudo-UCH domain. This ubiquitin C-terminal hydrolase (UCH)-like or ubiquitin specific protease (USP)-like domain is predicted to be catalytically inactive because it lacks the active site catalytic triad characteristic of thiol proteases, with residues at the equivalent structural positions that are incompatible with catalysis, and it cannot bind ubiquitin. It functions as a structural scaffold for intra- and intermolecular interactions in the complex. The linker, or PAN3 interaction domain (PID), between the WD40 repeats and the pseudo-UCH domain mediates interaction with pan3. Belongs to the peptidase C19 family. PAN2 subfamily. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The NB-protein (BchN-BchB) is the catalytic component of the complex. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per heterodimer. The cluster is bound at the heterodimer interface by residues from both subunits. Porphyrin-containing compound metabolism; bacteriochlorophyll biosynthesis (light-independent). Protochlorophyllide reductase is composed of three subunits; BchL, BchN and BchB. Forms a heterotetramer of two BchB and two BchN subunits. Belongs to the ChlB/BchB/BchZ family. +Secreted metalloproteinase that allows assimilation of proteinaceous substrates. Belongs to the peptidase M43B family. +Specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of cytidine at position 56 in tRNAs. cytidine(56) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(56) in tRNA + H(+) + S-adenosyl-L-homocysteine Homodimer. Belongs to the aTrm56 family. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpB that pull DNA away from mid-cell into both cell halves. Component of a cohesin-like complex composed of ScpA, ScpB and the Smc homodimer, in which ScpA and ScpB bind to the head domain of Smc. The presence of the three proteins is required for the association of the complex with DNA. Associated with two foci at the outer edges of the nucleoid region in young cells, and at four foci within both cell halves in older cells. Belongs to the ScpA family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Plays a role in lysophospholipid acylation. Transfers fatty acids to the 1-position via an enzyme-bound acyl-ACP intermediate in the presence of ATP and magnesium. Its physiological function is to regenerate phosphatidylethanolamine from 2-acyl-glycero-3-phosphoethanolamine (2-acyl-GPE) formed by transacylation reactions or degradation by phospholipase A1. a 2-acyl-sn-glycero-3-phosphoethanolamine + a fatty acyl-[ACP] = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + holo-[ACP] a long-chain fatty acid + ATP + holo-[ACP] = a long-chain fatty acyl-[ACP] + AMP + diphosphate In the N-terminal section; belongs to the 2-acyl-GPE acetyltransferase family. In the C-terminal section; belongs to the ATP-dependent AMP-binding enzyme family. +Putative epoxide hydrolase; part of the gene clusters that mediate the biosynthesis of the host-selective toxins (HSTs) AF-toxins responsible for Alternaria black spot of strawberry disease by the strawberry pathotype (Probable). AF-toxin I and III are valine derivatives of 2,3-dyhydroxy-isovaleric acid and 2-hydroxy-isovaleric acid respectively, while AF II is an isoleucine derivative of 2-hydroxy-valeric acid (PubMed:15066029, Ref.4, PubMed:22846083). These derivatives are bound to a 9,10-epoxy-8-hydroxy-9-methyl-decatrienoic acid (EDA) moiety (PubMed:15066029, Ref.4, PubMed:22846083). On cellular level, AF-toxins affect plasma membrane of susceptible cells and cause a sudden increase in loss of K(+) after a few minutes of toxin treatment (PubMed:22846083). The aldo-keto reductase AFTS1 catalyzes the conversion of 2-keto-isovaleric acid (2-KIV) to 2-hydroxy-isovaleric acid (2-HIV) by reduction of its ketone to an alcohol (PubMed:15066029). The acyl-CoA ligase AFT1, the hydrolase AFT2 and the enoyl-CoA hydratases AFT3 and AFT6, but also the polyketide synthase AFT9, the acyl-CoA dehydrogenase AFT10, the cytochrome P450 monooxygenase AFT11 and the oxidoreductase AFT12 are all involved in the biosynthesis of the AK-, AF- and ACT-toxin common EDA structural moiety (PubMed:12019223, Ref.4, PubMed:18986255). The exact function of each enzyme, and of additional enzymes identified within the AF-toxin clusters have still to be determined (PubMed:12019223, Ref.4, PubMed:18986255). Mycotoxin biosynthesis. Gene clusters encoding host-selective toxins (HSTs) are localized on conditionally dispensable chromosomes (CDCs), also called supernumerary chromosomes, where they are present in multiple copies (PubMed:12019223). The CDCs are not essential for saprophytic growth but controls host-selective pathogenicity (PubMed:12019223). Belongs to the peptidase S33 family. +Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA (By similarity). Component of the heptameric LSM1-LSM7 complex, which consists of lsm1, lsm2, lsm3, lsm4, lsm5, lsm6 and lsm7. Component of the heptameric LSM2-LSM8 complex, which consists of lsm2, lsm3, lsm4, lsm5, lsm6, lsm7 and lsm8. The LSm subunits form a seven-membered ring structure with a doughnut shape (By similarity). Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily. +Serine/threonine protein kinase involved in the cytoplasm to vacuole transport (Cvt) and found to be essential in autophagy, where it is required for the formation of autophagosomes. Involved in the clearance of protein aggregates which cannot be efficiently cleared by the proteasome. Required for selective autophagic degradation of the nucleus (nucleophagy) as well as for mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. Also involved in endoplasmic reticulum-specific autophagic process, in selective removal of ER-associated degradation (ERAD) substrates. Plays a key role in ATG9 and ATG23 cycling through the pre-autophagosomal structure and is necessary to promote ATG18 binding to ATG9 through phosphorylation of ATG9. Catalyzes phosphorylation of ATG4, decreasing the interaction between ATG4 and ATG8 and impairing deconjugation of PE-conjugated forms of ATG8. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Homodimer. Forms a ternary complex with ATG13 and ATG17. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. APG1/unc-51/ULK1 subfamily. +Common junctional plaque protein. The membrane-associated plaques are architectural elements in an important strategic position to influence the arrangement and function of both the cytoskeleton and the cells within the tissue. The presence of plakoglobin in both the desmosomes and in the intermediate junctions suggests that it plays a central role in the structure and function of submembranous plaques. Acts as a substrate for VE-PTP and is required by it to stimulate VE-cadherin function in endothelial cells. Can replace beta-catenin in E-cadherin/catenin adhesion complexes which are proposed to couple cadherins to the actin cytoskeleton (By similarity). Homodimer. Component of an E-cadherin/catenin adhesion complex composed of at least E-cadherin/CDH1 and gamma-catenin/JUP, and possibly alpha-catenin/CTNNA1; the complex is located to adherens junctions. The stable association of CTNNA1 is controversial as CTNNA1 was shown not to bind to F-actin when assembled in the complex. Interacts with MUC1. Interacts with CAV1 (By similarity). Interacts with PTPRJ. Interacts with DSG1. Interacts with DSC1 and DSC2. Interacts with PKP2. Cytoplasmic in a soluble and membrane-associated form. The entire ARM repeats region mediates binding to CDH1/E-cadherin. The N-terminus and first three ARM repeats are sufficient for binding to DSG1. The N-terminus and first ARM repeat are sufficient for association with CTNNA1. DSC1 association requires both ends of the ARM repeat region. May be phosphorylated by FER. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the beta-catenin family. Extended N-terminus. +Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein. Monomer. Belongs to the LolB family. +Present with 4190 molecules/cell in log phase SD medium. Belongs to the SMP-30/CGR1 family. +Catalyzes two subsequent steps in gluconeogenesis: the aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GA3P) to fructose-1,6-bisphosphate (FBP), and the dephosphorylation of FBP to fructose-6-phosphate (F6P). beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate Carbohydrate biosynthesis; gluconeogenesis. Homooctamer; dimer of tetramers. Consists of a single catalytic domain, but remodels its active-site architecture via a large structural change to exhibit dual activities. Belongs to the FBP aldolase/phosphatase family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways. AMP + ATP = 2 ADP Monomer. Predominantly mitochondrial. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. AK2 subfamily. +Protein 2A: implicated in RNA2 replication. Could also be required for nematode transmission of the virus (By similarity). Transports viral genome to neighboring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier. Acts by forming a tubular structure at the host plasmodesmata, enlarging it enough to allow free passage of virion capsids (By similarity). Assembles in tubules that are embedded within modified plasmodesmata (By similarity). Movement proteins are targeted preferentially to calreticulin-labeled foci within the youngest cross walls, where they assemble into tubules. During cell division, they colocalize in the cell plate with KNOLLE, a cytokinesis-specific syntaxin (By similarity). Specific enzymatic cleavages in vivo by the P1 encoded 3C-like protease yield mature proteins. Virions are comprised of 60 copies of the coat protein. Belongs to the nepoviruses RNA2 polyprotein family. +Guanine-nucleotide releasing factor that promotes the exchange of Ran-bound GDP by GTP, and thereby plays an important role in RAN-mediated functions in nuclear import and mitosis (PubMed:1944575, PubMed:17435751, PubMed:20668449, PubMed:22215983, PubMed:11336674). Contributes to the generation of high levels of chromosome-associated, GTP-bound RAN, which is important for mitotic spindle assembly and normal progress through mitosis (PubMed:12194828, PubMed:17435751, PubMed:22215983). Via its role in maintaining high levels of GTP-bound RAN in the nucleus, contributes to the release of cargo proteins from importins after nuclear import (PubMed:22215983). Involved in the regulation of onset of chromosome condensation in the S phase (PubMed:3678831). Binds both to the nucleosomes and double-stranded DNA (PubMed:17435751, PubMed:18762580). Interacts with RAN (PubMed:17435751, PubMed:18762580, PubMed:29040603, PubMed:11336674). Interacts (via N-terminus and RCC1 repeats) with KPNA4 (PubMed:29042532). Interacts with ARRB2; the interaction is detected in the nucleus upon OR1D2 stimulation (PubMed:16820410). Predominantly nuclear in interphase cells (PubMed:12194828). Binds to mitotic chromosomes (PubMed:12194828, PubMed:17435751, PubMed:20668449). N-terminal methylation by METTL11A/NTM1 is required for binding double-stranded DNA and stable chromatin association. Di- and trimethylation produce a permanent positive charge on the amino group, which facilitates electrostatic binding to the phosphate groups on DNA, while inhibiting histone-binding. Methylated tail helps retain RCC1 on chromosomes during nucleotide exchange on Ran. Patients with Raynaud disease produce antibodies that bind to RCC1. +Gap class segmentation protein that controls development of head structures. Belongs to the hunchback C2H2-type zinc-finger protein family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form the product. After dissociation, two additional enzymatic reactions on the tRNA convert PreQ1 to queuine (Q), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine). 7-aminomethyl-7-carbaguanine + guanosine(34) in tRNA = 7-aminomethyl-7-carbaguanosine(34) in tRNA + guanine Binds 1 zinc ion per subunit. tRNA modification; tRNA-queuosine biosynthesis. Homodimer. Within each dimer, one monomer is responsible for RNA recognition and catalysis, while the other monomer binds to the replacement base PreQ1. Belongs to the queuine tRNA-ribosyltransferase family. +Belongs to the hssA/B family. +Provides the (R)-glutamate required for cell wall biosynthesis. L-glutamate = D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the aspartate/glutamate racemases family. +Catalyzes the condensation of pyruvate and acetyl-coenzyme A to form (R)-citramalate. acetyl-CoA + H2O + pyruvate = (3R)-citramalate + CoA + H(+) Amino-acid biosynthesis; L-isoleucine biosynthesis; 2-oxobutanoate from pyruvate: step 1/3. Homodimer. Belongs to the alpha-IPM synthase/homocitrate synthase family. +Binds with low affinity to interleukin-13 (IL13). Together with IL4RA can form a functional receptor for IL13. Also serves as an alternate accessory protein to the common cytokine receptor gamma chain for interleukin-4 (IL4) signaling, but cannot replace the function of IL2RG in allowing enhanced interleukin-2 (IL2) binding activity. Interleukin-13 receptor is a complex of IL4R, IL13RA1, and possibly other components. Interacts with TRAF3IP1. Interacts with IL4 (PubMed:18243101). Ubiquitous. Highest levels in heart, liver, skeletal muscle and ovary; lowest levels in brain, lung and kidney. Also found in B-cells, T-cells and endothelial cells. The WSXWS motif appears to be necessary for proper protein folding and thereby efficient intracellular transport and cell-surface receptor binding. The box 1 motif is required for JAK interaction and/or activation. Belongs to the type I cytokine receptor family. Type 5 subfamily. +Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). Component of the Mediator complex. Belongs to the Mediator complex subunit 18 family. +Contributes to the regulation of lumenal Ca2+ release via the sarcoplasmic reticulum calcium release channels RYR1 and RYR2, a key step in triggering skeletal and heart muscle contraction. Required for normal organization of the triad junction, where T-tubules and the sarcoplasmic reticulum terminal cisternae are in close contact. Required for normal skeletal muscle strength. Plays a role in excitation-contraction coupling in the heart and in regulating the rate of heart beats. Homooligomer of variable subunit number; disulfide-linked. Interacts with CASQ1 and RYR1 in skeletal muscle (By similarity). Interacts with CASQ2. Detected in heart (at protein level). Skeletal and cardiac muscle. Phosphorylated by CaMK2. N-glycosylated. +Leucine-rich repeat receptor-like protein kinase that may play a role in vascular tissues development. Expressed in the vascular strands of cotyledons, the shoot apex, hypocotyls, roots, leaves, stems and flowers. The protein kinase domain is predicted to be catalytically inactive. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +Involved in a zinc uptake transport system. Belongs to the ABC transporter superfamily. +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems. G proteins are composed of 3 units; alpha, beta and gamma. The alpha chain contains the guanine nucleotide binding site. The helical domain (70-190) is required for self-activation. Belongs to the G-alpha family. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Cotranslationally removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides. Binds 2 divalent metal cations per subunit. Has a high-affinity and a low affinity metal-binding site. The true nature of the physiological cofactor is under debate. The enzyme is active with cobalt, zinc, manganese or divalent iron ions. Most likely, methionine aminopeptidases function as mononuclear Fe(2+)-metalloproteases under physiological conditions, and the catalytically relevant metal-binding site has been assigned to the histidine-containing high-affinity site. Belongs to the peptidase M24A family. Methionine aminopeptidase eukaryotic type 2 subfamily. +Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A. 3'-dephospho-CoA + ATP = ADP + CoA + H(+) Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 5/5. Belongs to the CoaE family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for potassium absorption in various tissues. ATP + H(+)(in) + H2O + K(+)(out) = ADP + 2 H(+)(out) + K(+)(in) + phosphate Composed of two subunits: alpha (catalytic) and beta. Found in skin, kidney and distal colon. Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIC subfamily. +Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I. di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 4 family. MraY subfamily. +Protease that deconjugates SUMO1, SUMO2 and SUMO3 from targeted proteins. Processes preferentially poly-SUMO2 and poly-SUMO3 chains, but does not efficiently process SUMO1, SUMO2 and SUMO3 precursors. Deconjugates SUMO1 from RXRA, leading to transcriptional activation. Involved in chromosome alignment and spindle assembly, by regulating the kinetochore CENPH-CENPI-CENPK complex. Desumoylates PML and CENPI, protecting them from degradation by the ubiquitin ligase RNF4, which targets polysumoylated proteins for proteasomal degradation. Desumoylates also RPA1, thus preventing recruitment of RAD51 to the DNA damage foci to initiate DNA repair through homologous recombination. Protein modification; protein sumoylation. Interacts with RXRA. Forms a complex with KAT5-TIP60 and UBE2I in response to UV irradiation. Interacts with RPA1 to maintain it in hyposumoylated state during S phase preventing DNA repair initiation. Highly expressed in reproductive organs, such as testis, ovary and prostate. Belongs to the peptidase C48 family. +GTP-binding component of the eukaryotic elongation factor 1 complex (eEF1). In its active GTP-bound form, binds to and delivers aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. In the presence of a correct codon-anticodon match between the aminoacyl-tRNA and the A-site codon of the ribosome-bound mRNA, the ribosome acts as a GTPase activator and the GTP is hydrolyzed. The inactive GDP-bound form leaves the ribosome and must be recycled by its guanine nucleotide exchange factor (GEF) (eEF1B subcomplex) before binding another molecule of aminoacyl-tRNA. Required for nuclear export of aminoacyl-tRNAs. May also be involved in translational quality control by targeting cotranslationally damaged proteins to the proteasome (By similarity). Protein biosynthesis; polypeptide chain elongation. Component of the eukaryotic elongation factor 1 complex (eEF1). Expressed in late sporogonial stages. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Involved in ubiquitin-mediated protein degradation. Regulatory factor in the ubiquitin/proteasome pathway that controls the turnover of proteasome substrates. Targets proteasomes to the nucleus and facilitates the degradation of nuclear proteins (By similarity). Binds the proteasome. Belongs to the cut8/STS1 family. +Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I. di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 4 family. MraY subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 4L family. +Catalyzes the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH 5,10-methenyltetrahydrofolate + H2O = (6S)-10-formyltetrahydrofolate + H(+) One-carbon metabolism; tetrahydrofolate interconversion. Homodimer. Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family. +Regulator of biological processes that recruits a histone deacetylase to control gene transcription. May play a role in the entry into mitosis, negatively regulating the cell proliferation. Formation of stable complexes with geminiviridae replication-associated proteins may create a cellular environment which favors viral DNA replication (By similarity). Belongs to the retinoblastoma protein (RB) family. +Critical mediator, in cooperation with CASP4, of endoplasmic reticulum-stress induced apoptosis. Required or the activation of CASP4 following endoplasmic reticulum stress (By similarity). Constitutively interacts with CASP4; required for the localization of procaspase 4 to the ER. Belongs to the TMEM214 family. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Belongs to the thiolase-like superfamily. UPF0219 family. +Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA. Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding. Interacts with PCNA. Three molecules of FEN1 bind to one PCNA trimer with each molecule binding to one PCNA monomer. PCNA stimulates the nuclease activity without altering cleavage specificity. Resides mostly in the nucleoli and relocalizes to the nucleoplasm upon DNA damage. Phosphorylated. Phosphorylation upon DNA damage induces relocalization to the nuclear plasma. Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily. +Putative viral proton channel. May play a role in virus entry (By similarity). Dimer. Belongs to the influenza viruses type B glycoprotein NB family. +Antimicrobial activity against Gram-negative bacterium E.coli. Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Brevinin subfamily. +Forms oligomers. Belongs to the MraZ family. +Rab effector protein acting as linker between gamma-adaptin and RAB5A. Involved in endocytic membrane fusion and membrane trafficking of recycling endosomes. Stimulates nucleotide exchange on RAB5A. Can act as a ubiquitin ligase. Heterodimer with RABEP1. The heterodimer binds RAB4A and RAB5A that have been activated by GTP-binding. Binds TSC2, GGA1, GGA2, GGA3, AP1G1 and AP1G2 (By similarity). Interacts with RAB21, and with 100-fold lower affinity also with RAB22 (By similarity). Interacts with ubiquitinated EGFR. Interacts with RGS14; the interaction is GTP-dependent (By similarity). Detected in brain. Monoubiquitinated. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +(S)-malate + a quinone = a quinol + oxaloacetate Carbohydrate metabolism; tricarboxylic acid cycle; oxaloacetate from (S)-malate (quinone route): step 1/1. Belongs to the MQO family. +May be involved in recombination. Belongs to the RdgC family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds a dinuclear copper A center per subunit. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Found in a complex with TMEM177, COA6, COX18, COX20, SCO1 and SCO2. Interacts with TMEM177 in a COX20-dependent manner. Interacts with COX20. Interacts with COX16 (By similarity). Belongs to the cytochrome c oxidase subunit 2 family. +Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides. Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low. Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids. Binds 2 manganese ions per subunit. Belongs to the peptidase M17 family. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +Cysteine dioxygenase involved in sulfite formation from cysteine. Required for keratin degradation and plays an important role in filamentous growth and virulence. L-cysteine + O2 = 3-sulfino-L-alanine + H(+) Binds 1 Fe cation per subunit. Induced by L-cysteine. The thioether cross-link between Cys-113 and Tyr-183 plays a structural role through stabilizing the Fe(2+) ion, and prevents the production of highly damaging free hydroxyl radicals by holding the oxygen radical via hydroxyl hydrogen. Leads to hypersensitivity to L-cysteine. Abolishes the ability to grow on human hair and nails as substrates. Belongs to the cysteine dioxygenase family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Cytoplasmic poly(A) RNA polymerase that adds successive AMP monomers to the 3'-end of specific RNAs, forming a poly(A) tail. In contrast to the canonical nuclear poly(A) RNA polymerase, it only adds poly(A) to selected cytoplasmic mRNAs. Required for formation of long term memory. ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide Interacts with Fmr1 and eIF-4E. Found in neuronal cytoplasm, present in discrete neuronal particles associated with mRNA control, and in nuclear puncta. Expressed in the brain. Expressed in larvae, pupae and adults. Belongs to the DNA polymerase type-B-like family. GLD2 subfamily. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Anther-specific aspartic protease involved in tapetal programmed cell death (PCD). Directly regulated by the transcription factor EAT1/DTD in anthers during tapetum PCD and degeneration. Belongs to the peptidase A1 family. +Divisome component that associates with the complex late in its assembly, after the Z-ring is formed, and is dependent on DivIC and PBP2B for its recruitment to the divisome. Together with EzrA, is a key component of the system that regulates PBP1 localization during cell cycle progression. Its main role could be the removal of PBP1 from the cell pole after pole maturation is completed. Also contributes to the recruitment of PBP1 to the division complex. Not essential for septum formation. Forms polymers through the coiled coil domains. Interacts with PBP1, MreC and EzrA. Shuttles between the lateral wall and the division site in a cell cycle-dependent manner. Belongs to the GpsB family. +Involved in transport of proteins into the mitochondrion. Essential for embryonic development (By similarity). Associates with the mitochondrial contact site and cristae organizing system (MICOS) complex (also known as MINOS or MitOS complex). Belongs to the metaxin family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Belongs to the UPF0306 family. +Synthesizes nicotianamine, a polyamine that is the first intermediate in the synthesis of the phytosiderophores of the mugineic acid type found in gramineae which serve as a sensor for the physiological iron status within the plant, and/or might be involved in the transport of iron. 3 S-adenosyl-L-methionine = 3 H(+) + nicotianamine + 3 S-methyl-5'-thioadenosine Expressed in leaves. By iron deficiency in roots. Down-regulated in chlorotic leaves by iron deficiency. Belongs to the nicotianamine synthase (NAS)-like family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +Almost completely overlaps YAL044W-A. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Belongs to the major facilitator superfamily. TCR/Tet family. +Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses molecular oxygen or nitrate as electron acceptor. a quinone + sn-glycerol 3-phosphate = a quinol + dihydroxyacetone phosphate Polyol metabolism; glycerol degradation via glycerol kinase pathway; glycerone phosphate from sn-glycerol 3-phosphate (aerobic route): step 1/1. There are two sn-glycerol-3-phosphate dehydrogenase isozymes in E.coli: one is aerobic, the other anaerobic. Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA. Homotetramer, a dimer of dimers. One homotetramer interacts with 1 SecA dimer. Belongs to the SecB family. +Splicing factor specifically required for neural cell differentiation. Acts in conjunction with nPTB/PTBP2 by binding directly to its regulated target transcripts and promotes neural-specific exon inclusion in many genes that function in neural cell differentiation. Required to promote the inclusion of neural-specific exon 10 in nPTB/PTBP2, leading to increased expression of neural-specific nPTB/PTBP2. Also promotes the inclusion of exon 16 in DAAM1 in neuron extracts (By similarity). Promotes alternative splicing of REST transcripts to produce REST isoform 3 (REST4) with greatly reduced repressive activity, thereby activating expression of REST targets in neural cells (PubMed:30684677). Plays an important role during embryonic development as well as in the proper functioning of the adult nervous system. Regulates alternative splicing events in genes with important neuronal functions (By similarity). Specifically expressed in neuronal cells (at protein level). Expressed in the cerebellum. Phosphorylated. Belongs to the nSR100 family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Mast cell degranulating peptide. Expressed by the venom gland. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +The GPI-anchor is attached to the protein in the endoplasmic reticulum and serves to target the protein to the cell surface. There, the glucosamine-inositol phospholipid moiety is cleaved off and the GPI-modified mannoprotein is covalently attached via its lipidless GPI glycan remnant to the 1,6-beta-glucan of the outer cell wall layer (By similarity). Belongs to the TOS6 family. +Sorting receptor that directs prohormones to the regulated secretory pathway. Acts also as a prohormone processing enzyme in neuro/endocrine cells, removing dibasic residues from the C-terminal end of peptide hormone precursors after initial endoprotease cleavage. Release of C-terminal arginine or lysine residues from polypeptides. Binds 1 zinc ion per subunit. Interacts with secretogranin III/SCG3. Associated with the secretory granule membrane through direct binding to lipid rafts in intragranular conditions. Defects in Cpe are the cause of the fat phenotype. Mice homozygous for the fat mutation develop obesity and hyperglycemia that can be suppressed by treatment with exogenous insulin. Belongs to the peptidase M14 family. +Thiol protease. Has dipeptidylpeptidase activity. Active against a broad range of dipeptide substrates composed of both polar and hydrophobic amino acids. Proline cannot occupy the P1 position and arginine cannot occupy the P2 position of the substrate. Can act as both an exopeptidase and endopeptidase. Activates serine proteases such as elastase, cathepsin G and granzymes A and B. Can also activate neuraminidase and factor XIII. Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, except when Xaa is Arg or Lys, or Yaa or Zaa is Pro. Binds 1 Cl(-) ion per heavy chain. Strongly inhibited by the cysteine peptidase inhibitors mersalyl acid, iodoacetic acid and cystatin. Inhibited by N-ethylmaleimide, Gly-Phe-diazomethane, TLCK, TPCK and, at low pH, by dithiodipyridine. Not inhibited by the serine peptidase inhibitor PMSF, the aminopeptidase inhibitor bestatin, or metal ion chelators. High activity at pH 4.5-6.8. Tetramer of heterotrimers consisting of exclusion domain, heavy- and light chains. Ubiquitous. Highly expressed in lung, kidney and placenta. Detected at intermediate levels in colon, small intestine, spleen and pancreas. Up-regulated in lymphocytes by IL2/interleukin-2. N-glycosylated. While glycosylation at Asn-53, Asn-119 and Asn-276 is mediated by STT3A-containing complexes, glycosylation at Asn-29 is mediated STT3B-containing complexes. In approximately 50% of the complexes the exclusion domain is cleaved at position 58 or 61. The two parts of the exclusion domain are held together by a disulfide bond. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the peptidase C1 family. Extended N-terminus. CTSC mutation db +Catalyzes the cross-linking of proteins and the conjugation of polyamines to proteins. L-glutaminyl-[protein] + L-lysyl-[protein] = [protein]-L-lysyl-N(6)-5-L-glutamyl-[protein] + NH4(+) Binds 1 Ca(2+) ion per subunit. Mainly expressed in hemocytes, hepatopancreas, and gastric tissues. On the other hand nothing was detected in the heart, intestine and muscle. Belongs to the transglutaminase superfamily. Transglutaminase family. +Component of a cytoskeletal structure that is required for membrane curvature. Does not display the endocytic, hyphal growth, virulence, or cell wall defects exhibited by disruption in related RVS161 or RVS167. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Binds the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +Essential cell division protein. May link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic. Part of a complex composed of FtsB, FtsL and FtsQ. Localizes to the division septum. Belongs to the FtsB family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +Mannosyltransferase involved in glycosylphosphatidylinositol-anchor biosynthesis. Transfers the second mannose to the glycosylphosphatidylinositol during GPI precursor assembly (By similarity). Glycolipid biosynthesis; glycosylphosphatidylinositol-anchor biosynthesis. Belongs to the PIGV family. +Involved in the biosynthesis of labdane-type diterpenoid including cleroda-dienols, and peregrinol lactones and furan derivatives, dopaminergic diterpenoids that can bind to dopamine receptors in the human pituitary gland, have probably ability to lower prolactin levels, and are used to treat menstrual cycle disorders (e.g. premenstrual syndrome and mastodynia) (Probable). Terpene synthase the catalyzes the conversion of peregrinol diphosphate to viteagnusin D and 9,13(R)-epoxy-labd-14-ene, and of syn-copalyl diphosophate to vitexifolin A (PubMed:29315936). 9alpha-copalyl diphosphate + H2O = (13S)-vitexifolin A + diphosphate peregrinol diphosphate = (13R)-9,13-epoxylabd-14-ene + diphosphate H2O + peregrinol diphosphate = diphosphate + viteagnusin D Binds 3 Mg(2+) ions per subunit. Secondary metabolite biosynthesis; terpenoid biosynthesis. Mostly expressed in trichomes of leaves and fruits. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg(2+). Belongs to the terpene synthase family. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. Required to maintain the reduced state of SoxR. Binds 3 [4Fe-4S] clusters. The complex is composed of six subunits: RsxA, RsxB, RsxC, RsxD, RsxE and RsxG. Belongs to the 4Fe4S bacterial-type ferredoxin family. RnfB subfamily. +The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-amino acid + H(+) Monomer. Belongs to the PTH family. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Low-affinity nitrate transporter involved in xylem-to-phloem transfer for redistributing nitrate into developing leaves. Not involved in dipeptides transport. Expressed in siliques, shoots and roots. Mainly detected in larger expanded leaves, in the companion cells of major veins. Nrt1.11 and nrt1.12 double mutant is defective in high-nitrate-enhanced growth. Belongs to the major facilitator superfamily. Proton-dependent oligopeptide transporter (POT/PTR) (TC 2.A.17) family. +Fimbriae (also called pili), polar filaments radiating from the surface of the bacterium to a length of 0.5-1.5 micrometers and numbering 100-300 per cell, enable bacteria to colonize the epithelium of specific host organs. Belongs to the fimbrial protein family. +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and/or repair of Fe-S clusters in biosynthetic enzymes. Belongs to the Fe(2+)-trafficking protein family. +Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation. cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). Binds 1 FAD per subunit. Binds 1 5,10-methenyltetrahydrofolate (MTHF) non-covalently per subunit. Monomer. There are only 10-20 molecules of photolyase per E.coli cell. Upon absorption of visible light electrons are transferred from Trp-307 through Trp-360 to Trp 383, and from there to FADH, giving rise to the fully reduced catalytic FADH(-). Belongs to the DNA photolyase class-1 family. +Belongs to the D-glutamate cyclase family. +One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS17 family. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Belongs to the bacterial ribosomal protein bS16 family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +Proton-conducting pore forming of the V0 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons. V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (By similarity). Involved in necrotic cell death. Required along with other vacuolar ATPase components for the removal of protein aggregates which form in immature oocytes in the distal gonad. This removal occurs as the oocytes mature and move to the proximal gonad, is triggered by the introduction of sperm through mating and occurs before fertilization. The introduction of sperm triggers V-ATPase accumulation in proximal oocytes and induces lysosomal acidification which leads to engulfing of protein aggregates by lysosomes and subsequent clearance of the aggregates. Lysosomal acidification also leads to changes in mitochondrial morphology and function. Mitochondria in distal immature oocytes are fragmented, produce high levels of reactive oxygen species (ROS) and have high membrane potential, indicative of metabolic inactivity. In contrast, mitochondria in proximal mature oocytes are tubular with lower ROS levels and membrane potential, indicative of an active metabolic state required for aggregate mobilization before clearance (By similarity). V-ATPase is a heteromultimeric enzyme made up of two complexes: the ATP-hydrolytic V1 complex and the proton translocation V0 complex (By similarity). The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H (By similarity). The proton translocation complex V0 consists of the proton transport subunit a, a ring of proteolipid subunits c9c'', rotary subunit d, subunits e and f, and the accessory subunits vah-19/Ac45 and vah-20/PRR (By similarity). Vha-11 and vha-3 are transcribed on a dicistronic transcript where vha-3 is the upstream transcript and vha-11 the downstream. Belongs to the V-ATPase proteolipid subunit family. +Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate. adenosylcob(III)inamide-GDP + alpha-ribazole = adenosylcob(III)alamin + GMP + H(+) adenosylcob(III)inamide-GDP + alpha-ribazole 5'-phosphate = adenosylcob(III)alamin 5'-phosphate + GMP + H(+) Cofactor biosynthesis; adenosylcobalamin biosynthesis; adenosylcobalamin from cob(II)yrinate a,c-diamide: step 7/7. Belongs to the CobS family. +Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Tryptophillin subfamily. +Endonuclease that is involved in the suppression of homologous recombination and may therefore have a key role in the control of bacterial genetic diversity. Homodimer. Belongs to the DNA mismatch repair MutS family. MutS2 subfamily. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Precursor of the Latency-associated peptide (LAP) and Transforming growth factor beta-2 (TGF-beta-2) chains, which constitute the regulatory and active subunit of TGF-beta-2, respectively. Required to maintain the Transforming growth factor beta-2 (TGF-beta-2) chain in a latent state during storage in extracellular matrix. Associates non-covalently with TGF-beta-2 and regulates its activation via interaction with 'milieu molecules', such as LTBP1 and LRRC32/GARP, that control activation of TGF-beta-2. Multifunctional protein that regulates various processes such as angiogenesis and heart development (By similarity). Activation into mature form follows different steps: following cleavage of the proprotein in the Golgi apparatus, Latency-associated peptide (LAP) and Transforming growth factor beta-2 (TGF-beta-2) chains remain non-covalently linked rendering TGF-beta-2 inactive during storage in extracellular matrix (By similarity). At the same time, LAP chain interacts with 'milieu molecules', such as LTBP1 and LRRC32/GARP, that control activation of TGF-beta-2 and maintain it in a latent state during storage in extracellular milieus (By similarity). Once activated following release of LAP, TGF-beta-2 acts by binding to TGF-beta receptors (TGFBR1 and TGFBR2), which transduce signal (By similarity). Interacts with Transforming growth factor beta-2 (TGF-beta-2) chain; interaction is non-covalent and maintains (TGF-beta-2) in a latent state (By similarity). Homodimer; disulfide-linked (By similarity). Interacts with TGF-beta receptors (TGFBR1 and TGFBR2), leading to signal transduction (By similarity). The precursor proprotein is cleaved in the Golgi apparatus to form Transforming growth factor beta-2 (TGF-beta-2) and Latency-associated peptide (LAP) chains, which remain non-covalently linked, rendering TGF-beta-2 inactive. Belongs to the TGF-beta family. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbK family. +Involved in the biosynthesis of aklavinone which is an important precursor common to the formation of the clinically significant anthracyclines such as carminomycin, daunorubicin (daunomycin), rhodomycin, aclacinomycin T (aklavin) and aclacinomycin A (aclarubicin). These compounds are aromatic polyketide antibiotics that exhibit high cytotoxicity and are widely applied in the chemotherapy of a variety of cancers. Catalyzes the NADPH-specific conversion of aklaviketone to yield aklavinone. It can also convert maggiemycin and 7-oxodaunomycinone to epsilon-rhodomycinone and daunomycinone, respectively. aklavinone + NADP(+) = aklaviketone + 2 H(+) + NADPH Antibiotic biosynthesis; daunorubicin biosynthesis. Antibiotic biosynthesis; carminomycin biosynthesis. Antibiotic biosynthesis; rhodomycin biosynthesis. Antibiotic biosynthesis; aclacinomycin biosynthesis. Cells lacking this gene accumulate maggiemycin. In the absence of the aklavinone intermediate, aklaviketone is apparently hydroxylated at C-11 to form maggiemycin. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Catalyzes the epimerization of trans-4-hydroxy-L-proline (t4LHyp) to cis-4-hydroxy-D-proline (c4DHyp). Is likely involved in a degradation pathway that converts t4LHyp to alpha-ketoglutarate. Displays no proline racemase activity. trans-4-hydroxy-L-proline = cis-4-hydroxy-D-proline Belongs to the proline racemase family. +Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis. beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate Binds 2 Zn(2+) ions per subunit. One is catalytic and the other provides a structural contribution. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 4/4. Belongs to the class II fructose-bisphosphate aldolase family. +Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids. Binds 2 magnesium ions per subunit. Homodimer. Belongs to the UPP synthase family. +Involved in peptidoglycan biosynthesis. Transports lipid-linked peptidoglycan precursors from the inner to the outer leaflet of the cytoplasmic membrane. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurJ/MviN family. +Probable membrane-anchored myosin receptors. Truncated N-terminus. Truncated N-terminus. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +D-glyceraldehyde 3-phosphate + NADP(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADPH D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5. Homotetramer. Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. +Acts as a ligand for FGFR1, FGFR2, FGFR3 and FGFR4 (By similarity). Also acts as an integrin ligand which is required for FGF2 signaling (By similarity). Binds to integrin ITGAV:ITGB3 (By similarity). Plays an important role in the regulation of cell survival, cell division, cell differentiation and cell migration (By similarity). Functions as a potent mitogen in vitro (By similarity). Can induce angiogenesis (By similarity). Mediates phosphorylation of ERK1/2 and thereby promotes retinal lens fiber differentiation (By similarity). Monomer. Homodimer. Interacts with FGFR1, FGFR2, FGFR3 and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. Interacts with CSPG4, FGFBP1 and TEC. Found in a complex with FGFBP1, FGF1 and FGF2. Interacts with FGFBP3. Interacts with integrin ITGAV:ITGB3; the interaction is required for FGF2 signaling. Interacts with SNORC (via the extracellular domain). Interacts with glypican GPC3. Exported from cells by an endoplasmic reticulum (ER)/Golgi-independent mechanism (By similarity). Unconventional secretion of FGF2 occurs by direct translocation across the plasma membrane (By similarity). Binding of exogenous FGF2 to FGFR facilitates endocytosis followed by translocation of FGF2 across endosomal membrane into the cytosol (By similarity). Nuclear import from the cytosol requires the classical nuclear import machinery, involving proteins KPNA1 and KPNB1, as well as CEP57 (By similarity). The N-terminus of isoform 2 is blocked. Phosphorylation at Tyr-97 regulates FGF2 unconventional secretion. Belongs to the heparin-binding growth factors family. The correction of the frameshifts allows to extend the similarity to the human sequence and is based on partial amino-acid sequencing. +Catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides. Release of any N-terminal amino acid, including proline, that is linked to proline, even from a dipeptide or tripeptide. Binds 2 manganese ions per subunit. Belongs to the peptidase M24B family. +Involved in the biosynthesis of the antibiotic, phenazine, a nitrogen-containing heterocyclic molecule having important roles in virulence, competition and biological control. chorismate + L-glutamine = anthranilate + H(+) + L-glutamate + pyruvate Antibiotic biosynthesis; phenazine biosynthesis. Component I catalyzes the formation of anthranilate using ammonia rather than glutamine, whereas component II provides glutamine amidotransferase activity. +Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline. carbamoyl phosphate + L-ornithine = H(+) + L-citrulline + phosphate Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 1/3. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. OTCase family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase delta chain family. +Inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. Acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase. Binds 1 zinc ion. Interacts with GyrB. Belongs to the DNA gyrase inhibitor YacG family. +Part of the gene cluster B that mediates the biosynthesis of the fungal meroterpenoid acetoxydehydroaustin (PubMed:29076725). The first step of the pathway is the synthesis of 3,5-dimethylorsellinic acid by the polyketide synthase ausA (By similarity). 3,5-dimethylorsellinic acid is then prenylated by the polyprenyl transferase ausN (By similarity). Further epoxidation by the FAD-dependent monooxygenase ausM and cyclization by the probable terpene cyclase ausL lead to the formation of protoaustinoid A (By similarity). Protoaustinoid A is then oxidized to spiro-lactone preaustinoid A3 by the combined action of the FAD-binding monooxygenases ausB and ausC, and the dioxygenase ausE (By similarity). Acid-catalyzed keto-rearrangement and ring contraction of the tetraketide portion of preaustinoid A3 by ausJ lead to the formation of preaustinoid A4 (By similarity). The aldo-keto reductase ausK, with the help of ausH, is involved in the next step by transforming preaustinoid A4 into isoaustinone which is in turn hydroxylated by the P450 monooxygenase ausI to form austinolide (By similarity). The cytochrome P450 monooxygenase ausG then modifies austinolide to austinol (By similarity). Austinol is further acetylated to austin by the O-acetyltransferase ausP, which spontaneously changes to dehydroaustin (PubMed:29076725). The cytochrome P450 monooxygenase then converts dehydroaustin is into 7-dehydrodehydroaustin (PubMed:29076725). The hydroxylation catalyzed by ausR permits the second O-acetyltransferase ausQ to add an additional acetyl group to the molecule, leading to the formation of acetoxydehydroaustin (PubMed:29076725). Due to genetic rearrangements of the clusters and the subsequent loss of some enzymes, the end product of the Penicillium brasilianum austinoid biosynthesis clusters is acetoxydehydroaustin (PubMed:29076725). AusS is necessary for austinoids production and may play a possible function as a regulator (By similarity). Secondary metabolite biosynthesis; terpenoid biosynthesis. Homodimer. In A.calidoustus, the austinoid gene cluster lies on a contiguous DNA region, while clusters from E.nidulans and P.brasilianum are split in their respective genomes. Genetic rearrangements provoked variability among the clusters and E.nidulans produces the least number of austionoid derivatives with the end products austinol and dehydroaustinol, while P.brasilianum can produce until acetoxydehydroaustin, and A.calidoustus produces the highest number of identified derivatives. Belongs to the trt14 isomerase family. +Acts as a molecular chaperone for G protein-coupled receptors, regulating their biogenesis and exit from the ER. Associated with the cytosolic side. +Required for normal Golgi function. Homodimer (PubMed:27448097). Component of the conserved oligomeric Golgi complex which is composed of eight different subunits and is required for normal Golgi morphology and localization (Probable). Interacts with COG3, COG6, COG7 and COG8 (PubMed:27448097). Belongs to the COG5 family. +Tip subunit of the minor fimbriae. These filamentous pili are attached to the cell surface; they mediate biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome (PubMed:24118823, PubMed:26001707). They play an important role in invasion of periodontal tissues and are recognized as major virulence factors. Fimbrium subunits from different strains have highly divergent sequences, and this correlates with pathogenicity (Probable). Component of the fimbrium tip (PubMed:24118823). Minor fimbriae are composed of a structural subunit, most often Mfa1, and the accessory subunits Mfa3, Mfa4 and Mfa5 (PubMed:19589838, PubMed:24118823, PubMed:26001707). Fimbrium assembly occurs by linear, head-to-tail oligomerization of fimbrial subunits. This is mediated via insertion of a C-terminal beta-strand from one subunit into a groove in the N-terminal domain of the following subunit (Probable). Mfa3 is required for Mfa4 and Mfa5 insertion into the fimbrium (PubMed:24118823). Targeted to the outer membrane as a palmitoylated precursor. The lipid modification is no longer present after proteolytic processing to the mature form (PubMed:26437277). Detected at the tip of the fimbriae (PubMed:24118823). Mildly increased autoaggregation. The name (minor fimbrium subunit) does not indicate the abundance of the protein, but is derived from the greater length of the major fimbriae. In strain ATCC 33277 and strain ATCC BAA-1703 / FDC 381, major fimbriae are 300 - 1600 nM in length and about 5 nm in diameter. In contrast, minor fimbriae are only about 80 - 120 nm long. This length difference is observed only in a small number of strains, including strain ATCC 33277 and strain ATCC BAA-1703 / FDC 381, and is due to a loss of function mutation in FimB, a protein that restricts fimbrial length in other strains. Belongs to the bacteroidetes fimbrillin superfamily. FimB/Mfa2 family. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Homodimer. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 3 subfamily. +Catalyzes the oxidation of long-chain aliphatic aldehydes to acids. May be implicated in controlling luminescence as it catalyzes the oxidation of the fatty aldehyde substrate for the light-emitting reaction. an aldehyde + H2O + NADP(+) = a carboxylate + 2 H(+) + NADPH Homodimer. Belongs to the aldehyde dehydrogenase family. +Probable GTP-binding protein that may be involved in cell development. Belongs to the TRAFAC class dynamin-like GTPase superfamily. GB1/RHD3 GTPase family. RHD3 subfamily. +During nodulation, plays a central role in bacterial infection and contributes to nodule organogenesis (PubMed:22874912). Protein kinase that recognizes the calcium spiking induced by Nod factors and translates this signal to components controlling nodulation and mycorrhizal infection responses. May phosphorylate the NSP1 protein (PubMed:14963335, PubMed:15070781). Required in epidermal and cortical cells to promote infection thread (IT) formation in root hairs (PubMed:22874912). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by calcium. Autophosphorylation may play an important role in the regulation of the kinase activity (By similarity). Interacts with IPD3. Highly expressed in roots (PubMed:17722695, PubMed:22874912). Expressed in root hairs and nodules (PubMed:17722695, PubMed:22874912). Expressed at low levels in flowers. Not detected in leaves or stems (PubMed:22874912). In non inoculated roots, present at low levels in both epidermis and cortex. Levels increase two days after inoculation with Sinorhizobium meliloti, especially in root hair cells. During infection, mostly expressed in cortical cells where infection thread (IT) progresses and in underlying layers. Detected in the whole cortex of young nodules. In mature nodules, localized in the infection zone. Small up-regulation in nodules. Autophosphorylation. Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. CaMK subfamily. +Required for normal cell proliferation and chromosome stability. Plays a role in DNA repair during replication. ATP + H2O = ADP + H(+) + phosphate Uncoordinated and sterile with cell proliferation defects in germ and somatic cells. Hermaphrodite gonads have fewer cells with 13% of homozygotes having only one gonad arm. Most hermaphrodite mutants contain sperm but only 20% contain oocytes that develop as far as diakinesis and those that develop exhibit abnormal karyotypes. Mutant adults contain significantly fewer D neurons and seam cells than wild type. No poly-guanine tract deletions but double mutants of chl-1 and dog-1 display increased deletion frequency when compared to dog-1 mutants. Belongs to the DEAD box helicase family. DEAH subfamily. DDX11/CHL1 sub-subfamily. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. Belongs to the radical SAM superfamily. Lipoyl synthase family. +Essential antioxidant peroxidase that directly reduces phospholipid hydroperoxide even if they are incorporated in membranes and lipoproteins (By similarity). Can also reduce fatty acid hydroperoxide, cholesterol hydroperoxide and thymine hydroperoxide (By similarity). Plays a key role in protecting cells from oxidative damage by preventing membrane lipid peroxidation (By similarity). Required to prevent cells from ferroptosis, a non-apoptotic cell death resulting from an iron-dependent accumulation of lipid reactive oxygen species (By similarity). The presence of selenocysteine (Sec) versus Cys at the active site is essential for life: it provides resistance to overoxidation and prevents cells against ferroptosis (By similarity). The presence of Sec at the active site is also essential for the survival of a specific type of parvalbumin-positive interneurons, thereby preventing against fatal epileptic seizures (By similarity). May be required to protect cells from the toxicity of ingested lipid hydroperoxides (By similarity). Required for normal sperm development and male fertility (By similarity). Essential for maturation and survival of photoreceptor cells (By similarity). Plays a role in a primary T-cell response to viral and parasitic infection by protecting T-cells from ferroptosis and by supporting T-cell expansion (By similarity). Plays a role of glutathione peroxidase in platelets in the arachidonic acid metabolism (By similarity). Reduces hydroperoxy ester lipids formed by a 15-lipoxygenase that may play a role as down-regulator of the cellular 15-lipoxygenase pathway (By similarity). a hydroperoxy polyunsaturated fatty acid + 2 glutathione = a hydroxy polyunsaturated fatty acid + glutathione disulfide + H2O (12S)-hydroperoxy-(5Z,8Z,10E,14Z)-eicosatetraenoate + 2 glutathione = (12S)-hydroxy-(5Z,8Z,10E,14Z)-eicosatetraenoate + glutathione disulfide + H2O (13S)-hydroperoxy-(9Z,11E)-octadecadienoate + 2 glutathione = (13S)-hydroxy-(9Z,11E)-octadecadienoate + glutathione disulfide + H2O Monomer. Has a tendency to form higher mass oligomers. Expressed very intensively in the testis and weakly in lung, heart, and cerebellum. Belongs to the glutathione peroxidase family. +To H.influenzae HI_1709. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 49 kDa subunit family. +Seems to have no detectable effect on transcription elongation in vitro. Interacts with TCEA2 and ELOA. May be due to an intron retention. Belongs to the REXO1/REXO3 family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Involved in synthesis of starch. Catalyzes the synthesis of ADP-glucose, a molecule that serves as an activated glycosyl donor for alpha-1,4-glucan synthesis. Essential for starch synthesis in leaf chloroplasts. alpha-D-glucose 1-phosphate + ATP + H(+) = ADP-alpha-D-glucose + diphosphate Activated by 3'phosphoglycerate, inhibited by orthophosphate. Allosteric regulation. Glycan biosynthesis; starch biosynthesis. Heterotetramer composed of two small and two large subunits. Expressed in leaves and stems. Expressed in developing seeds from 1 to 20 days after flowering (DAF). Induced by sucrose and glucose. Belongs to the bacterial/plant glucose-1-phosphate adenylyltransferase family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Involved in the biosynthesis of ent-kaurene diterpenoids natural products such as oridonin, miltiradiene, eriocalyxin B and nezukol, known to exhibit antitumor, anti-inflammatory and antibacterial activities (PubMed:28381502). Catalyzes the conversion of ent-copalyl diphosphate (ent-CPP) to ent-isopimaradiene like compounds (PubMed:28381502). Binds 3 Mg(2+) ions per subunit. Secondary metabolite biosynthesis; terpenoid biosynthesis. Highly expressed in leaves. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg(2+). Abietane diterpenoids (e.g. miltiradiene, abietatriene and ferruginol) accumulate specifically in the periderm of roots (PubMed:28381502). The ent-kaurene diterpenoid oridonin, main constituent of Isodon rubescens, accumulates in leaves (PubMed:28381502). Belongs to the terpene synthase family. +Belongs to the FAM214 family. Contaminating sequence. Potential poly-A sequence. Extended N-terminus. Extended N-terminus. +Catalyzes the conversion of threonine to alpha-keto butyrate in isoleucine (Ile) biosynthesis (PubMed:17085687). Required for JA-Ile biosynthesis, a signaling molecule involved in defense and resistance to the herbivore Manduca sexta caterpillars (PubMed:17085687). L-threonine = 2-oxobutanoate + NH4(+) Amino-acid biosynthesis; L-isoleucine biosynthesis; 2-oxobutanoate from L-threonine: step 1/1. Induced by methyl jasmonate and feeding with the herbivore Manduca sexta caterpillars. Plants silencing TD exhibit a stunt growth phenotype. Belongs to the serine/threonine dehydratase family. +DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase (By similarity). a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the PolIII' complex. PolIII' associates with the gamma complex (composed of gamma, delta, delta', psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex (By similarity). Belongs to the DNA polymerase type-C family. DnaE subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Involved in nuclear export of spliced and unspliced mRNA. Assembling component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. May undergo several rounds of ATP hydrolysis during assembly of TREX to drive subsequent loading of components such as ALYREF/THOC and CHTOP onto mRNA. Also associates with pre-mRNA independent of ALYREF/THOC4 and the THO complex. Involved in the nuclear export of intronless mRNA; the ATP-bound form is proposed to recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP hydrolysis is thought to trigger the dissociation from RNA to allow the association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in transcription elongation and genome stability. Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2; the effect of ALYREF/THOC4 is reported conflictingly with [] reporting a stimulatory effect. ATP + H2O = ADP + H(+) + phosphate Homodimer, and heterodimer with DDX39A. Component of the transcription/export (TREX) complex at least composed of ALYREF/THOC4, DDX39B, SARNP/CIP29, CHTOP and the THO subcomplex; TREX seems to have dynamic structure involving ATP-dependent remodeling; in the complex bridges ALYREF/THOC4 and the THO complex, and, in a ATP-dependent manner, ALYREF/THOC4 and SARNP/CIP29. Component of the spliceosome. Interacts directly with U2AF2. Interacts with RBM8A, RNPS1 and SRRM1, FYTTD1/UIF, THOC1, MX1 and POLDIP3. Interacts with LUZP4. Can translocate to the cytoplasm in the presence of MX1. The helicase C-terminal domain mediates interaction with ALYREF/THOC4. Belongs to the DEAD box helicase family. DECD subfamily. +Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. Laminin is a complex glycoprotein, consisting of three different polypeptide chains (alpha, beta, gamma), which are bound to each other by disulfide bonds into a cross-shaped molecule comprising one long and three short arms with globules at each end. Beta-3 is a subunit of laminin-5 (laminin-332 or epiligrin/kalinin/nicein). Interacts with ECM1 (By similarity). Found in the basement membranes (major component). The alpha-helical domains I and II are thought to interact with other laminin chains to form a coiled coil structure. Domain VI is globular. +Exchanges the guanine residue with 7-cyano-7-deazaguanine (preQ0) at position 15 in the dihydrouridine loop (D-loop) of archaeal tRNAs. 7-cyano-7-deazaguanine + guanosine(15) in tRNA = 7-cyano-7-carbaguanosine(15) in tRNA + guanine Binds 1 zinc ion per subunit. tRNA modification; archaeosine-tRNA biosynthesis. Belongs to the archaeosine tRNA-ribosyltransferase family. +Required for insertion of 4Fe-4S clusters for at least IspG. Binds 1 iron-sulfur cluster per subunit. Homodimer. Belongs to the HesB/IscA family. +NADPH-dependent alcohol-forming fatty acyl-coenzyme A reductase that catalyzes the reduction of fatty acyl-CoA to fatty alcohols. The recombinant enzyme accepts saturated and mono-unsaturated fatty acyl-CoAs of 16 to 22 carbons. a long-chain fatty acyl-CoA + 2 H(+) + 2 NADPH = a long-chain primary fatty alcohol + CoA + 2 NADP(+) Belongs to the fatty acyl-CoA reductase family. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG. Belongs to the NqrB/RnfD family. +Specifically methylates the guanosine in position 1516 of 16S rRNA. guanosine(1516) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(2)-methylguanosine(1516) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmJ family. +Male determiner protein (M-factor) that controls male somatic sexual differentiation. Acts as a dominant factor that regulates the mRNA splicing of transformer (tra) and doublesex (dsx) transcripts and promotes expression of male splice forms of tra and dsx (By similarity). Probably acts as a component of the spliceosome C complex required for mRNA splicing factor and exon-junction complex (EJC) assembly (By similarity). Hinders eIF4AIII from non-specifically binding RNA and escorts it to the splicing machinery to promote EJC assembly on mature mRNAs (By similarity). Component of the spliceosome C complex. Specifically expressed in early male embryos. Zygotic expression first appears in 2- to 3-hour-old embryos (cellularized blastoderm stage). Expression is then maintained throughout male development until adulthood. The M.domestica genome only codes for one male determiner Mdmd protein, which is encoded in the M region, and can be located at different loci on the genome (chromosomes II, III, V or Y). The M region contains a cluster of tandemly repeated Mdmd copies with only one intact copy: other copies are degenerate with large truncations and frameshifts and are assumed to be non-functional. The presence of multiple copies in the M region may preserve its integrity in a hostile non-recombining environment. This protein is encoded on chromosome V. Belongs to the CWC22 family. +Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA. Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule. Binds 2 Zn(2+) ions. Homodimer. Belongs to the RNase Z family. +Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). Contains 4 disulfide bonds. Belongs to the short scorpion toxin superfamily. Potassium channel inhibitor family. Alpha-KTx 27 subfamily. +Probably deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs), playing an important role in chemotaxis. H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Belongs to the CheD family. +Belongs to the bacterial ribosomal protein bL27 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +Essential sporozoite protein (By similarity). In the mosquito vector, required for sporozoite development in the oocyst, migration through the vector hemolymph and entry into the vector salivary glands (By similarity). In the vertebrate host, required for sporozoite migration through the host dermis and infection of host hepatocytes (By similarity). Binds to highly sulfated heparan sulfate proteoglycans (HSPGs) on the surface of host hepatocytes (By similarity). In the vertebrate host, binds to highly sulfated heparan sulfate proteoglycans (HSPGs) on the surface of host hepatocytes and is required for sporozoite invasion of the host hepatocytes. Localizes to the cytoplasm and the cell membrane in oocysts at day 6 post infection and then gradually distributes over the entire cell surface of the sporoblast and the budding sporozoites. The N-terminus is involved in the initial binding to heparan sulfate proteoglycans (HSPGs) on the surface of host hepatocytes (By similarity). The N-terminus masks the TSP type-1 (TSR) domain which maintains the sporozoites in a migratory state, enabling them to complete their journey to the salivary gland in the mosquito vector and then to the host liver. The unmasking of the TSP type-1 (TSR) domain when the sporozoite interacts with the host hepatocyte also protects sporozoites from host antibodies (By similarity). The TSP type-1 (TSR) domain is required for sporozoite development and invasion. CSP has two conformational states, an adhesive conformation in which the TSP type-1 (TSR) domain is exposed and a nonadhesive conformation in which the TSR is masked by the N-terminus. TSR-exposed conformation occurs during sporozoite development in the oocyst in the mosquito vector and during host hepatocyte invasion. TSR-masked conformation occurs during sporozoite migration through the hemolymph to salivary glands in the mosquito vector and in the host dermis. The GPI-anchor is essential for cell membrane localization and for sporozoite formation inside the oocyst. During host cell invasion, proteolytically cleaved at the cell membrane in the region I by a papain-like cysteine protease of parasite origin (By similarity). Cleavage is triggered by the sporozoite contact with highly sulfated heparan sulfate proteoglycans (HSPGs) present on the host hepatocyte cell surface (By similarity). Cleavage exposes the TSP type-1 (TSR) domain and is required for productive invasion of host hepatocytes but not for adhesion to the host cell membrane (By similarity). Cleavage is dispensable for sporozoite development in the oocyst, motility and for traversal of host and vector cells (By similarity). O-glycosylated; maybe by POFUT2. The sequence of the repeats varies across Plasmodium species and strains. Belongs to the plasmodium circumsporozoite protein family. +GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel. Rho-2 GABA receptor could play a role in retinal neurotransmission (By similarity). Generally pentameric. There are five types of GABA(A) receptor chains: alpha, beta, gamma, delta, and rho. Interacts with SQSTM1 (By similarity). Isoform 2 could be translated from an upstream initiator ATG located in frame within the first coding exon. The probability of a signal peptide within this isoform is very low. Belongs to the ligand-gated ion channel (TC 1.A.9) family. Gamma-aminobutyric acid receptor (TC 1.A.9.5) subfamily. GABRR2 sub-subfamily. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +Component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Together with TOM20 and TOM22 functions as the transit peptide receptor at the surface of the mitochondrion outer membrane and facilitates the movement of preproteins into the TOM40 translocation pore (By similarity). Forms part of the TOM (translocase of outer membrane) complex that consists of at least 7 different proteins (TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70). In the complex interacts with TOM22. Interacts with TOM37. Belongs to the Tom70 family. +Belongs to the universal ribosomal protein uL29 family. +Bifunctional serine/threonine kinase and phosphorylase involved in the regulation of the pyruvate, phosphate dikinase (PPDK) by catalyzing its phosphorylation/dephosphorylation. ADP + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] = AMP + H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] + phosphate = diphosphate + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] Belongs to the pyruvate, phosphate/water dikinase regulatory protein family. PDRP subfamily. +Belongs to the peptidase S1 family. Plasma kallikrein subfamily. Although related to peptidase S1 family, lacks the essential His, Asp, and Ser residues of the catalytic triad at positions 73, 119 and 210 and is therefore predicted to have lost protease activity. +Cell wall formation. ATP + L-alanine + UDP-N-acetyl-alpha-D-muramate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Functions as an E3 ubiquitin ligase. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +Component of the cytosolic iron-sulfur (Fe/S) protein assembly machinery. Required for maturation of extramitochondrial Fe/S proteins (By similarity). Arrest at the L2-L3 stage in 90% oxygen. Belongs to the NARF family. +Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH. Belongs to the CcmE/CycJ family. +DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate. Belongs to the ATP-dependent DNA ligase family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +3'-5' exonuclease that prefers single-stranded DNA and RNA. May play a role in the H(2)O(2)-induced DNA damage repair. Monomer. Belongs to the metallo-dependent hydrolases superfamily. TatD-type hydrolase family. TatD subfamily. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway. a 3-demethylubiquinol + S-adenosyl-L-methionine = a ubiquinol + H(+) + S-adenosyl-L-homocysteine a 3-(all-trans-polyprenyl)benzene-1,2-diol + S-adenosyl-L-methionine = a 2-methoxy-6-(all-trans-polyprenyl)phenol + H(+) + S-adenosyl-L-homocysteine Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the methyltransferase superfamily. UbiG/COQ3 family. +Belongs to the UPF0178 family. +Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell. Belongs to the MinE family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Seed storage protein. Might be integrated via inter-chain disulfide bonds within the glutenin polymer (By similarity). Contains disulfide bonds. Belongs to the prolamin family. +Catalyzes the oxidation of erythronate-4-phosphate to 3-hydroxy-2-oxo-4-phosphonooxybutanoate. 4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + H(+) + NADH Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 2/5. Homodimer. Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Cytokine that stimulates the growth and differentiation of hematopoietic precursor cells from various lineages, including granulocytes, macrophages, eosinophils and erythrocytes. Monomer. The signaling GM-CSF receptor complex is a dodecamer of two head-to-head hexamers of two alpha, two beta, and two ligand subunits (By similarity). Belongs to the GM-CSF family. +Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate. (S)-dihydroorotate + H2O = H(+) + N-carbamoyl-L-aspartate Binds 2 Zn(2+) ions per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 3/3. Homodimer. Belongs to the metallo-dependent hydrolases superfamily. DHOase family. Class II DHOase subfamily. +Part of the ABC transporter complex MalEFGK involved in maltose/maltodextrin import. Probably responsible for the translocation of the substrate across the membrane. The complex is composed of two ATP-binding proteins (MalK), two transmembrane proteins (MalG and MalF) and a solute-binding protein (MalE). Belongs to the binding-protein-dependent transport system permease family. MalFG subfamily. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Endoglycosidase that releases N-glycans from glycoproteins by cleaving the beta-1,4-glycosidic bond in the N,N'-diacetylchitobiose core. Involved in the processing of free oligosaccharides in the cytosol (By similarity). Endohydrolysis of the N,N'-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -[Man(GlcNAc)2]Asn- structure. One N-acetyl-D-glucosamine residue remains attached to the protein, the rest of the oligosaccharide is released intact. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the glycosyl hydrolase 85 family. Wrong choice of CDS. +Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional pre-initiation complex with RNA polymerase II and the general transcription factors (By similarity). Functions downstream of receptor let-23 and let-60/Ras during vulval induction likely by down-regulating the expression of phosphatase dep-1 and lin-12/Notch in vulva precursor cell descendants with a primary cell fate (PubMed:7557379, PubMed:15901674). Acts to repress beta-catenin target genes (PubMed:12130541). Required for asymmetric division of T-cells (PubMed:15790964). Plays a role in responses to M.nematophilum-mediated bacterial infection by promoting tail swelling and preventing constipation (PubMed:15268855). Component of the Mediator complex (By similarity). Interacts with let-19/mdt-13. Highest levels in embryos and larvae. Expressed in vulval precursor cells at the time of vulval determination. Belongs to the Mediator complex subunit 23 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 3 family. +Snake venom phospholipase A2 (PLA2) that shows myotoxic activities. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides (By similarity). a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) Binds 1 Ca(2+) ion. When tested as a monomer. Monomer. Expressed by the venom gland. Contains 7 disulfide bonds. Belongs to the phospholipase A2 family. Group II subfamily. D49 sub-subfamily. +Belongs to the UPF0306 family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. +Belongs to the LDH/MDH superfamily. MDH type 2 family. +Modulates transcription in response to changes in cellular NADH/NAD(+) redox state. Homodimer. Belongs to the transcriptional regulatory Rex family. +Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P). D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate from glycerone phosphate: step 1/1. Homodimer. Belongs to the triosephosphate isomerase family. +Iridoid glucosyltransferase acting exclusively on 7-deoxyloganetin. No activity with 7-deoxyloganetic acid. 7-deoxyloganetin + UDP-alpha-D-glucose = 7-deoxyloganin + H(+) + UDP kcat is 0.0355 sec(-1) for 7-deoxyloganetin. kcat is 0.0320 sec(-1) for UPD-glucose. Expressed in roots. Belongs to the UDP-glycosyltransferase family. +Inhibits the mitochondrial pyruvate dehydrogenase complex by phosphorylation of the E1 alpha subunit, thus contributing to the regulation of glucose metabolism. ATP + L-seryl-[pyruvate dehydrogenase E1 alpha subunit] = ADP + H(+) + O-phospho-L-seryl-[pyruvate dehydrogenase E1 alpha subunit] Belongs to the PDK/BCKDK protein kinase family. +Belongs to the UPF0735 family. +Catalyzes the condensation of ribulose 5-phosphate with formaldehyde to form 3-hexulose 6-phosphate. D-ribulose 5-phosphate + formaldehyde = D-arabino-hex-3-ulose 6-phosphate One-carbon metabolism; formaldehyde assimilation via RuMP pathway; D-fructose 6-phosphate from D-ribulose 5-phosphate and formaldehyde: step 1/2. Belongs to the HPS/KGPDC family. HPS subfamily. +Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA). NADP(+) + shikimate = 3-dehydroshikimate + H(+) + NADPH Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 4/7. Homodimer. Belongs to the shikimate dehydrogenase family. +Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + H(+) + holo-[ACP] Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxD subfamily. +Involved in intraflagellar protein (IFT) transport in photoreceptor cilia. Interacts with NINL (PubMed:18826961). Interacts with OFD1 (PubMed:19800048). Interacts with FAM161A (PubMed:22940612). Interacts with components of the IFT complex B (PubMed:21606596). In non- ciliated cells, localizes to the centrosome and its associated microtubule array (PubMed:17546029). Colocalizes with IFT complex A and B proteins in the connecting cilium in primary cilia of hTERT-RPE1 cells (PubMed:21606596). Widely expressed. The disease is caused by variants affecting the gene represented in this entry. Belongs to the LCA5 family. +Enone oxidoreductase involved in the biosynthesis of 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF or furaneol), the key flavor compound in strawberries. Can use both NADH and NADPH as the electron donor. 4-hydroxy-2,5-dimethyl-furan-3(2H)-one + NADP(+) = 4-hydroxy-5-methyl-2-methylenefuran-3(2H)-one + H(+) + NADPH kcat is 1.94 sec(-1) with EDHMF as substrate. kcat is 2.69 sec(-1) with HMPDF as substrate. kcat is 1.43 sec(-1) with BDHMF as substrate. Monomer. Up-regulated during ripening. The N-terminus is blocked. Belongs to the zinc-containing alcohol dehydrogenase family. Quinone oxidoreductase subfamily. +Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system. ATP + H2O + phosphate(out) = ADP + H(+) + 2 phosphate(in) The complex is composed of two ATP-binding proteins (PstB), two transmembrane proteins (PstC and PstA) and a solute-binding protein (PstS). Belongs to the ABC transporter superfamily. Phosphate importer (TC 3.A.1.7) family. Truncated N-terminus. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. Interacts with UvrB in an incision complex. This bacterium is considerably more resistant to UV and gamma irradiation than E.coli; the E.coli-like SOS regulon model is not an appropriate model for DNA repair in this cyanobacterium. Belongs to the UvrC family. +Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate + thiamine phosphate 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine phosphate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; thiamine diphosphate biosynthesis; thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1. Belongs to the thiamine-phosphate synthase family. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor, and NADPH and FADH(2) as the reductant. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP + H(+) + NADPH = (6S)-5,6,7,8-tetrahydrofolate + dTMP + NADP(+) Binds 4 FAD per tetramer. Each FAD binding site is formed by three monomers. Pyrimidine metabolism; dTTP biosynthesis. Homotetramer. Belongs to the thymidylate synthase ThyX family. +E3 ubiquitin ligase essential for DNA replication origin activation during S phase. Acts as a replication origin selector which selects the origins to be fired and catalyzes the multi-mono-ubiquitination of a subset of chromatin-bound ORC3 and ORC5 during S-phase. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Associates with ORC complex. Binds to chromatin; association is cell cycle-regulated, absent from mitotic chromosomes, is associated with chromatin from G1 and partially released from chromatin from mid S-phase. Association to chromatin is cell cycle-regulated, absent from mitotic chromosomes, is associated with chromatin from G1 and partially released from chromatin from mid S-phase. Auto-ubiquitinated. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Flavoenzyme involved in polyamine back-conversion (PubMed:24634478). Catalyzes the oxidation of the secondary amino group of polyamines, such as spermine, spermidine and their acetyl derivatives (PubMed:24634478). Substrate preference is spermine > spermidine > N(1)-acetylspermine > N(1)-acetylspermidine > norspermine > thermospermine (PubMed:24634478). No activity detected when putrescine is used as substrate (PubMed:24634478). May play a role in producing hydrogen peroxide for secondary wall thickening through lignin formation during anther development (Probable). H2O + O2 + spermine = 3-aminopropanal + H2O2 + spermidine H2O + N(1)-acetylspermine + O2 = 3-acetamidopropanal + H2O2 + spermidine H2O + norspermine + O2 = 3-aminopropanal + H2O2 + norspermidine H2O + O2 + spermidine = 3-aminopropanal + H2O2 + putrescine H2O + N(1)-acetylspermidine + O2 = 3-acetamidopropanal + H2O2 + putrescine H2O + O2 + thermospermine = 3-aminopropanal + H2O2 + spermidine Binds 1 FAD per subunit. Optimum pH is 7.0 with spermidine as substrate (PubMed:24634478). Optimum pH is 6.5 with spermine as substrate (PubMed:24634478). Optimum temperature is 37 degrees Celsius with spermidine as substrate (PubMed:24634478). Optimum temperature is 30 degrees Celsius with spermine as substrate (PubMed:24634478). Amine and polyamine degradation; spermidine degradation. Amine and polyamine degradation; spermine degradation. Specifically expressed during anther development, from the meiosis/tetrad pollen stage to the tricellular pollen stage, with a peak at the bicellular pollen stage. Belongs to the flavin monoamine oxidase family. Truncated N-terminus. Truncated N-terminus. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. +May be due to a competing donor splice site. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins (By similarity). Essential protein required for chloroplast development and integrity (PubMed:16705403, PubMed:17241447). Essential for Embryogenesis (PubMed:23548781). Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Component of the chloroplastic Clp protease core complex which consist of at least 16 proteins: CLPP4 (3 copies), CLPP5 (3 copies), CLPR4 (2 copies), ClpP1 (1 copy), CLPP6 (1 copy), CLPR2 (1 copy), CLPT1 (1 copy), CLPT2 (1 copy) and 3 copies of CLPP3 and/or CLPR1 and/or CLPR3 (PubMed:11278690, PubMed:14593120, PubMed:16766689, PubMed:16980539). Interacts with CHIP (PubMed:17241447). The core complex is organized in two heptameric rings, one containing CLPP3,4,5,6 in a 1:2:3:1 ratio and the other CLPP1 and CLPR1,2,3,4 in a 3:1:1:1:1 ratio (PubMed:21712416). Mostly expressed in leaves. Also detected in stems, and to a lower extent, in roots (at protein level). Repressed in darkness. Levels decrease in leaves during aging (at protein level). Slightly and transiently repressed by high light stress (at protein level). Ubiquitinated by CHIP. Embryo lethal when homozygous. Belongs to the peptidase S14 family. Extended N-terminus. Truncated N-terminus. +Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). Belongs to the AP2/ERF transcription factor family. RAV subfamily. +Essential cell division protein. May link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic. Part of a complex composed of FtsB, FtsL and FtsQ. Localizes to the division septum. Belongs to the FtsB family. +Interferes with one step of hemostasis (modulation of platelet aggregation, or coagulation cascade, for example). Heterodimer; disulfide-linked. Expressed by the venom gland. Shows greater sequence similarity to the alpha than beta subunits compared to other heterodimer snaclecs. Belongs to the snaclec family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. Binds 1 heme group covalently. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, petD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer (By similarity). Belongs to the cytochrome f family. +Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell. Belongs to the MinE family. +Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress. These functions might be dependent on each isozyme/isoform in each plant tissue. 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit. Binds 2 calcium ions per subunit. Slightly expressed in roots. By methyl jasmonate, a plant defense-related signaling molecule. There are 73 peroxidase genes in A.thaliana. Belongs to the peroxidase family. Classical plant (class III) peroxidase subfamily. +May act as a transcriptional coregulator during muscle development through its interaction with SNW1. Has lost its ancestral function as a Na,K-ATPase beta-subunit (By similarity). Associates with a SMAD7-transcriptional complex. Interacts with TOR1AIP1. Does not associate with known Na,K-ATPase alpha-subunits (By similarity). Interacts with SNW1. Detected in nuclear envelops. Expressed in skeletal muscle (at protein level). Expressed during postnatal development in skeletal muscle and heart. Expressed in embryo 15.5 dpc, onward. Belongs to the X(+)/potassium ATPases subunit beta family. +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily. +Catalyzes the NADPH-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5-carboxylate. L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 2/2. Belongs to the gamma-glutamyl phosphate reductase family. +Belongs to the UPF0235 family. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homotetramer; dimer of dimers. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Belongs to the bacterial ribosomal protein bL32 family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. Together with TatC, TatB is part of a receptor directly interacting with Tat signal peptides. TatB may form an oligomeric binding site that transiently accommodates folded Tat precursor proteins before their translocation. The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. Belongs to the TatB family. +Catalyzes the NAD(+)-dependent oxidation of formate to carbon dioxide. Formate oxidation is the final step in the methanol oxidation pathway in methylotrophic microorganisms. Has a role in the detoxification of exogenous formate in non-methylotrophic organisms. formate + NAD(+) = CO2 + NADH Cu(2+), Hg and p-chloromercuribenzoate are strong inhibitors of enzyme activity and Ca(2+), Mg(2+), Zn(2+), Mn(2+), Cd(2+) and Sn(2+) have no effect on activity indicating a cysteine residue in the protein is essential for enzyme activity or to maintain the proper structure of the enzyme. Nitrite and nitrate inhibit some enzyme activity, however cyanide, azide, thiocyanate and cyanate are strong inhibitors of the enzymatic reaction. The inhibition of cyanide is competitive with formate and reversible. Optimum pH is 7.5-8.5. Broad temperature optima between 45 and 55 degrees Celsius. Reaction rate increases steeply up to 55 degrees Celsius. 50% of activity lost after incubation for 20 minutes at 57 degrees Celsius. Thermal stability increases in the presence of glycerol. Homodimer. Expression is strongly induced by methanol, but is completely repressed in the presence of glucose. However, methanol induced expression is equally strong in cells grown on glucose when formate, methylamine or choline is added. No expression is detected in cells grown on glycerol. When formate, methylamine or choline is added to the culture medium of glycerol- or glucose-grown cells, they exhibit an induction of FDH1 expression. Is able to grow on methanol in a batch culture experiment, but its growth is greatly inhibited and a toxic level of formate accumulates in the medium. Formate is not detected in the medium in a methanol-limited chemostat culture but deletion mutant shows only one-fourth of the growth yield of the wild-type. Ideal catalyst for synthesizing chiral compounds of high enantiomeric purity from prochiral precursors due to a favorable thermodynamic equilibrium, the oxidation of formate to carbon dioxide while also reducing NAD to NADH. However, the necessesity for the presence of large quantities of the enzyme and its rapid inactivation under biotransformation conditions results in higher costs for the biocatalyst industry. In order to make this enzymatic reduction viable and to perform it on a larger scale a more efficient and cost effective process has been established. Site-directed mutagenesis has been effective in stabilizing this commercially important enzyme for its application in the biotransformation of trimethyl pyruvate to L-tert leucine. Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. FDH subfamily. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Regulates negatively salt stress responses and Na(+) homeostasis (PubMed:29272523, PubMed:30701352). Prevents Na(+) efflux, disturbs reactive oxygen species (ROS) homeostasis, and represses the expression of nuclear salt stress-responsive genes (PubMed:30701352). Involved in resistance to abiotic stress (PubMed:29272523). Heterodimers (PubMed:29272523). Interacts with CYSTM7 and WIH1/CYSTM13 (PubMed:29272523). Mostly expressed in leaves and flowers and, to a lower extent, in stems, siliques, shoots and roots. Induced by salt, cold and drought. Increased tolerance to high salinity with reduced reactive oxygen species (ROS) levels and associated with an over-activation of nuclear salt stress-responsive genes. Belongs to the CYSTM1 family. +Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to TFIIK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. In transcription, TFIIH has an essential role in transcription initiation. When the pre-initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module TFIIK controls the initiation of transcription. Component of the 7-subunit TFIIH core complex composed of XPB/SSL2, XPD/RAD3, SSL1, TFB1, TFB2, TFB4 and TFB5, which is active in NER. The core complex associates with the 3-subunit CTD-kinase module TFIIK composed of CCL1, KIN28 and TFB3 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription. Belongs to the TFB4 family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. +May modulate chromatin structure by regulation of nucleosome assembly/disassembly. The acidic domain is probably involved in the interaction with histones. Belongs to the nucleosome assembly protein (NAP) family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Belongs to the bacterial ribosomal protein bL27 family. +Required for chromosome condensation and partitioning. Homodimer. Contains large globular domains required for ATP hydrolysis at each terminus and a third globular domain forming a flexible SMC hinge near the middle of the molecule. These domains are separated by coiled-coil structures. Belongs to the SMC family. +Tropomyosin, in association with the troponin complex, plays a central role in the calcium dependent regulation of muscle contraction. Homodimer. The molecule is in a coiled coil structure that is formed by 2 polypeptide chains. The sequence exhibits a prominent seven-residues periodicity. Causes an allergic reaction in human. Binds to IgE of patients allergic to shellfish (mollusks and crustaceans). Belongs to the tropomyosin family. +Catalyzes the deamination of various vicinal amino-alcohols to oxo compounds. Allows this organism to utilize ethanolamine as the sole source of nitrogen and carbon in the presence of external vitamin B12. ethanolamine = acetaldehyde + NH4(+) Binds between the large and small subunits. Amine and polyamine degradation; ethanolamine degradation. The basic unit is a heterodimer which dimerizes to form tetramers. The heterotetramers trimerize; 6 large subunits form a core ring with 6 small subunits projecting outwards. Belongs to the EutC family. +an acyl phosphate + H2O = a carboxylate + H(+) + phosphate Belongs to the acylphosphatase family. +Beta-mannosyltransferase involved in cell wall biosynthesis. Initiates the beta-mannosylation of core N-linked glycans (By similarity). Belongs to the BMT family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Metalloproteinase. Inhibited by human TIMP1 and TIMP2 and the broad MMP inhibitors BB94 (Batimastat) and CT543. The conserved cysteine present in the cysteine-switch motif binds the catalytic zinc ion, thus inhibiting the enzyme. The dissociation of the cysteine from the zinc ion upon the activation-peptide release activates the enzyme. Belongs to the peptidase M10A family. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys) Binds 3 Mg(2+) ions per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +diphosphate + H2O = H(+) + 2 phosphate Belongs to the HAD-like hydrolase superfamily. PpaX family. +Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. 2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2 The D1/D2 heterodimer binds P680, chlorophylls that are the primary electron donor of PSII, and subsequent electron acceptors. It shares a non-heme iron and each subunit binds pheophytin, quinone, additional chlorophylls, carotenoids and lipids. D1 provides most of the ligands for the Mn4-Ca-O5 cluster of the oxygen-evolving complex (OEC). There is also a Cl(-1) ion associated with D1 and D2, which is required for oxygen evolution. The PSII complex binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. PSII is more abundant in mesophyll than bundle sheath cells and more abundant in grana than stroma lamellae in mesophyll cells. Phosphorylated in both bundle sheath and mesophyll cells, phosphorylation increases when cells are grown under high rather than low light regimes (70 vs 900 umol photons/m-2/s). PSII is subject to light-induced damage, in particular to D1. Damaged protein is degraded by Deg1 and FtsH proteases and replaced. In maize mesophyll cells D1 degradation is less extensive in grana (stacked) vs stroma (unstacked) lamellae, in part due to exclusion of FtsH from the grana. D1 degradation is faster in bundle sheath cells. Tyr-161 forms a radical intermediate that is referred to as redox-active TyrZ, YZ or Y-Z. C-terminally processed by CTPA; processing is essential to allow assembly of the oxygen-evolving complex and thus photosynthetic growth. 2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water. Herbicides such as atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer. Belongs to the reaction center PufL/M/PsbA/D family. +Catalyzes the deamination of three SAM-derived enzymatic products, namely 5'-deoxyadenosine, S-adenosyl-L-homocysteine, and 5'-methylthioadenosine, to produce the inosine analogs. Can also deaminate adenosine. The preferred substrate for this enzyme is 5'-deoxyadenosine, but all these substrates are efficiently deaminated. Likely functions in a S-adenosyl-L-methionine (SAM) recycling pathway from S-adenosyl-L-homocysteine (SAH) produced from SAM-dependent methylation reactions. May also be involved in the recycling of 5'-deoxyadenosine, whereupon the 5'-deoxyribose moiety of 5'-deoxyinosine is further metabolized to deoxyhexoses used for the biosynthesis of aromatic amino acids in methanogens. 5'-deoxyadenosine + H(+) + H2O = 5'-deoxyinosine + NH4(+) H(+) + H2O + S-adenosyl-L-homocysteine = NH4(+) + S-inosyl-L-homocysteine H(+) + H2O + S-methyl-5'-thioadenosine = NH4(+) + S-methyl-5'-thioinosine adenosine + H(+) + H2O = inosine + NH4(+) Binds 1 zinc ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis. Homotetramer. SAH is a product of SAM methyltransferases and is known to be a feedback inhibitor of these enzymes. As a result of this inhibition, organisms have evolved efficient enzymes to metabolize SAH via different pathways. The pathway found in methanogens differs from the canonical pathway, it uses the deamination of S-adenosyl-L-homocysteine to form S-inosyl-L-homocysteine for the regeneration of SAM from S-adenosyl-L-homocysteine. 5'-deoxyadenosine is a radical SAM enzyme reaction product which strongly inhibits radical SAM enzymes. A pathway for removing this product must be present in methanogens where the MTA/SAH nucleosidase which normally metabolizes this compound is absent. Belongs to the metallo-dependent hydrolases superfamily. MTA/SAH deaminase family. +Cation-chloride cotransporter which mediates the electroneutral transport of chloride, potassium and/or sodium ions across the membrane (PubMed:32294086). Plays a vital role in the regulation of ionic balance and cell volume. Inhibited by bumetanide (PubMed:7629105, PubMed:32081947). Activated by WNK3 (PubMed:21613606). Homodimer. Expressed in many tissues. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the SLC12A transporter family. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +(6S)-5,6,7,8-tetrahydrofolate + ATP + formate = (6S)-10-formyltetrahydrofolate + ADP + phosphate One-carbon metabolism; tetrahydrofolate interconversion. Belongs to the formate--tetrahydrofolate ligase family. +Partially overlaps NUP53. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. ATP + NAD(+) = ADP + H(+) + NADP(+) Belongs to the NAD kinase family. +Part of the accessory SecA2/SecY2 system specifically required for export of possible cell wall proteins. The central subunit of a protein translocation channel. Component of the accessory SecA2/SecY2 protein translocase complex required to export cell wall proteins. May form heterotrimers with SecE and SecG subunits. Belongs to the SecY/SEC61-alpha family. SecY2 subfamily. +Belongs to the UDP-glycosyltransferase family. This sequence is shorter than orthologs and has a completely different amino acid sequence after position 289 due to a single nucleotide insertion. This protein is not functional which could partially explain the failure of M.bovis derivatives to produce the full-length PGL. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Belongs to the DMRL synthase family. +Belongs to the UPF0201 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase gamma chain family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved. Distribution is 50-50. Belongs to the SecA family. +1-(5-phospho-beta-D-ribosyl)-ATP + H2O = 1-(5-phospho-beta-D-ribosyl)-5'-AMP + diphosphate + H(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 2/9. Belongs to the PRA-PH family. +Regulatory subunit (beta subunit) of the cytosolic type I platelet-activating factor (PAF) acetylhydrolase (PAF-AH (I)), an enzyme that catalyzes the hydrolyze of the acetyl group at the sn-2 position of PAF and its analogs and participates in PAF inactivation. Regulates the PAF-AH (I) activity in a catalytic dimer composition-dependent manner (By similarity). Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes such as the maintenance of Golgi integrity, the peripheral transport of microtubule fragments and the coupling of the nucleus and centrosome. May be required for proliferation of neuronal precursors and neuronal migration. Can self-associate. Component of the cytosolic PAF-AH (I) heterotetrameric enzyme, which is composed of PAFAH1B1 (beta), PAFAH1B2 (alpha2) and PAFAH1B3 (alpha1) subunits. The catalytic activity of the enzyme resides in the alpha1 (PAFAH1B3) and alpha2 (PAFAH1B2) subunits, whereas the beta subunit (PAFAH1B1) has regulatory activity. Trimer formation is not essential for the catalytic activity (By similarity). Interacts with dynein, dynactin, nde1 and ndel1. Localizes to the plus end of microtubules and to the centrosome. Dimerization mediated by the LisH domain may be required to activate dynein. Belongs to the WD repeat LIS1/nudF family. +May be involved in B-cell and macrophage adhesion processes. In B-cells, may act by coupling the B-cell receptor (BCR) to integrin activation. May play a role in src signaling pathway. Homodimer (By similarity). Interacts with PTPNS1. Part of a complex consisting of SKAP2, FYB1 and PTPNS1. Part of a complex consisting of SKAP2, FYB1 and LILRB3. May interact with actin (By similarity). Interacts with FYB1, which is required for SKAP2 protein stability. Interacts with LAT, GRB2, PTK2B and PRAM1. May interact with FYN, HCK and LYN. Interacts with FASLG. Ubiquitously expressed. Present in platelets (at protein level). By retinoic acid. The SH3 domain interacts with FYB1 and PTK2B. Phosphorylated in resting platelets. Phosphorylated by FYN on Tyr-261 upon T-cell activation (Probable). Dephosphorylated on Tyr-75 by PTPN22. Belongs to the SKAP family. +Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. [sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Monomer. Belongs to the methylthiotransferase family. MiaB subfamily. +Receptor for abscisic acid (ABA) required for ABA-mediated responses such as stomatal closure and germination inhibition. Inhibits the activity of group-A protein phosphatases type 2C (PP2Cs) in an ABA-independent manner but more efficiently when activated by ABA (PubMed:23844015, PubMed:21658606). Can be activated by both (-)-ABA and (+)-ABA (PubMed:23844015). Monomer (PubMed:21658606). Forms heterodimer with PYL13, thus antagonizing PP2Cs-binding and ABA-independent inhibition of PP2Cs (PubMed:24165892). Homodimer. Binds ABA on one subunit only. Binds to CARs protein in an ABA-independent manner, both at the plasma membrane and in the nucleus (By similarity). Interacts with ABI1 and HAB1, and possibly with other PP2Cs, in an ABA-independent manner (PubMed:19874541, PubMed:21658606). Localizes at the plasma membrane in the presence of a CAR protein. Upon interaction with ABA, the 'latch' and 'gate' loops change in conformation leading to a tight dimerization and the creation a surface that enables the receptor to dock into and inhibit the PP2C active site. Belongs to the PYR/PYL/RCAR abscisic acid intracellular receptor family. +Involved in the control of energetic metabolism and significantly contribute to cell fitness, especially under respiratory growth conditions. Belongs to the RGI1 family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP. Allosterically activated by GTP. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uracil: step 1/1. Belongs to the UPRTase family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Nitric oxide-sensitive repressor of genes involved in protecting the cell against nitrosative stress. May require iron for activity. Binds 1 [2Fe-2S] cluster per subunit. +Mediates electron transfer from NADH to oxygen, reducing it to water. This modular protein has 3 redox cofactors, in other organisms the same activity requires 2 or 3 proteins (By similarity). Binds 2 iron ions per subunit. By homology with NorV in E.coli, may be involved in nitric oxide detoxification. In the N-terminal section; belongs to the zinc metallo-hydrolase group 3 family. In the C-terminal section; belongs to the flavodoxin reductase family. +Catalyzes the interconversion between UDP-glucose and UDP-galactose (Ref.6, PubMed:16644739, PubMed:19754426). Cooperates with UGE3 in pollen development and with UGE4 in cell wall carbohydrate biosynthesis and growth (PubMed:17496119). UDP-alpha-D-glucose = UDP-alpha-D-galactose Enhanced activity by NaCl. Enhanced activity by NAD(+). Strongly inhibited by UDP. Optimum pH is 7.0-9.0. Optimum temperature is 40 degrees Celsius. Carbohydrate metabolism; galactose metabolism. Forms homodimers and heterodimers. Widely expressed (PubMed:12419184, PubMed:16644739, PubMed:17496119, Ref.6). Most highly expressed in stems and flowers (PubMed:17496119). No visible phenotype under normal growth conditions. Uge2 and uge3 double mutant is almost completely sterile. Uge2 and uge4 double mutant displays a reduction in rosette and root growth, hypocotyl elongation, and secondary hypocotyl thickening. Belongs to the NAD(P)-dependent epimerase/dehydratase family. +Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Binds vitamin B12 and delivers it to the periplasmic surface of BtuC. The complex is composed of two ATP-binding proteins (BtuD), two transmembrane proteins (BtuC) and a solute-binding protein (BtuF). Belongs to the BtuF family. +an acyl phosphate + H2O = a carboxylate + H(+) + phosphate Belongs to the acylphosphatase family. +RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit. Belongs to the RnpA family. +Putative deoxyribonuclease. Binds 2 divalent metal cations per subunit. Belongs to the metallo-dependent hydrolases superfamily. TatD-type hydrolase family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Homodimer. Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily. +Member of the two-component regulatory system DegS/DegU, which plays an important role in the transition growth phase. Involved in the control of expression of different cellular functions, including production of degradative enzymes such as the neutral and alkaline proteases, flagellum formation, biofilm formation, and competence for DNA uptake. Positively or negatively regulates expression of many different genes. The phosphorylated form is required for synthesis of degradative enzymes, flagellum formation and biofilm formation. The unphosphorylated form is required for expression of genetic competence, via induction of comK. Phosphorylated and unphosphorylated forms are both active and have different functions. A low concentration of phospho-DegU is sufficient to activate transcription of flagellar genes, but a higher concentration of phospho-DegU is required for transcription of other genes. Phosphorylated DegU is stabilized by DegR. Phosphorylated DegU activates its own expression. The N-terminal region acts as an inhibitor, whereas the C-terminal region carries enhancing activity. Phosphorylated and dephosphorylated by DegS. +Nitrate reductase is a key enzyme involved in the first step of nitrate assimilation in plants, fungi and bacteria. H2O + NAD(+) + nitrite = H(+) + NADH + nitrate Binds 1 FAD per subunit. Binds 1 heme group per subunit. Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit. Homodimer. Belongs to the nitrate reductase family. +Plays a role in electron transfer. The fas operon encodes genes involved in cytokinin production and in host plant fasciation (leafy gall). Binds 1 [3Fe-4S] cluster. During the interaction with host plants. In the C-terminal section; belongs to the transketolase family. +Plays a crucial role in elastic fiber formation in tissue, and in the formation of ultrastructural connections between elastic laminae and smooth muscle cells in the aorta, therefore participates in terminal differentiation and maturation of smooth muscle cell (SMC) and in the mechanical properties and wall integrity maintenance of the aorta (PubMed:16478991, PubMed:19855011, PubMed:20019329, PubMed:26486174, PubMed:26711913, PubMed:28508064). In addition, is involved in the control of collagen fibril assembly in tissue throught proteolytic activation of LOX leading to cross- linking of collagen and elastin (PubMed:26690653, PubMed:26711913, PubMed:26220971, PubMed:26178373). Also promotes ELN coacervation and participates in the deposition of ELN coacervates on to microfibrils but also regulates ELN cross- linking through LOX interaction (PubMed:17324935). Moreover adheres to the cells through heparin binding in a calcium-dependent manner and regulates vascularlar smooth muscle cells proliferation through angiotensin signaling (PubMed:23636094). Homodimer; disulfide-linked (By similarity). Multimer; allows heparin binding (By similarity). Monomer (PubMed:17324935). Binds preferentially to p53 mutants (PubMed:10380882). Interacts with FBN1 (via N-terminal domain); this interaction inhibits EFEMP2 binding to LOX and ELN (By similarity). Interacts with ELN with moderate affinity; this interaction regulates ELN self-assembly maturation stage (PubMed:16478991, PubMed:17324935). Interacts with PCOLCE (PubMed:26220971). Interacts with collagen type IV trimer (COL4A1-COL4A1-COL4A2), NID2 and moderately with COL15A1-derived endostatin (PubMed:17324935). Interacts with EMILIN1; this interaction promotes the incorporation of EFEMP2 into the extracellular matrix (PubMed:28717224). Interacts with LTBP4; the LTBP4 long form (LTBP4L) has a stronger binding affinity than the LTBP4 short form and the LTBP4 long form promotes fibrillar deposition of EFEMP2 (PubMed:25713297). Interacts with LOX (via propeptide); this interaction is strong and facilitates formation of ternary complexes with ELN during elastic fiber assembly; this interaction limits interaction of EFEMP2 with FBLN5 (By similarity). Interacts with PITX2 (By similarity). Interacts with FBLN5 with moderate affinity (By similarity). Interacts with LOXL1 (via propeptide), LTBP1 and TGFB1 stronger than with LOXL2 and LTBP3 (By similarity). Localizes on the microfibrils surrounding ELN cores. Expressed in elastic fibers of the skin, near the dermal-epidermal junction, surrounding the hair follicles and throughout the dermis (PubMed:26178373). Expressed in tendon around tenocytes (PubMed:26711913). Prominently expressed in cartilage, bone, perichondrium and ligaments. Also detected in bone marrow stroma (PubMed:26690653). Expressed in aorta, lung, and esophagus (PubMed:17324935). At E(15), found in the perichondrium of the developing bone. At E(14) detected in the lung parenchyma. N-glycosylated; contains mostly complex-type glycans. Not O-glycosylated. Cleaved by ELANE; produces a 50-55 kDa fragment. Cleaved by MMP2 and MMP9; produces several fragments. Homozygous mice for the EFEMP2 gene appear to be outwardly normal (PubMed:16478991, PubMed:28508064). Homozygous mice exhibit severe lung and vascular defects including emphysema, artery tortuosity, irregularity, aneurysm, rupture, and resulting hemorrhages (PubMed:16478991, PubMed:19855011, PubMed:26178373, PubMed:28508064). Mice died perinatally (PubMed:16478991, PubMed:19855011). Mice with conditional knockout of EFEMP2, in vascular smooth muscle, grow normally, are fertile and exhibit an arterial stiffness (PubMed:19855011). Mice with conditional knockout of EFEMP2, in endothelial cell (EC) are healthy with an normal aorta (PubMed:20019329). Mice with conditional knockout of EFEMP2, in smooth muscle cells, die spontaneously at approximately 2 months of age despite absence of embryonic or neonatal lethality. Aortae exhibit large aneurysms exclusively in the ascending aorta. Aneurysms are observed with complete penetrance (PubMed:20019329, PubMed:26486174, PubMed:23636094, PubMed:26220971). Homozygous mice for the EFEMP2 gene die within 1-2 days after birth. Embryos at 19 dpc show bilateral forelimb contractures (PubMed:26711913, PubMed:26690653). Newborn homozygous mice demonstrate normal morphology of the skeleton (PubMed:26690653). Aneurysm may be prevent with postnatal administration of ACE inhibitor and/or angiotensin II receptor blocker (ARB). Belongs to the fibulin family. +Negative regulator of sphingolipid synthesis. Widely expressed. Expressed in adult and fetal heart, brain, lung, liver, skeletal muscle and kidney. Expressed in adult pancreas and placenta and in fetal spleen abd thymus. Expressed at intermediate level in pancreas, placenta and brain but low in skeletal muscle and lung. Belongs to the ORM family. +Specifically methylates the cytosine at position 1962 (m5C1962) of 23S rRNA. cytidine(1962) in 23S rRNA + S-adenosyl-L-methionine = 5-methylcytidine(1962) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RlmI family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Partially overlaps DDR48. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Rho GTPase activating protein that suppresses F-actin polymerization by inhibiting Rho. Rho GTPase activating proteins act by converting Rho-type GTPases to an inactive GDP-bound state. Plays a key role in tissue tension and 3D tissue shape by regulating cortical actomyosin network formation. Acts downstream of YAP1 and inhibits actin polymerization, which in turn reduces nuclear localization of YAP1. Regulates cell shape, spreading, and migration (By similarity). Interacts with MPHOSPH6. Widely expressed: expressed in most organs, except small intestine. +Binds the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +Catalyzes the oxidation of sulfhydryl groups in peptide and protein thiols to disulfides with the reduction of oxygen to hydrogen peroxide. May contribute to disulfide bond formation in a variety of secreted proteins (By similarity). O2 + 2 R'C(R)SH = H2O2 + R'C(R)S-S(R)CR' +Plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons. Its association with pi-bodies suggests a participation in the primary piRNAs metabolic process. Required prior to the pachytene stage to facilitate the production of multiple types of piRNAs, including those associated with repeats involved in the regulation of retrotransposons. May act by mediating protein-protein interactions during germ cell maturation (By similarity). Interacts with DDX4, PIWIL1, RANBP9 and TDRD1. Component of the meiotic nuage, also named P granule, a germ-cell-specific organelle required to repress transposon activity during meiosis. Specifically localizes to pi-bodies, a subset of the nuage which contains primary piRNAs (By similarity). +Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate. ATP + L-glutamate = ADP + L-glutamyl 5-phosphate Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 1/2. Belongs to the glutamate 5-kinase family. +Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL. ATP + H2O + L-glutamine + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide = 2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ADP + H(+) + L-glutamate + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole from N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide: step 1/2. Monomer. Part of the FGAM synthase complex composed of 1 PurL, 1 PurQ and 2 PurS subunits. Belongs to the FGAMS family. +Involved in the RNA silencing pathway. Cleaves double-stranded RNA to produce microRNAs (miRNAs) of 21-24 nucleotides which target the selective destruction of complementary RNAs. Regulates by this way the development of the plant. May not be involved in small interfering RNAs (siRNAs) production. May interact with ARGONAUTE1 or PINHEAD through their common PAZ domains. Severe dwarfism and dark green color. Seedling viability compromised. Belongs to the helicase family. Dicer subfamily. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides (By similarity). Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low. Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids. Binds 2 manganese ions per subunit. Belongs to the peptidase M17 family. +Belongs to the bacterial ribosomal protein bL33 family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis: the synthesis of N-acetylglutamate from glutamate and acetyl-CoA as the acetyl donor, and of ornithine by transacetylation between N(2)-acetylornithine and glutamate. L-glutamate + N(2)-acetyl-L-ornithine = L-ornithine + N-acetyl-L-glutamate acetyl-CoA + L-glutamate = CoA + H(+) + N-acetyl-L-glutamate Amino-acid biosynthesis; L-arginine biosynthesis; L-ornithine and N-acetyl-L-glutamate from L-glutamate and N(2)-acetyl-L-ornithine (cyclic): step 1/1. Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 1/4. Heterotetramer of two alpha and two beta chains. Some bacteria possess a monofunctional ArgJ, i.e. capable of catalyzing only the fifth step of the arginine biosynthetic pathway. Belongs to the ArgJ family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Binds 1 Fe(2+) ion per subunit. Belongs to the OGFOD3 family. +Synthesizes alpha-1,4-glucan chains using ADP-glucose. [(1->4)-alpha-D-glucosyl](n) + ADP-alpha-D-glucose = [(1->4)-alpha-D-glucosyl](n+1) + ADP + H(+) Glycan biosynthesis; glycogen biosynthesis. Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily. +Has lytic and hemolytic activities. Its hemolytic activity is inhibited by phospholipids, but not by cholesterol. Has antibacterial activity with a broad spectrum against various species of bacteria including both Gram-positive and Gram-negative groups. Has ichthyotoxic activity. Exists as aggregates of 3-4 molecules. Expressed by the skin glands. LD(50) is 4.0 ug/ml against killifish. Belongs to the grammistin family. Group 2 subfamily. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +(R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Belongs to the prokaryotic pantothenate kinase family. +Expressed at high levels in normal and psoriatic skin, but not in normal keratinocytes, A-431 cells, or any of the other cell lines or tissues tested. +Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+) Binds 1 dipyrromethane group covalently. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. The porphobilinogen subunits are added to the dipyrromethane group. Belongs to the HMBS family. +A terminal oxidase that catalyzes quinol-dependent, Na(+)-independent oxygen uptake. Prefers menadiol over other quinols although ubiquinol was not tested (PubMed:8626304). Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H(2)O, transferring 1 proton/electron. 2 a ubiquinol + n H(+)(in) + O2 = 2 a ubiquinone + n H(+)(out) + 2 H2O May bind up to 3 heme groups per complex. Inhibited by cyanide; is more sensitive to cyanide than cytochrome bd-I oxidase. Energy metabolism; oxidative phosphorylation. Heterodimer of subunits I and II. Induced when bacterial cultures reach stationary phase; synthesis is triggered by phosphate starvation or a shift from aerobic to anaerobic conditions. 3-fold decreased ubiquinone levels but no change in redox levels of the ubiquinone pool (in aerobically grown minimal medium with glucose). Belongs to the cytochrome ubiquinol oxidase subunit 2 family. Was originally thought not to translocate protons. +Involved in innate immunity. Required for the expression of defense-related genes PR1A, LOX2 and CHS1 upon biotic stresses. Required for basal resistance to the fungal blast (M.grisea), bacterial blight (X.oryzae pv. oryzae, Xoo) and the herbivorous insect brown planthopper (N.lugens, BPH). May be involved in several defense signaling pathways. Involved in the promotion of seed germination. Required for the expression of alpha-amylase genes during seed germination (By similarity). Involved in resistance against the herbivorous insect brown planthopper (N.lugens, BPH). Member of the BPH3 (BPH resistance locus 3) cluster which contains LECRK1, LECRK2 and LECRK3 (PubMed:25485617). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +Belongs to the UPF0306 family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Expressed only in the forespore compartment of sporulating cells. Belongs to the Tlp family. +Oxidoreductase involved in lignan biosynthesis (PubMed:11606193). Catalyzes the NADPH-dependent reduction of phenylcoumaran benzylic ethers (PubMed:11606193). Converts dehydrodiconiferyl alcohol (DDC) to isodihydrodehydrodiconiferyl alcohol (IDDDC) (PubMed:11606193). (-)-dehydrodiconiferyl alcohol + H(+) + NADPH = (S)-isodihydrodehydrodiconiferyl alcohol + NADP(+) (+)-dehydrodiconiferyl alcohol + H(+) + NADPH = (R)-isodihydrodehydrodiconiferyl alcohol + NADP(+) May cause an allergic reaction in human (PubMed:11606193). Binds to IgE from patients allergic to pear fruit (PubMed:11606193). Induces histamine release from basophils of patient allergic to the pear fruit protein Pyr c 5 (PubMed:11606193). Exhibits cross-reactivity with IgE from patients allergic to other fruits, vegetables and birch pollen (PubMed:11606193). May be a minor allergen of pear fruit (PubMed:11606193). Belongs to the NmrA-type oxidoreductase family. Isoflavone reductase subfamily. +Antitoxin component of a type II toxin-antitoxin (TA) system. A labile antitoxin (half-life of 5.9 minutes) that inhibits the endonuclease activity of cognate toxin LsoA but not that of non-cognate toxin RnlA. Can form a complex with cognate toxin LsoA. This plasmid is only found in Sakai-derived strains of E.coli O157. +A major RuBisCO chaperone. Acts after GroEL-GroES chaperonin to fold and/or assemble the large subunit of RuBisCO (ccbL, rbcL). Cooperates with RbcX in RbcL folding, plays the major role in assembly of dimers into RbcL(8)-Raf1(8) intermediate complexes. RbcS replaces Raf1, leading to holoenzyme formation. Required for optimal reconstitution of RuBisCO upon expression of rbcL-rbcS subunits in E.coli. Only interacts with the large subunit (cbbL, rbcL). Probably acts in the final stages of RuBisCO assembly, possibly participating in the addition of the small subunit (ccbS, rbcS). Homodimer. Forms an RbcL(8)-Raf1(8) complex. Forms complexes of many stoichiometries with RbcL with and without RbcS. RbcX and Raf1 can bind simultaneously to RbcL. Interacts with the large subunit of RuBisCO in the cytoplasm. Has 3 domains, the N-terminal alpha-helical domain, an extended flexible linker and the C-terminal beta-sheet domain. The 2 C-terminal beta-sheet domains are swapped and pack against each other to form the dimer interface. Belongs to the RAF family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity and assembly of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Interacts with TMEM242 (By similarity). Belongs to the complex I subunit 2 family. +Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. ATP + CoA + succinate = ADP + phosphate + succinyl-CoA Binds 1 Mg(2+) ion per subunit. Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. Heterotetramer of two alpha and two beta subunits. Belongs to the succinate/malate CoA ligase beta subunit family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Removes the pyruvyl group from chorismate, with concomitant aromatization of the ring, to provide 4-hydroxybenzoate (4HB) for the ubiquinone pathway. chorismate = 4-hydroxybenzoate + pyruvate Cofactor biosynthesis; ubiquinone biosynthesis. Monomer. Belongs to the UbiC family. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the cyclophilin-type PPIase family. +Belongs to the helicase family. SKI2 subfamily. +Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids. Binds 2 magnesium ions per subunit. Homodimer. Belongs to the UPP synthase family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7. Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family. +Seems to be required for the assembly of the photosystem I complex. Belongs to the Ycf4 family. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'-nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Magnesium is required for nucleotidyltransferase activity. Nickel for phosphatase activity. Monomer. Can also form homodimers and oligomers. Comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain associated with both phosphodiesterase and phosphatase activities. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 1 subfamily. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +The different products prevent the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) and IFN-gamma signaling pathways. They inhibit IFN-alpha/beta induced tyrosine phosphorylation of STAT1 and STAT2. Blocking the IFN-alpha/beta pathway requires binding to STAT1 in the cytoplasm. They inhibit IFN-gamma induced serine phosphorylation of STAT1. Block the IFN-gamma pathway by binding to and stabilizing the parallel form of the STAT1 dimer, further inducing high-molecular-weight complex formation and inhibition of transcription by IFN-gamma. May also have a role in preventing the cell to enter apoptosis. Modulate regulation of viral transcription and replication. Overexpression inhibits the viral RNA polymerase. The absence of all C', C and Y1 proteins leads to viral delayed growth. Plays an important role in virion particles release. Modulates virion shape. The different isoforms interact (via C-terminus) with unphosphorylated and phosphorylated human STAT1 (via N-terminus), favoring the formation of parallel STAT1 homodimers. The different isoforms do not interact with host STAT2. C protein interacts with L protein; this interaction has an inhibitory effect on viral transcription and replication. Protein C' seems to localize around the Golgi. The disordered region at the N-terminus is involved in C protein self-degradation in trans. This self-degradation of C protein may play a role in the regulation of viral RNA synthesis. The disordered region at the N-terminus is also involved in the host STAT1 degradation in order to counteract the host innate antiviral response. Protein Y1 is produced not only by alternative initiation, but also by proteolytic cleavage of C'. Only alternative initiation is detected in vitro, whereas in vivo cleavage seems to be predominant. The C protein is found in virion at a ratio of approximately 40 molecules per virion, presumably associated with the nucleocapsid. The P/V/C gene has two overlapping open reading frames. One encodes the P/V/W proteins and the other the C/Y proteins. The initiator methionine is coded by an unusual start codon ACG. Most abundant isoform in infected cells. Belongs to the respirovirus protein C family. The C' protein uses an unusual ACG start codon. +Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. Binds to the 16 bp palindromic sequence 5'-CTGTATATATATACAG-3'. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair. Hydrolysis of Ala-|-Gly bond in repressor LexA. Homodimer. Belongs to the peptidase S24 family. +PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin. hnu + oxidized [2Fe-2S]-[ferredoxin] + reduced [plastocyanin] = oxidized [plastocyanin] + reduced [2Fe-2S]-[ferredoxin] P700 is a chlorophyll a/chlorophyll a' dimer, A0 is one or more chlorophyll a, A1 is one or both phylloquinones and FX is a shared 4Fe-4S iron-sulfur center. The PsaA/B heterodimer binds the P700 chlorophyll special pair and subsequent electron acceptors. PSI consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The eukaryotic PSI reaction center is composed of at least 11 subunits. Belongs to the PsaA/PsaB family. +Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. Contains one covalently linked tetrapyrrole chromophore. In the N-terminal section; belongs to the phytochrome family. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +Snake venom phospholipase A2 (PLA2) that displays moderate myotoxic activity in vivo, and cytotoxic activity in vitro. In vitro, shows anticoagulant activity on human plasma and in mice causes inflammatory cell infiltration and myonecrosis in the gastrocnemius muscles of CD-1 mice 3 hours after injection (100 ug). PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) Homopentamer. Expressed by the venom gland. Belongs to the phospholipase A2 family. Group I subfamily. D49 sub-subfamily. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress. These functions might be dependent on each isozyme/isoform in each plant tissue. 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit. Binds 2 calcium ions per subunit. Belongs to the peroxidase family. Classical plant (class III) peroxidase subfamily. +Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. Monomer. Belongs to the glycosyl hydrolase 5 (cellulase A) family. +Catalyzes the NAD(+)-dependent oxidation of L-carnitine to 3-dehydrocarnitine. Is specific for L-carnitine and NAD(+) as substrates. D,L-3-hydroxybutyrate, L-lactate, ethanol, L-malate and D,L-isocitrate are not substrates. Is involved in a L-carnitine degradation pathway that allows P.aeruginosa to grow on L-carnitine as the sole source of carbon and nitrogen. carnitine + NAD(+) = 3-dehydrocarnitine + H(+) + NADH Analogs of L-carnitine such as D-carnitine, glycine betaine and choline, are competitive inhibitors of L-carnitine oxidation. Optimum pH is 9-9.5 for the forward reaction (oxidation) and 7.0 for the reverse reaction (reduction). Optimum temperature is 35 degrees Celsius for the reaction in both directions. Amine and polyamine metabolism; carnitine metabolism. Homodimer. Highly induced by carnitine via the CdhR transcriptional regulator. Not induced by glycine betaine or pyruvate. Cells are incapable of growth on carnitine. Belongs to the 3-hydroxyacyl-CoA dehydrogenase family. L-carnitine dehydrogenase subfamily. +Involved in maceration and soft-rotting of plant tissue. Hydrolyzes the 1,4-alpha glycosidic bonds of de-esterified pectate in the smooth region of the plant cell wall. (1,4-alpha-D-galacturonosyl)n+m + H2O = (1,4-alpha-D-galacturonosyl)n + (1,4-alpha-D-galacturonosyl)m. Belongs to the glycosyl hydrolase 28 family. +Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems. The G(s) protein is involved in hormonal regulation of adenylate cyclase: it activates the cyclase. Participates in olfactory signal transduction. G proteins are composed of 3 units; alpha, beta and gamma. The alpha chain contains the guanine nucleotide binding site. Belongs to the G-alpha family. G(s) subfamily. +Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units. Binds 1 Ca(2+) ion per subunit. Binds 1 Cl(-) ion per subunit. Monomer. Midgut and fat body. Expressed during second and third larval instars, but not in the adult. Belongs to the glycosyl hydrolase 13 family. +RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs. Homohexamer. Belongs to the Hfq family. +Catalyzes the ATP-dependent condensation of GlcN-Ins and L-cysteine to form L-Cys-GlcN-Ins. 1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside + ATP + L-cysteine = 1D-myo-inositol 2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranoside + AMP + diphosphate + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. MshC subfamily. +Binds, preferentially, to the Maundrell ARS consensus sequence within ARS3002. Interacts with mcm10. +Belongs to the FAM151 family. +Gamma chains make up the fetal hemoglobin F, in combination with alpha chains. Heterotetramer of two alpha chains and two gamma chains in fetal hemoglobin (Hb F). Red blood cells. Belongs to the globin family. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. Belongs to the FlgH family. +Transcriptional regulator involved in the global control of Brucella gene expression. Mediates the effects of the quorum sensing autoinducer C12-HSL (N-dodecanoyl-homoserine lactone) on a large and diverse number of genes. +Catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PNAG, also referred to as PIA), a biofilm adhesin polysaccharide. N-deacetylation is crucial for attachment of the polysaccharide to the bacterial cell surface; it leads to the introduction of positive charges in the otherwise neutral PIA polymer, allowing electrostatic interactions (By similarity). Attached to the cell surface. Belongs to the polysaccharide deacetylase family. +Catalyzes the NADPH-dependent reduction of N-acetyl-5-glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde. N-acetyl-L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + N-acetyl-L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 3/4. Belongs to the NAGSA dehydrogenase family. Type 1 subfamily. +Specifically catalyzes the beta-elimination of phosphate from L-phosphoserine and the beta-addition of sulfite to the dehydroalanine intermediate to produce L-cysteate. Does not display threonine synthase activity like the paralog protein ThrC. H(+) + O-phospho-L-serine + sulfite = L-cysteate + phosphate Is inhibited by AP3 (DL-2-amino-3-phosphonopropionate) and, to a lesser extent, by L-aspartate or AP4 (DL-2-amino-4-phosphonobutyrate). Is also inhibited by EDTA in vitro. Cofactor biosynthesis; coenzyme M biosynthesis. Homotrimer. Belongs to the threonine synthase family. Cysteate synthase subfamily. +Histone-binding protein required for histone H4 methyltransferase activity of PRMT5. Specifically required for histone H4 'Arg-3' methylation mediated by PRMT5, but not histone H3 'Arg-8' methylation, suggesting that it modulates the substrate specificity of PRMT5. Specifically interacts with the N-terminus of histone H4 but not with histone H3, suggesting that it acts by promoting the association between histone H4 and PRMT5. Involved in CCNE1 promoter repression (By similarity). Plays a role in muscle cell differentiation by modulating the recruitment of PRMT5 to the promoter of genes involved in the coordination between cell cycle exit and muscle differentiation (By similarity). Interacts with PRMT5. Interacts with histone H4; specifically interacts with the N-terminus of histone H4 but not with histone H3. Interacts with CBFB. Found in a complex with PRMT5, RUNX1 and CBFB. +Acts as a co-chaperone for HSP90AA1. Mediates the association of the molecular chaperones HSPA8/HSC70 and HSP90. Probably forms a complex composed of chaperones HSP90 and HSP70, co-chaperones STIP1/HOP, CDC37, PPP5C, PTGES3/p23, TSC1 and client protein TSC2. Forms a complex with HSPA8/HSC70, HSPCA/HSP-86 and HSPCB/HSP-84. Interacts with PACRG. Interacts with EEF1AKMT3 (By similarity). Interacts with HSP90/HSP90AA1; the interaction dissociates the PPP5C:HSP90AA1 interaction. Interacts with FLCN, FNIP1 and FNIP2. Interacts with HSPA8/HSC70. Interacts with HSP90AB1; upon SMYD2-dependent HSP90AB1 methylation. The TPR 1 repeat interacts with the C-terminal of HSC70. The TPR 4, 5 and 6 repeats (also called TPR2A domain) and TPR 7, 8 and 9 repeats (also called TPR2B domain) interact with HSP90 (By similarity). +Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions. Belongs to the ELOF1 family. +One nucleotide addition (T) at position 1821 changed the reading frame of the known B gene by erasing the stop codon and consequently fusing the B gene with C gene. +Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor. (S)-dihydroorotate + NAD(+) = H(+) + NADH + orotate Binds 1 FMN per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (NAD(+) route): step 1/1. Heterotetramer of 2 PyrK and 2 PyrD type B subunits. Belongs to the dihydroorotate dehydrogenase family. Type 1 subfamily. +Belongs to the UPF0346 family. +Expression of the protease correlates with blood-feeding and suggests a role for the protease in blood digestion. At low level in the third and fourth-stage larvae, and abundant in adult worms. Belongs to the peptidase C1 family. +Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides. Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low. Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids. Binds 2 manganese ions per subunit. Belongs to the peptidase M17 family. +Maintains high levels of reduced glutathione in the chloroplast. 2 glutathione + NADP(+) = glutathione disulfide + H(+) + NADPH Binds 1 FAD per subunit. The active site is a redox-active disulfide bond. Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. +Strong inhibitor of fluid secretion by the Malpighian tubules. Uses cGMP as a second messenger and inhibits fluid production by decreasing cAMP concentration. Reduces isosmotic fluid secretion by inhibiting electroneutral and non-conductive transport pathways. Reverses the stimulatory effect of diuretic hormone I. To T.molitor cuticular protein LPCP29 C-terminal region. +Transcription factor that, in osteoblasts, activates the decoy receptor for RANKL, TNFRSF11B, which in turn regulates osteoclast differentiation. Acts in synergy with the Wnt-responsive LEF1/CTNNB1 pathway. Recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). Forms either a homodimer or a heterodimer with a related family member (By similarity). Interacts with SIX1 (PubMed:27923061). Belongs to the COE family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. Interacts with UvrB in an incision complex. Belongs to the UvrC family. +Belongs to the UPF0374 family. +The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. Belongs to the RecF family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion. alpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + NH4(+) Allosterically activated by N-acetylglucosamine 6-phosphate (GlcNAc6P). Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 5/5. Homohexamer. Belongs to the glucosamine/galactosamine-6-phosphate isomerase family. NagB subfamily. +Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS8 family. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +Belongs to the nematode receptor-like protein sra family. +FMRFamides and FMRFamide-like peptides are neuropeptides. Belongs to the FARP (FMRF amide related peptide) family. +Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. (2E,6E,10E)-geranylgeranyl diphosphate + sn-glycerol 1-phosphate = diphosphate + sn-3-O-(geranylgeranyl)glycerol 1-phosphate Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the GGGP/HepGP synthase family. Group II subfamily. +Does not exhibit cutinase activity. Belongs to the cutinase family. +Tachykinins are active peptides which excite neurons, evoke behavioral responses, are potent vasodilators and secretagogues, and contract (directly or indirectly) many smooth muscles. Associated with sex-specific or age/division of labor-selective behavior and/or physiology of honeybees. Strong expression was detected in the queen and forager heads, while weak and almost no significant expression was detected in the nurse and drone heads, respectively. Incompletely processed peptide. Partial peptide processing. Partial peptide processing. Partial peptide processing. Belongs to the tachykinin family. Intron retention. Intron retention. Intron retention. +May catalyze the synthesis of indole-3-acetic acid (IAA)-amino acid conjugates, providing a mechanism for the plant to cope with the presence of excess auxin. Expressed in etiolated seedlings and roots. At low level by auxin. Belongs to the IAA-amido conjugating enzyme family. +Translocates 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol (alpha-L-Ara4N-phosphoundecaprenol) from the cytoplasmic to the periplasmic side of the inner membrane. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Heterodimer of ArnE and ArnF. Belongs to the ArnE family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Can also synthesize a number of adenyl dinucleotides (in particular AppppA). These dinucleotides have been proposed to act as modulators of the heat-shock response and stress response. ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys) Binds 3 Mg(2+) ions per subunit. The third one is coordinated by ATP. Homodimer. There are two lysyl-tRNA ligases in E.coli: lysS is expressed constitutively, while lysU is heat inducible. Belongs to the class-II aminoacyl-tRNA synthetase family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +Probable transcription factor. Expressed in the endoderm of mid-gastrula embryos. At neurula stage, expressed in the notochord and in ciliated cells of the epithelium. During tailbud stages, expressed throughout the endoderm as well as in the notochord and neural floor plate. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Cell wall formation. NADP(+) + UDP-N-acetyl-alpha-D-muramate = H(+) + NADPH + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurB family. +Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and/or repair of Fe-S clusters in biosynthetic enzymes. Belongs to the Fe(2+)-trafficking protein family. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. +Belongs to the UPF0482 family. +Catalyzes the conversion of 7,8-dihydroneopterin triphosphate (H2NTP) to 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) and acetaldehyde. 7,8-dihydroneopterin 3'-triphosphate + H2O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + 2 H(+) + triphosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. The active site is at the interface between 2 subunits. The proton acceptor Cys is on one subunit, and the charge relay system is on the other subunit (By similarity). Belongs to the PTPS family. QueD subfamily. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and probably 6 low-molecular weight proteins. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Belongs to the TACO1 family. +Required for formate dehydrogenase (FDH) activity. Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH. Belongs to the FdhD family. +This protein is either not expressed, expressed at low levels or rapidly degraded. To the N-terminal of nitrogenase iron protein (NifH). Has lost the ATP-binding site. +Belongs to the universal ribosomal protein uS2 family. +This form constitutes the precursor of the pore-forming protein: upon cleavage, the released N-terminal moiety (Gasdermin-A2, N-terminal) binds to membranes and forms pores, triggering cell death. Pore-forming protein that causes membrane permeabilization and pyroptosis. Released upon cleavage of Gasdermin-A2, and binds to membrane inner leaflet lipids. Homooligomerizes within the membrane and forms pores of 10-15 nanometers (nm) of inner diameter, triggering pyroptosis. Binds to membrane inner leaflet lipids, such as phosphatidylinositol (4,5)-bisphosphate. The functional mechanisms and physiological proteases that cleave and activate this pore-forming protein are unknown. The full-length protein before cleavage is inactive: intramolecular interactions between N- and C-terminal domains mediate autoinhibition in the absence of activation signal. The intrinsic pyroptosis-inducing activity is carried by the released N-terminal moiety (Gasdermin-A2, N-terminal). Homooligomer; homooligomeric ring-shaped pore complex containing 27-28 subunits when inserted in the membrane. Expressed in the gastrointestinal tract, specifically from the middle to the upper region of the gastric mucosa in the glandular stomach. Expression is first detected at 16.6-17.5 dpc. Intramolecular interactions between N- and C-terminal domains are important for autoinhibition in the absence of activation signal. The intrinsic pyroptosis-inducing activity is carried by the N-terminal domain. Cleavage relieves autoinhibition by releasing the N-terminal moiety (Gasdermin-A2, N-terminal) that initiates pyroptosis. Belongs to the gasdermin family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges. Belongs to the universal ribosomal protein uL14 family. +Part of the ABC transporter complex DrrABC involved in doxorubicin resistance. Probably responsible for the translocation of the substrate across the membrane. The complex is composed of two ATP-binding proteins (DrrA) and two transmembrane proteins (DrrB and DrrC). Was identified as a high-confidence drug target. Belongs to the ABC-2 integral membrane protein family. +Involved in the biosynthesis of germacrene-derived sesquiterpene lactones (PubMed:30468448). Component of the parthenolide biosynthetic pathway; parthenolide and conjugates are promising anti-cancer drugs highly active against colon cancer cells (PubMed:30468448). Hydroxylates germacrene A acid to 6-alpha-hydroxy-germacrene A acid, a precursor of sesquiterpene lactones that spontaneously undergoes a lactonization which yields costunolide (PubMed:24704560). germacra-1(10),4,11(13)-trien-12-oate + O2 + reduced [NADPH--hemoprotein reductase] = (+)-costunolide + 2 H2O + oxidized [NADPH--hemoprotein reductase] Secondary metabolite biosynthesis; terpenoid biosynthesis. Expressed in floral glandular trichomes. During ovary development, accumulates until the stage 3 and fades out progressively to disappear at stage 6. Belongs to the cytochrome P450 family. +Belongs to the IIV-6 261R/396L/443R family. +Endonuclease that is involved in the suppression of homologous recombination and may therefore have a key role in the control of bacterial genetic diversity. Homodimer. Belongs to the DNA mismatch repair MutS family. MutS2 subfamily. +Modulates the structure and function of the apical ectodermal ridge (AER) that controls embryonic limb development (PubMed:21575622). Functions in cell-cell adhesion, cell migration and axon guidance, exerting an attractive or repulsive role depending on its interaction partners. Plays a role in the spatial organization of brain neurons. Plays a role in vascular development. Plays a role in cell-cell adhesion via its interaction with latrophilins that are expressed at the surface of adjacent cells. Mediates axon attraction towards cells expressing NTN1. Mediates axon growth cone collapse and plays a repulsive role in neuron guidance via its interaction with UNC-5 family members. Plays a role in the regulation of the density of glutamaergic synapses. Plays a role in fibroblast growth factor-mediated signaling cascades. Required for normal morphogenesis during embryonic development, but not for normal embryonic patterning (By similarity). Detected on dendritic punctae that colocalize in part with glutamaergic synapses, but not with GABAergic synapses. Proteolytic cleavage in the juxtamembrane region gives rise to a shedded ectodomain. Detected in distal ectodermal cells at Hamburger Hamilton stage 18 (18HH). Becomes restricted to the apical ectodermal ridge (AER) (at protein level). At stage 11HH, detected in neural ectoderm, developing optic placodes, the neural crest around the otic placodes, and along the anterior-posterior axis in somites. Detected in the ectoderm of the limb bud at 16HH to 18HH. Becomes restricted to the dermomyotome closer to the neural tube at stage 18HH. At 19HH and 23HH, detected in the apical ectodermal ridge, the developing eye and branchial arches. N-glycosylated. Proteolytic cleavage in the juxtamembrane region gives rise to a soluble ectodomain. Cleavage is probably effected by a metalloprotease. +Acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. Binds to short interfering RNAs (siRNAs) with high affinity. Acts as a molecular caliper to specifically select siRNAs based on the length of the duplex region of the RNA (By similarity). Homodimer. Belongs to the tombusviruses protein p19 family. +Catalyzes the hydrolytic cleavage of the carbon-nitrogen bond in imidazolone-5-propanoate to yield N-formimidoyl-L-glutamate. It is the third step in the universal histidine degradation pathway. 4-imidazolone-5-propanoate + H2O = N-formimidoyl-L-glutamate Binds 1 zinc or iron ion per subunit. Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 3/3. Belongs to the metallo-dependent hydrolases superfamily. HutI family. +Essential component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. Seems to control the nucleotide-dependent binding of mtHSP70 (hsp70-5) to substrate proteins (By similarity). Component of the PAM complex, at least composed of hsp70-5/ssc1, grpe/mge1, tim44, un-4/pam16, pam17 and tim14/pam18. Belongs to the GrpE family. +Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily. +Cysteine protease that plays a key role in autophagy by mediating both proteolytic activation and delipidation of ATG8 family proteins (PubMed:15169837, PubMed:15187094, PubMed:17347651, PubMed:19322194, PubMed:21177865, PubMed:26378241, PubMed:29232556, PubMed:28821708, PubMed:30443548, PubMed:30661429, PubMed:22302004, PubMed:27527864, PubMed:28633005, PubMed:30076329). Required for canonical autophagy (macroautophagy), non-canonical autophagy as well as for mitophagy (PubMed:33773106, PubMed:33909989). The protease activity is required for proteolytic activation of ATG8 family proteins: cleaves the C-terminal amino acid of ATG8 proteins MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAPL1, GABARAPL2 and GABARAP, to reveal a C-terminal glycine (PubMed:15169837, PubMed:15187094, PubMed:17347651, PubMed:20818167, PubMed:19322194, PubMed:21177865, PubMed:22302004, PubMed:27527864, PubMed:28633005, PubMed:29458288, PubMed:30661429, PubMed:28287329). Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy (PubMed:15169837, PubMed:15187094, PubMed:17347651, PubMed:19322194, PubMed:21177865, PubMed:22302004). Protease activity is also required to counteract formation of high-molecular weight conjugates of ATG8 proteins (ATG8ylation): acts as a deubiquitinating-like enzyme that removes ATG8 conjugated to other proteins, such as ATG3 (PubMed:31315929, PubMed:33773106). In addition to the protease activity, also mediates delipidation of ATG8 family proteins (PubMed:15187094, PubMed:28633005, PubMed:29458288, PubMed:32686895, PubMed:33909989, PubMed:19322194). Catalyzes delipidation of PE-conjugated forms of ATG8 proteins during macroautophagy (PubMed:15187094, PubMed:29458288, PubMed:32686895, PubMed:33909989, PubMed:19322194). Also involved in non-canonical autophagy, a parallel pathway involving conjugation of ATG8 proteins to single membranes at endolysosomal compartments, by catalyzing delipidation of ATG8 proteins conjugated to phosphatidylserine (PS) (PubMed:33909989). Compared to other members of the family (ATG4A, ATG4C or ATG4C), constitutes the major protein for proteolytic activation of ATG8 proteins, while it displays weaker delipidation activity than other ATG4 paralogs (PubMed:29458288, PubMed:30661429). Involved in phagophore growth during mitophagy independently of its protease activity and of ATG8 proteins: acts by regulating ATG9A trafficking to mitochondria and promoting phagophore-endoplasmic reticulum contacts during the lipid transfer phase of mitophagy (PubMed:33773106). [protein]-C-terminal L-amino acid-glycyl-phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine [protein]-C-terminal L-amino acid-glycyl-phosphatidylserine + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phospho-L-serine Inhibited by N-ethylmaleimide (PubMed:21177865). Redox-regulated during autophagy since reducing conditions activate ATG4A whereas an oxidizing environment such as the presence of H(2)O(2) inhibits its activity (PubMed:17347651). The cysteine protease activity compounds is inhibited by styrylquinoline compounds 4-28 and LV-320 (PubMed:30076329). Interacts with PFKP; promoting phosphorylation of ATG4B at Ser-34 (PubMed:33607258). Interacts with GBP7 (By similarity). Mainly localizes to the cytoplasm, including cytosol (PubMed:29165041). A samll potion localizes to mitochondria; phosphorylation at Ser-34 promotes localization to mitochondria (PubMed:29165041). The LIR motif (LC3-interacting region) is required for the interaction with ATG8 family proteins MAP1LC3A, MAP1LC3B, MAP1LC3C and GABARAPL1 (PubMed:28287329). Required for proteolytic activation and delipidation of ATG8 proteins (PubMed:29458288, PubMed:28287329). Phosphorylation at Ser-383 and Ser-392 promotes autophagy by increasing protein delipidation activity without affecting proteolytic activation of ATG8 proteins (PubMed:26378241). Phosphorylation at Ser-316 by ULK1 inhibits autophagy by decreasing both proteolytic activation and delipidation activities (PubMed:28821708). Phosphorylation at Ser-316 is dephosphorylated by protein phosphatase 2A (PP2A) (PubMed:28821708). Phosphorylation at Ser-34 by AKT2 promotes its hydrolase activity, leading to increased proteolytic activation and delipidation of ATG8 family proteins (PubMed:30443548). Phosphorylation at Ser-34 by AKT1 promotes mitochondrial localization and inhibition of the F1F0-ATP synthase activity, leading to elevation of mitochondrial reactive oxygen species (ROS) (PubMed:29165041). Ubiquitinated by RNF5, leading to its degradation by the proteasome. S-nitrosylation at Cys-189 and Cys-292 in response to high glucose decreases both proteolytic activation and delipidation activities. O-glycosylated by OGT, leading to increase protease activity, thereby promoting the proteolytic activation of ATG8 family proteins. Forms reversible intrachain disulfide bonds in response to oxidative stress (PubMed:31880198). Forms interchain disulfide bonds, leading to formation of homooligomers in response to oxidation (PubMed:31880198). Belongs to the peptidase C54 family. A paper describing ATG4B tissue expression has been retracted, due to concerns of image duplication in some of the figures. Extended N-terminus. Extended N-terminus. +Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate. 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 6/7. Monomer. Belongs to the EPSP synthase family. +This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA. Binds to the 5S rRNA independently of L5 and L18. Belongs to the bacterial ribosomal protein bL25 family. CTC subfamily. +Capsid proteins VP1, VP2, and VP3 form a closed capsid enclosing the viral positive strand RNA genome (PubMed:25327248, PubMed:28074040). All these proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:25327248). Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms (PubMed:25327248). VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (PubMed:25327248). The naked capsid interacts with the host receptor HAVCR1 to provide virion attachment to and probably entry into the target cell (PubMed:9658108, PubMed:11134285, PubMed:29437974). Capsid proteins VP1, VP2, and VP3 form a closed capsid enclosing the viral positive strand RNA genome (PubMed:25327248, PubMed:28074040). All these proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:25327248). Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms (PubMed:25327248). VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (PubMed:25327248). The naked capsid interacts with the host receptor HAVCR1 to provide virion attachment to and probably entry into the target cell (PubMed:9658108, PubMed:11134285, PubMed:29437974). Capsid proteins VP1, VP2, and VP3 form a closed capsid enclosing the viral positive strand RNA genome (PubMed:25327248, PubMed:28074040). All these proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:25327248). Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms (PubMed:25327248). VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (PubMed:25327248). The naked capsid interacts with the host receptor HAVCR1 to provide virion attachment to and probably entry into the target cell (PubMed:9658108, PubMed:11134285, PubMed:29437974). VP0 precursor is a component of the immature procapsids. Plays a role in the assembly of the 12 pentamers into an icosahedral structure. Has not been detected in mature virions, supposedly owing to its small size. Precursor component of immature procapsids that corresponds to an extended form of the structural protein VP1 (PubMed:9988685, PubMed:12097562). After maturation, possibly by the host Cathepsin L, the assembly signal 2A is cleaved to give rise to the mature VP1 protein (PubMed:9988685). Functions as a viroporin (PubMed:26515753). Affects membrane integrity and causes an increase in membrane permeability (PubMed:9875331). Involved in host intracellular membrane rearrangements probably to give rise to the viral factories (PubMed:9344908). Does not disrupt calcium homeostasis or glycoprotein trafficking (PubMed:18216106). Antagonizes the innate immune response of the host by suppressing IFN-beta synthesis, which it achieves by interfering with the DDX58/IFIH1 (RIG-I/MDA5) pathway (PubMed:18559929). Affects membrane integrity and causes an increase in membrane permeability. Associates with and induces structural rearrangements of intracellular membranes (PubMed:9344908). Displays RNA-binding activity (PubMed:9645199). The precursor 3ABC is targeted to the mitochondrial membrane where protease 3C activity cleaves and inhibits the host antiviral protein MAVS, thereby disrupting activation of IRF3 through the IFIH1/MDA5 pathway (PubMed:17438296). In vivo, the protease activity of 3ABC precursor is more efficient in cleaving the 2BC precursor than that of protein 3C. The 3ABC precursor may therefore play a role in the proteolytic processing of the polyprotein (PubMed:10559299). Interacts with the 3CD precursor and with RNA structures found at both the 5'- and 3'-termini of the viral genome (PubMed:10562502). Since the 3AB precursor contains the hydrophobic domain 3A, it probably anchors the whole viral replicase complex to intracellular membranes on which viral RNA synthesis occurs (PubMed:9705870). May serve as membrane anchor to the 3AB and 3ABC precursors via its hydrophobic domain (PubMed:9705870). May interact with RNA (PubMed:10562502). Acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome. Cysteine protease that generates mature viral proteins from the precursor polyprotein (PubMed:1850033). In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication (PubMed:15361063). RNA and substrate bind cooperatively to the protease (PubMed:9032381). Cleaves IKBKG/NEMO to impair innate immune signaling (PubMed:24920812). Cleaves host PABPC1 which may participate in the switch of viral translation to RNA synthesis (PubMed:17726047). Interacts with the 3AB precursor and with RNA structures found at both the 5'- and 3'-termini of the viral genome (PubMed:10562502). Disrupts TLR3 signaling by degrading the host adapter protein TICAM1/TRIF (PubMed:21931545). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. Homodimer. Homomultimer; probably interacts with membranes in a multimeric form (PubMed:26515753). Seems to assemble into amyloid-like fibers (PubMed:25589659). Interacts with host ACBD3 (PubMed:23572552). Homodimer. Monomer (PubMed:9705870). Interacts with protein 3CD (PubMed:10562502). Interacts with protein 3AB (PubMed:10562502). Interacts with human MAVS (PubMed:17438296). Homodimer; disulfide-linked (PubMed:15361063). Homopentamer (PubMed:12782637). Homooligomer (PubMed:18823593, PubMed:12782637). Interacts with capsid protein VP2 (PubMed:25327248, PubMed:28074040). Interacts with capsid protein VP3 (PubMed:25327248, PubMed:28074040). Interacts with capsid protein VP1 (PubMed:25327248, PubMed:28074040). Interacts with capsid protein VP3 (PubMed:25327248, PubMed:28074040). Interacts with capsid protein VP1 (PubMed:25327248, PubMed:28074040). Interacts with capsid protein VP2 (PubMed:25327248, PubMed:28074040). The egress of newly formed virions occurs through an exosome-like mechanism involving endosomal budding of viral capsids into multivesicular bodies. The egress of newly formed virions occurs through an exosome-like mechanism involving endosomal budding of viral capsids into multivesicular bodies. The egress of newly formed virions occurs through an exosome-like mechanism involving endosomal budding of viral capsids into multivesicular bodies. Present in the full mature virion (PubMed:25327248). The egress of newly formed virions occurs through an exosome-like mechanism involving endosomal budding of viral capsids into multivesicular bodies (Probable). Probably localizes to intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. Probably localizes to intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. May associate with membranes through a N-terminal amphipathic helix. Probably localizes to intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. Probably localizes to intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. Probably localizes to intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. Interacts with membranes in a complex with viral protein 3AB. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum. The assembly signal 2A region mediates pentamerization of P1-2A. Late-budding domains (L domains) are short sequence motifs essential for viral particle budding (Probable). They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins (Probable). The genome polyprotein contains two L domains: a tandem of (L)YPX(n)L domain which is known to bind the PDCD6IP/ALIX adaptater protein (PubMed:23542590). Late-budding domains (L domains) are short sequence motifs essential for viral particle budding (Probable). They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins (Probable). Capsid protein VP2 contains two L domains: a tandem of (L)YPX(n)L domain which is known to bind the Alix adaptater protein (PubMed:23542590). The C-terminus displays a membrane-penetrating ability. Specific enzymatic cleavages by viral protease in vivo yield a variety of precursors and mature proteins. Polyprotein processing intermediates are produced, such as P1-2A which is a functional precursor of the structural proteins, VP0 which is a VP4-VP2 precursor, VP1-2A precursor, 3ABC precursor which is a stable and catalytically active precursor of 3A, 3B and 3C proteins, 3AB and 3CD precursors (PubMed:7483265, PubMed:1850033, PubMed:8382411, PubMed:8291234, PubMed:9060697, PubMed:9733840, PubMed:8259663, PubMed:7853510, PubMed:10559299). The assembly signal 2A is removed from VP1-2A by a host protease, possibly host Cathepsin L (PubMed:18823593). This cleavage occurs over a region of 3 amino-acids probably generating VP1 proteins with heterogeneous C-termini (PubMed:10364353). During virion maturation, immature virions are rendered infectious following cleavage of VP0 into VP4 and VP2. This maturation seems to be an autocatalytic event triggered by the presence of RNA in the capsid and is followed by a conformational change of the particle (PubMed:12782637, PubMed:8291234, PubMed:9060697, PubMed:9733840). The assembly signal 2A is removed from VP1-2A by a host protease, possibly host Cathepsin L in naked virions (PubMed:18823593). This cleavage does not occur in enveloped virions (PubMed:28490497). This cleavage occurs over a region of 3 amino-acids probably generating VP1 proteins with heterogeneous C-termini (PubMed:10364353). VPg is uridylylated prior to priming replication into VPg-pUpU. Unlike other picornaviruses, does not seem to be myristoylated. The need for an intact eIF4G factor for the initiation of translation of HAV results in an inability to shut off host protein synthesis by a mechanism similar to that of other picornaviruses. During infection, enveloped virions (eHAV) are released from cells (PubMed:23542590). These eHAV are cloaked in host-derived membranes and resemble exosomes (PubMed:28490497). The membrane of eHAV is devoid of viral proteins and thus prevents their neutralization by antibodies (PubMed:23542590). eHAV budding is dependent on ESCRT-associated proteins VPS4B and PDCD6IP/ALIX (PubMed:23542590). eHAV are produced and released in the serum and plasma, but not in bile and feces which only contain the naked, nonenveloped virions (Probable). It is likely that eHAV also use HAVCR1 as a functional receptor to infect cells, an evolutionary trait that may enhance HAV infectivity (PubMed:29437974). Wild-type HM175 (HM175/wt) comes from a sample isolated from a patient in Australia in 1976 and subsequently passaged three times in marmosets. HM175/7 is an attenuated strain derived from HM175 by 32 passages in African green monkey kidney cells. HM175/18f, HM175/24a, and HM175/43c are cytopathic isolates derived from HM175 by serial passages in FRhK-4 cells. Mutations in proteins 2B and 2C seem to be essential for strain HM175 adaptation to growth in cell culture. Belongs to the picornaviridae polyprotein family. It is uncertain whether Met-1 or Met-3 is the initiator. In vitro, both are used, with a preference for Met-3. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL2 family. +Catalyzes the hydrolytic cleavage of the carbon-nitrogen bond in imidazolone-5-propanoate to yield N-formimidoyl-L-glutamate. It is the third step in the universal histidine degradation pathway. 4-imidazolone-5-propanoate + H2O = N-formimidoyl-L-glutamate Binds 1 zinc or iron ion per subunit. Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 3/3. Belongs to the metallo-dependent hydrolases superfamily. HutI family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. Interacts with UvrB in an incision complex. Belongs to the UvrC family. +Part of a K(+) efflux system which is required for the adaptation of R.meliloti to alkaline pH as well as for the infection process during symbiotic nodule development. May form a hetero-oligomeric complex that consists of six subunits: PhaAB, PhaC, PhaD, PhaE, PhaF and PhaG. Belongs to the CPA3 antiporters (TC 2.A.63) subunit C family. +Attaches the virus to host cellular receptor, inducing clathrin-dependent endocytosis of the virion. In the endosome, the acidic pH induces conformational changes in the glycoprotein trimer, which trigger fusion between virus and endosomal membrane. In neurons, neo-synthesized glycoproteins are sorted to the dendrites, where the virus buds (By similarity). Homotrimer. The cytoplasmic domain sorts the protein to neurons dentrites instead of axons. When expressed in ex vivo polarized cells like epithelial cells, it sorts the protein to the basolateral side (By similarity). Glycosylated by host. Palmitoylated by host on Cys-489 (By similarity). Used to pseudotype many virus-like particles like lentiviral vector, because of its broad spectrum of host cell tropism. Also used in viral vectors studies in cancer therapy. Belongs to the vesiculovirus glycoprotein family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Belongs to the imidazoleglycerol-phosphate dehydratase family. +Probably required for nitrate uptake under anoxic conditions. Also possibly involved in excretion of nitrite produced by the dissimilatory reduction of nitrate (By similarity). Positively regulated by the two-component system NreB/NreC. Belongs to the major facilitator superfamily. Nitrate/nitrite porter (TC 2.A.1.8) family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Part of the ABC transporter complex LolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone, LolA. Responsible for the formation of the LolA-lipoprotein complex in an ATP-dependent manner. The complex is composed of two ATP-binding proteins (LolD) and two transmembrane proteins (LolC and LolE). Belongs to the ABC transporter superfamily. Lipoprotein translocase (TC 3.A.1.125) family. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Exoglycosidase that cleaves the single beta-linked mannose residue from the non-reducing end of all N-linked glycoprotein oligosaccharides. Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides. Optimum pH is 5. Glycan metabolism; N-glycan degradation. Monomer. Detected in kidney (at protein level) (PubMed:1556126). Found in spleen and to a lesser extent in liver. Not detected in kidney or brain. N-glycosylated. Defects in MANBA cause beta-mannosidosis, a severe disorder that affects peripheral and central nervous system myelin resulting in tremor, nystagmus, ataxia and early death. The primary storage products associated with the enzyme deficiency are the trisaccharide Man-beta-1-4-GlcNAc-beta-1-4-GlcNAc and the disaccharide Man-beta-1-4-GlcNAc. Belongs to the glycosyl hydrolase 2 family. +Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide. 6-carboxyhexanoyl-[ACP] + H(+) + L-alanine = (8S)-8-amino-7-oxononanoate + CO2 + holo-[ACP] Cofactor biosynthesis; biotin biosynthesis. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient (By similarity). a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 5 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 13 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 4L family. +Part of the ABC transporter complex FbpABC involved in Fe(3+) ions import. Responsible for energy coupling to the transport system. ATP + Fe(3+)(out) + H2O = ADP + Fe(3+)(in) + H(+) + phosphate The complex is composed of two ATP-binding proteins (FbpC), two transmembrane proteins (FbpB) and a solute-binding protein (FbpA). Belongs to the ABC transporter superfamily. Fe(3+) ion importer (TC 3.A.1.10) family. +Involved in ubiquitination and subsequent proteasomal degradation of target proteins. Regulator of mitotic processes which plays a role during gametogenesis and embryogenesis. Together with SKP1, RBX1 and a F-box protein, it forms a SCF complex. The functional specificity of this complex depends of the type of F-box protein. SCF(UFO) is implicated in floral organ development. SCF(TIR1) is involved in auxin signaling pathway. SCF(COI1) regulates responses to jasmonates. SCF(EID1) and SCF(AFR) are implicated in phytochrome A light signaling. SCF(ADO1/ZTL), SCF(ADO2/LKP2), SCF(ADO3/FKF1) are related to the circadian clock. SCF(ORE9) seems to be involved in senescence. SCF(EBF1/EBF2) may regulate ethylene signaling. Protein modification; protein ubiquitination. Part of E3 ubiquitin ligase SCF complexes such as SCF(TIR1) and SCF(COI1). SCF(TIR1) is composed of CUL1, SKP1 (SKP1A or SKP1B), RBX1 (RBX1A or RBX1B) and TIR1, while SCF(COI1) is composed of CUL1, SKP1, RBX1 and COI1. A SNF1-related protein kinase (KIN10 and KIN11) can also be part of these SCF complexes. SCF(TIR1) is able to interact with the COP9 signalosome (CSN) complex. Interacts directly with some F-box proteins such as DOR, SKIP14, FBW2/SKIP18, SKIP19/FBL20 and SKIP28/MEE11. Interacts with CAND1. Mainly nuclear during interphase and preprophase, but also weakly cytoplasmic during interphase. Associated to mitotic spindle during metaphase, and to the phragmoplast during telophase. Expressed constitutively in roots, seedlings, stems, leaves and flowers. Strong accumulation in embryos (at protein level). Neddylated (rubylated). Deneddylation occurs upon interaction with the COP9 signalosome (CSN) complex. Belongs to the cullin family. +Transcription factor expressed in neurons of the brain that regulates the excitatory-inhibitory balance within neural circuits and is required for contextual memory in the hippocampus (By similarity). Plays a key role in the structural and functional plasticity of neurons (By similarity). Acts as an early-response transcription factor in both excitatory and inhibitory neurons, where it induces distinct but overlapping sets of late-response genes in these two types of neurons, allowing the synapses that form on inhibitory and excitatory neurons to be modified by neuronal activity in a manner specific to their function within a circuit, thereby facilitating appropriate circuit responses to sensory experience (By similarity). In excitatory neurons, activates transcription of BDNF, which in turn controls the number of GABA-releasing synapses that form on excitatory neurons, thereby promoting an increased number of inhibitory synapses on excitatory neurons (By similarity). In inhibitory neurons, regulates a distinct set of target genes that serve to increase excitatory input onto somatostatin neurons, probably resulting in enhanced feedback inhibition within cortical circuits (By similarity). The excitatory and inhibitory balance in neurons affects a number of processes, such as short-term and long-term memory, acquisition of experience, fear memory, response to stress and social behavior (PubMed:21887312). Acts as a regulator of dendritic spine development in olfactory bulb granule cells in a sensory-experience-dependent manner by regulating expression of MDM2 (By similarity). Efficient DNA binding requires dimerization with another bHLH protein, such as ARNT, ARNT2 or BMAL1 (By similarity). Can activate the CME (CNS midline enhancer) element (By similarity). Efficient DNA binding requires dimerization with another bHLH protein. Heterodimer; forms a heterodimer with ARNT, ARNT2 or BMAL1. Specifically expressed in neurons (PubMed:18815592). Expressed in the lateral nucleus of the amygdala (at protein level) (PubMed:21887312). Expression is regulated by neuronal activity (PubMed:18815592). Induced in excitatory neurons specifically upon calcium influx (PubMed:18815592). Induced in the lateral nucleus of the amygdala in a learning-dependent manner (at protein level) (PubMed:21887312). Ubiquitinated, leading to degradation by the proteosome. +Cleavage of the Leu-|-Leu bond in synthetic tetradecapeptide renin substrate, to produce angiotensin I, but not active on natural angiotensinogen. Also hydrolyzes Bz-Arg-p-nitroanilide. Belongs to the peptidase S1 family. Kallikrein subfamily. +Involved in the secretion of a lactococcin. Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Component of the triterpene saponins (e.g. ginsenosides or panaxosides) and phytosterols biosynthetic pathways (PubMed:29378087). Catalyzes the biosynthesis of squalene (By similarity). 2 (2E,6E)-farnesyl diphosphate + H(+) + NADH = 2 diphosphate + NAD(+) + squalene 2 (2E,6E)-farnesyl diphosphate + H(+) + NADPH = 2 diphosphate + NADP(+) + squalene Terpene metabolism; lanosterol biosynthesis; lanosterol from farnesyl diphosphate: step 1/3. Induced methyl jasmonate (MeJA) in adventitious roots. Belongs to the phytoene/squalene synthase family. +Involved in the biosynthesis of the polyketide antibiotic aureothin (PubMed:14700630, PubMed:15038705). Catalyzes the oxidation of p-aminobenzoate (pABA) to p-nitrobenzoate (pNBA), an unusual polyketide synthase starter unit (PubMed:15038705, PubMed:16927313, PubMed:20798054, PubMed:18458342). Reaction mechanism involves the generation of a peroxodiiron(III/III) intermediate, which effects the initial oxidation of p-aminobenzoate to p-hydroxylaminobenzoate (Ar-NHOH) (PubMed:19731912, PubMed:20798054). Ar-NHOH is then probably directly converted to the fully oxidized p-nitrobenzoate via a four-electron N-oxidation, bypassing the formation of a nitroso compound (PubMed:20798054). 4-aminobenzoate + AH2 + 2 O2 = 4-nitrobenzoate + A + 2 H2O Contains a nonheme dinuclear iron cluster that stabilizes a peroxo intermediate (PubMed:16927313, PubMed:18458342, PubMed:19731912, PubMed:20798054). Was originally suggested to contain a binuclear manganese cluster or an heterodinuclear manganese/iron cluster (PubMed:17765264, PubMed:17718517). kcat is 6.21 min(-1) with p-aminobenzoate as substrate. Antibiotic biosynthesis. Homodimer. Deletion of the gene abolishes both N-oxidation activity and aureothin production. Belongs to the AurF N-oxygenase family. +Water-repellent structural protein required for surface hydrophobicity and formation of aerial hyphae during filamentous growth. Highly expressed in filamentous form. Regulated by the mating type loci. +Belongs to the UPF0398 family. +Catalyzes the conversion of heme O to heme A by two successive hydroxylations of the methyl group at C8. The first hydroxylation forms heme I, the second hydroxylation results in an unstable dihydroxymethyl group, which spontaneously dehydrates, resulting in the formyl group of heme A. 2 A + Fe(II)-heme o + H2O = 2 AH2 + Fe(II)-heme a Porphyrin-containing compound metabolism; heme A biosynthesis; heme A from heme O: step 1/1. Interacts with CtaB. Belongs to the COX15/CtaA family. Type 2 subfamily. +Assembles to form an icosahedral capsid with a T=7 symmetry. The icosahedral capsid is about 60 nm in diameter and composed of 415 major capsid proteins. The assembly is primed by the interaction between capsid assembly protease and portal dodecamer, and major capsid proteins assemble cooperatively to form the procapsid with the help of capsid scaffolding protein. Major capsid protein forms hexons and pentons of the icosahedron. Viral genomic DNA is packaged into the procapsid through the portal vertex (By similarity). The packaging triggers a dramatic reconfiguration of the capsid shell, expanding from roughly 50nm to 60nm while the capsid thickness decreases. The capsid decoration protein binds the expanded capsid and stabilizes it. Homomultimer (PubMed:265585, PubMed:8411174). Interacts with FI protein (PubMed:22801427). Forms the capsid icosahedric shell. Belongs to the lambda phage major capsid protein family. Some of the E protein may be covalently linked with an equimolar amount of protein C and cleaved to yield minor capsid proteins X1 and X2. But recent data fail to detect cleavage products. +Interacts with subunit of G(i) alpha proteins and regulates the activation of G(i) alpha proteins. The GoLoco 1 and/or GoLoco 3 domains exhibit GDI activity towards GDP-bound G(i) alpha protein, but not the GoLoco 2 domain. +Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP. Allosterically activated by GTP. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uracil: step 1/1. Belongs to the UPRTase family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form the product. After dissociation, two additional enzymatic reactions on the tRNA convert PreQ1 to queuine (Q), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine). 7-aminomethyl-7-carbaguanine + guanosine(34) in tRNA = 7-aminomethyl-7-carbaguanosine(34) in tRNA + guanine Binds 1 zinc ion per subunit. tRNA modification; tRNA-queuosine biosynthesis. Homodimer. Within each dimer, one monomer is responsible for RNA recognition and catalysis, while the other monomer binds to the replacement base PreQ1. Belongs to the queuine tRNA-ribosyltransferase family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway. D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = beta-D-fructose 6-phosphate + D-erythrose 4-phosphate Carbohydrate degradation; pentose phosphate pathway; D-glyceraldehyde 3-phosphate and beta-D-fructose 6-phosphate from D-ribose 5-phosphate and D-xylulose 5-phosphate (non-oxidative stage): step 2/3. Belongs to the transaldolase family. Type 2 subfamily. +RNA binding protein that binds to the poly-A tract of mRNA molecules. Associates with the 40S ribosomal subunit and with polysomes. Plays a role in the regulation of mRNA translation. Plays a role in the regulation of cell morphology and cytoskeletal organization. Interacts (via N-terminal region) with PABPC1. Interacts with RACK1. Localized throughout the cytosol. Partially localized in stress granules in response to arsenite treatment. +Golgi-localized palmitoyltransferase that catalyzes the addition of palmitate onto various protein substrates and therefore functions in several unrelated biological processes (Probable). Has no stringent fatty acid selectivity and in addition to palmitate can also transfer onto target proteins myristate from tetradecanoyl-CoA and stearate from octadecanoyl-CoA (Probable). hexadecanoyl-CoA + L-cysteinyl-[protein] = CoA + S-hexadecanoyl-L-cysteinyl-[protein] L-cysteinyl-[protein] + tetradecanoyl-CoA = CoA + S-tetradecanoyl-L-cysteinyl-[protein] L-cysteinyl-[protein] + octadecanoyl-CoA = CoA + S-octadecanoyl-L-cysteinyl-[protein] Homooligomers. Probably maternally supplied. No zygotic expression is detected before 7.5 hpf. The DHHC domain is required for palmitoyltransferase activity. Autopalmitoylated. Belongs to the DHHC palmitoyltransferase family. +Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NAD(+) (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADPH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NADP(+) Belongs to the MnmG family. TrmFO subfamily. +Catalyzes the attachment of glycine to tRNA(Gly). ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP. an acyl phosphate + sn-glycerol 3-phosphate = a 1-acyl-sn-glycero-3-phosphate + phosphate Lipid metabolism; phospholipid metabolism. Probably interacts with PlsX. Belongs to the PlsY family. +Belongs to the bacterial ribosomal protein bS16 family. +Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. 2 H(+) + 2 superoxide = H2O2 + O2 Binds 1 Mn(2+) ion per subunit. Homotetramer. Nitrated under oxidative stress. Nitration coupled with oxidation inhibits the catalytic activity. Acetylation at Lys-122 decreases enzymatic activity. Deacetylated by SIRT3 upon exposure to ionizing radiations or after long fasting (By similarity). Polyubiquitinated; leading to proteasomal degradation. Deubiquitinated by USP36 which increases protein stability. Belongs to the iron/manganese superoxide dismutase family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Binds together with S18 to 16S ribosomal RNA. Part of the 30S ribosomal subunit (PubMed:328274, PubMed:10094780, PubMed:12809609, PubMed:16272117, PubMed:27934701, PubMed:12244297, PubMed:27906160, PubMed:27906161, PubMed:28077875). Interacts weakly with L2 in one of the 3.5 A resolved structures (PubMed:16272117). 5 different forms of the protein, varying only in the number of C-terminal glutamate residues, were isolated. The sequence shown is form S6-6, which is the longest. The first two Glu are encoded by the rpsF gene, the other Glu are added post-translationally by the RimK enzyme. Belongs to the bacterial ribosomal protein bS6 family. Up to 4 Glu residues can be added post-translationally. Up to 4 Glu residues can be added post-translationally. Up to 4 Glu residues can be added post-translationally. Up to 4 Glu residues can be added post-translationally. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. +During ventral cord development, required for axon fasciculation and navigation, mediating both pioneer and follower axon extension, guidance and track formation (PubMed:20876647, PubMed:22442082, PubMed:23376536, PubMed:28846083). Acts in CEPsh glia and SubL neurons to guide follower axons into the nerve ring (PubMed:28846083). Promotes motorneuron development by positively regulating the extension of the anterior neurite of ventral D-type GABAergic motorneurons along the anterior-posterior axis of the ventral nerve cord (PubMed:23376536). Plays a role in synaptogenesis by regulating synaptic vesicle accumulation at GABAergic and cholinergic neuromuscular junctions (PubMed:22442082). In embryos, localizes to axons in the nerve ring, the tail and along dendrites of sensory neurons. Expressed in a region of neuropil around the nerve ring and the ventral cord (at protein level) (PubMed:22442082). Expressed in the head, tail, ventral cord, nerve ring and neurons including HSN neurons (PubMed:20876647). Expressed in DA, VA, and VB and weakly in the DB cholinergic neurons (PubMed:22442082). Not expressed in ventral D-type GABAergic motorneurons (PubMed:22442082). Expressed throughout development (PubMed:20876647). In embryos, first expressed in neuronal precursor cells during gastrulation (PubMed:20876647). At the comma and 1.5-fold embryonic stage, expressed in neurons in the head, the tail and along the ventral cord (PubMed:20876647). In 1.5-fold stage embryos, expressed in the nerve ring bundle (PubMed:28846083). At the L1 larval stage, expressed in the ventral nerve cord and in a subset of dorsal D-type GABAergic motorneurons (PubMed:22442082, PubMed:23376536). At the L2 larval stage, expressed along the ventral nerve cord (PubMed:23376536). Not expressed in ventral D-type GABAergic motorneurons at the L2 larval stage (PubMed:23376536). Belongs to the G-protein coupled receptor 2 family. LN-TM7 subfamily. +Plays an important role in the elongation step of protein synthesis. A number of isoforms are produced. According to EST sequences. Belongs to the eukaryotic ribosomal protein P1/P2 family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Belongs to the peptidase S8 family. +1-(5-phospho-beta-D-ribosyl)-ATP + H2O = 1-(5-phospho-beta-D-ribosyl)-5'-AMP + diphosphate + H(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 2/9. Belongs to the PRA-PH family. +The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis. phosphate + thymidine = 2-deoxy-alpha-D-ribose 1-phosphate + thymine Pyrimidine metabolism; dTMP biosynthesis via salvage pathway; dTMP from thymine: step 1/2. Homodimer. Belongs to the thymidine/pyrimidine-nucleoside phosphorylase family. +Probably acts as a GEF (guanine nucleotide exchange factor) for the Rho family of small GTP-binding proteins (G proteins) that stimulates the dissociation of GDP to enable subsequent binding of GTP (By similarity). May also chaperone the processing and/or trafficking of small GTPases independently of GEF activity (By similarity). May be involved in the control of polarized cell growth via CDC42-mediated signaling (By similarity). May also be involved in the control of cell-wall organization via RHO1-mediated signaling (By similarity). +Receptor tyrosine kinase which binds promiscuously GPI-anchored ephrin-A family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. Among GPI-anchored ephrin-A ligands, EFNA5 most probably constitutes the cognate/functional ligand for EPHA5. Functions as an axon guidance molecule during development and may be involved in the development of the retinotectal, entorhino-hippocampal and hippocamposeptal pathways. Together with EFNA5 plays also a role in synaptic plasticity in adult brain through regulation of synaptogenesis. In addition to its function in the nervous system, the interaction of EPHA5 with EFNA5 mediates communication between pancreatic islet cells to regulate glucose-stimulated insulin secretion (By similarity). ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein] Heterotetramer upon binding of the ligand. The heterotetramer is composed of an ephrin dimer and a receptor dimer. Oligomerization is probably required to induce biological responses (By similarity). Interacts (via SAM domain) with SAMD5 (via SAM domain) (By similarity). Additional isoforms seem to exist. Almost exclusively expressed in the nervous system in cortical neurons, cerebellar Purkinje cells and pyramidal neurons within the cortex and hippocampus. Display an increasing gradient of expression from the forebrain to hindbrain and spinal cord. Phosphorylated. Phosphorylation is stimulated by the ligand EFNA5. Dephosphorylation upon stimulation by glucose, inhibits EPHA5 forward signaling and results in insulin secretion (By similarity). Belongs to the protein kinase superfamily. Tyr protein kinase family. Ephrin receptor subfamily. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +Unconventional myosin that functions as actin-based motor protein with ATPase activity (PubMed:30467170). Binds to membranes enriched in phosphatidylinositol 4-5-bisphosphate, and can glide along actin filaments when anchored to a lipid bilayer (PubMed:30467170). Generates left-right asymmetry at the level of single cells, organs and the whole body via its interaction with the actin cytoskeleton, both in the embryo and the adult (PubMed:16598258, PubMed:16598259, PubMed:18521948, PubMed:26073018, PubMed:25659376, PubMed:30467170). Normal left-right asymmetry of the larval midgut and hindgut requires expression in the embryonic hindgut epithelium during a critical time period, 10 to 12.75 hours after egg laying (PubMed:18521948). This period corresponds to a late stage of germband retraction, and precedes left-right asymmetric morphogenesis (PubMed:18521948). Expression in segment H1 of the imaginal ring is required at 0 to 24 hours after pupation for changes of cell shape and orientation in the H2 segment, which then gives rise to normal, dextral looping of the adult hindgut (PubMed:16598258, PubMed:26073018). Required during a critical period, 126-132 hours after egg laying, for normal, dextral rotation of the adult male genitalia (PubMed:16598258, PubMed:16598259, PubMed:22491943, PubMed:26073018, PubMed:25659376). Has a double role by promoting dextral rotation in the posterior compartment of segment A8 of the male genital disk, and in repressing sinistral looping in the anterior compartment (PubMed:16598259). Binds to F-actin (PubMed:7589814). Interacts with arm (PubMed:16598259, PubMed:22491943). Interacts with shg (PubMed:22491943). Interacts with ds (via intracellular region) (PubMed:26073018). Detected throughout the cytoplasm. Detected primarily in the basolateral cytoplasmic region of immature enterocytes. Detected also in the apical cytoplasmic region in midgut enterocytes and follicle cells (PubMed:7589814). Colocalizes with the actin cytoskeleton (PubMed:7589814, PubMed:16598258, PubMed:16598259, PubMed:25659376). Colocalizes with arm at adherens junctions (PubMed:16598259). Colocalizes with ds at cell junctions (PubMed:26073018). In the embryo, expressed in gastric caeca, midgut cells of the proventriculus, and in the mid and hindgut. In the larval gut brush border, expression is in the terminal web domain. In the adult gut brush border, expression remains in the web domain and has also moved into the microvilli. Also expressed at low levels in follicle cells during oogenesis. Expressed both maternally and zygotically throughout development to adulthood with highest levels at the end of larval development. Expression in embryogenesis is correlated with the formation of a brush border within the alimentary canal. Detected in the developing hindgut and midgut in stage 12 and stage 14 embryos (at protein level) (PubMed:16598258). In third instar larvae, detected in a symmetrical, double chevron-like pattern in the ventral section of segment A8 of the male genital disk, with one chevron in the anterior and the other in the posterior part of this segment (PubMed:16598259, PubMed:22491943). Detected in the H1 domain of the larval imaginal disk (PubMed:26073018). Detected in embryonic anterior and posterior midgut, hindgut, and in salivary gland (PubMed:25659376). The myosin motor domain contains the derminants for dextral twisting. The two IQ domains are essential for activity in determining left-right asymmetry. The actin-binding domain is essential for activity in determining left-right asymmetry. Viable and fertile (PubMed:16598258). Mutant embryos and adults display normal foregut left-right asymmetry, but inverted left-right asymmetry of the midgut and hindgut (PubMed:16598258, PubMed:18521948). RNAi-mediated knockdown in the hindgut at 0 to 24 hours after pupation leads to inverted left-right asymmetry of the adult hindgut, but knockdown at later stages has little or no effect (PubMed:16598258, PubMed:26073018). Adults display inverted left-right asymmetry of the male genitalia (PubMed:16598258). RNAi-mediated knockdown in the anterior and the posterior part of segment A8 of the male genital disk causes loss of the normal dextral rotation of the genital plate and inverted, sinistral spermiduct looping (PubMed:16598259, PubMed:26073018). Selective RNAi-mediated down-regulation in the anterior part of segment A8 of the male genital disk leads to partial dextral rotation of the genitalia, while RNAi-mediated down-regulation in the posterior part of segment A8 leads to non-rotated genitalia (PubMed:16598259). Combined RNAi-mediated knockdown of both ds and Myo31DF in the H1 segment of the imaginal ring causes mislooping of the adult hindgut (PubMed:26073018). Overexpression throughout the embryo reverses the normal left-right asymmetry of the embryonic gut, giving rise to a gut that is a mirror-image of the wild-type (PubMed:16598258). Ectopic expression in the larval epidermis causes dextral twisting of the entire larval body. Ectopic expression in tracheal precursor cells causes dextral spiraling of tracheal branches, giving rise to a spiraling ribbon shape instead of the normal smooth tube. Ectopic expression in epithelial cells causes increased elongation and a clear shift of the membrane orientation toward one side, so that the membrane is no longer perpendicular to the anterior-posterior axis (PubMed:30467170). Belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Myosin family. Represents an unconventional myosin that should not be confused with the conventional myosin-1. +Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons. Belongs to the HrcA family. +Pollen specific. Activated during early microspore development. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Specifically methylates the N7 position of guanine in position 535 of 16S rRNA. Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Implicated in the defense of plants against pathogens. Hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans. Is expressed primarily in epidermal cell of healthy plant, and following induction by ethylene, accumulates in mesophyll cells. By ethylene. Belongs to the glycosyl hydrolase 17 family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The NB-protein (ChlN-ChlB) is the catalytic component of the complex. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per heterodimer. The cluster is bound at the heterodimer interface by residues from both subunits. Porphyrin-containing compound metabolism; chlorophyll biosynthesis (light-independent). Protochlorophyllide reductase is composed of three subunits; ChlL, ChlN and ChlB. Forms a heterotetramer of two ChlB and two ChlN subunits. Belongs to the ChlB/BchB/BchZ family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase. Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Prokaryotic type I sub-subfamily. +Catalyzes the anaerobic oxidation of oxalate using a broad range of electron acceptors, including ferredoxin and the nickel-dependent carbon monoxide dehydrogenase. Does not require coenzyme A as cosubstrate. Enables anaerobic growth on oxalate which is used as energy source by the bacteria. oxalate + oxidized 2[4Fe-4S]-[ferredoxin] = 2 CO2 + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Kinetic parameters determined with the heterodimer oxalate oxidoreductase complex. Optimum pH is 8.7. Dimer of heterotrimer of one alpha, one beta and one delta subunit. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 2 family. +Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Could accept sulfur from TusD (By similarity). Interacts with the TusBCD complex. Interacts with MnmA (By similarity). Belongs to the DsrC/TusE family. +In Dictyostelium the holoenzyme is a dimer composed of a regulatory (R) and a catalytic (C) subunit. In the presence of cAMP it dissociates into the active C subunit and an R monomer. In other eukaryotes the holoenzyme is a tetramer composed of 2 regulatory (R) and 2 catalytic (C) subunits. In the presence of cAMP it dissociates into active monomeric C subunits and an R dimer. Lacks the N-terminal domain required for the association of regulatory subunits into dimers in other eukaryotes. The pseudophosphorylation site binds to the substrate-binding region of the catalytic chain but is not phosphorylated. The physiological significance of phosphorylations by other kinases is unclear. AcaA and pkaR double mutant shows no abolition of the ability to sporulate. In D.discoideum each R subunit carries only 1 high-affinity cAMP binding site (2 in other eukaryotes). Belongs to the cAMP-dependent kinase regulatory chain family. +Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). Belongs to the AP2/ERF transcription factor family. ERF subfamily. +Catalyzes the deamination of dCTP to dUTP. dCTP + H(+) + H2O = dUTP + NH4(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 1/2. Homotrimer. Belongs to the dCTP deaminase family. +Belongs to the UPF0102 family. +Associated component of the MCM complex that acts as a regulator of DNA replication. Binds to the MCM complex during late S phase and may act by promoting the disassembly of the MCM complex from chromatin. Required for sister chromatid cohesion. Interacts with the MCM complex. Associates with the replisome complex. Expression is regulated by E2FA and E2FB. Serrated leaves due to cell cycle inhibition and to a stringent late G2 cell cycle arrest. The leaf blade area is almost normal while the average abaxial pavement cell area increases significantly in the mutant plants, accompanied with a decrease in cell number per leaf. At the bolting stage, younger leaves display a slightly elongated and serrated leaf phenotype. In addition, the root growth rate of the mutant plants is significantly reduced. Belongs to the MCMBP family. +Probable S-adenosyl-L-methionine-dependent methyltransferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. May methylate the carboxyl group of leucine residues to form alpha-leucine ester residues (By similarity). 7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-methionine = 7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-homocysteine 7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine(37) in tRNA(Phe) + CO2 + S-adenosyl-L-methionine = 2 H(+) + S-adenosyl-L-homocysteine + wybutosine(37) in tRNA(Phe) tRNA modification; wybutosine-tRNA(Phe) biosynthesis. Belongs to the methyltransferase superfamily. LCMT family. +Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell attachment to the extracellular matrix, remodeling of the extracellular matrix, cell migration, differentiation, survival and cell proliferation. Collagen binding triggers a signaling pathway that involves SRC and leads to the activation of MAP kinases. Regulates remodeling of the extracellular matrix by up-regulation of the matrix metalloproteinases MMP2, MMP7 and MMP9, and thereby facilitates cell migration and wound healing. Required for normal blastocyst implantation during pregnancy, for normal mammary gland differentiation and normal lactation. Required for normal ear morphology and normal hearing (By similarity). Promotes smooth muscle cell migration, and thereby contributes to arterial wound healing. Also plays a role in tumor cell invasion. Phosphorylates PTPN11. ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein] Inhibited by the multi-targeted cancer drugs imatinib and ponatinib. Homodimer. Interacts (via PPxY motif) with WWC1 (via WW domains) in a collagen-regulated manner. Forms a tripartite complex with WWC1 and PRKCZ, but predominantly in the absence of collagen. Interacts (tyrosine phosphorylated) with SHC1. Interacts with SRC. Interacts with MYH9. Interacts with CDH1. Interacts with PTPN11. Interacts with NCK2. Detected in T-47D, MDA-MB-175 and HBL-100 breast carcinoma cells, A-431 epidermoid carcinoma cells, SW48 and SNU-C2B colon carcinoma cells and Hs 294T melanoma cells (at protein level). Expressed at low levels in most adult tissues and is highest in the brain, lung, placenta and kidney. Lower levels of expression are detected in melanocytes, heart, liver, skeletal muscle and pancreas. Abundant in breast carcinoma cell lines. In the colonic mucosa, expressed in epithelia but not in the connective tissue of the lamina propria. In the thyroid gland, expressed in the epithelium of the thyroid follicles. In pancreas, expressed in the islets of Langerhans cells, but not in the surrounding epithelial cells of the exocrine pancreas. In kidney, expressed in the epithelia of the distal tubules. Not expressed in connective tissue, endothelial cells, adipose tissue, muscle cells or cells of hematopoietic origin. The Gly/Pro-rich domains may be required for an unusual geometry of interaction with ligand or substrates. Autophosphorylated in response to fibrillar collagen binding. Glycosylation of Asn-211, but apparently not of Asn-260 or Asn-394, prevents autophosphorylation from occurring in the absence of collagen. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the protein kinase superfamily. Tyr protein kinase family. Insulin receptor subfamily. The mutant Gln-371 studied is still likely to be glycosylated at Asn-370, but study did not include mutagenesis of Asn-370. Truncated C-terminus. Extended N-terminus. +Binds lactose. May play a role in fruiting body formation (By similarity). Homotetramer. Oligomerization is required for carbohydrate binding. Detected in extracellular matrix, cell wall and cytoplasmic membrane-bound bodies. Most abundant in fruiting bodies. Very low levels of expression in asexual vegetative mycelia. Most abundant prior to premeiotic S-phase, remains high from karyogamy to early pachytene, declines drastically by late pachytene and diplotene, and is undetectable by sterigma stage. Repressed by continuous light. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine Purine metabolism; AMP biosynthesis via salvage pathway; AMP from adenine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)). 7-carboxy-7-deazaguanine + ATP + NH4(+) = 7-cyano-7-deazaguanine + ADP + H(+) + H2O + phosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. Homodimer. Belongs to the QueC family. +Catalyzes the cleavage of 5-oxoproline to form L-glutamate coupled to the hydrolysis of ATP to ADP and inorganic phosphate. 5-oxo-L-proline + ATP + 2 H2O = ADP + H(+) + L-glutamate + phosphate Forms a complex composed of PxpA, PxpB and PxpC. Belongs to the LamB/PxpA family. +ATP-dependent chaperone which uses the energy provided by ATP hydrolysis to generate mechanical force to disassemble protein complexes (By similarity). Required for various steps of embryonic mitosis including centrosome duplication, spindle assembly, ER dynamics and cell cycle progression (PubMed:15716356, PubMed:18854144). Regulates the stability and activity of kinase air-2, a component of the chromosomal passenger complex (CPC) (PubMed:18854144). Inhibits air-2 kinase activity from metaphase to late telophase and negatively regulates air-2 stability during mitotic exit (PubMed:18854144). Controls ER transition into sheet-like structures at the onset of mitosis, possibly by regulating homotypic membrane fusion (PubMed:15716356). ATP + H2O = ADP + H(+) + phosphate Homohexamer; ATP binding induces oligomerization (By similarity). Forms a ring-shaped particle of about 12 nm diameter, that displays 6-fold radial symmetry (By similarity). Interacts (via N-terminus) with kinase air-2; the interaction is direct and inhibits air-2 kinase activity in an ATPase-dependent manner. The first ATP-binding region binds ATP with low affinity whereas the second ATP-binding region binds ATP with high affinity. RNAi-mediated knockdown causes embryonic lethality (PubMed:15716356, PubMed:18854144). The first embryonic cell divisions have mitotic spindle and chromosome segregation defects, and mitotic progression is significantly delayed (PubMed:18854144). At late telophase/G1, air-2 accumulates at the spindle midbody abnormally persisting following cleavage furrow ingression and into the next mitotic cycle (PubMed:18854144). Loss of inhibition of air-2 kinase activity (PubMed:18854144). Also, causes defects in ER dynamics characterized by a failure of the ER to form a sheet structure at the onset of mitosis and remains in large aggregates throughout mitosis (PubMed:15716356). In an air-2 (os207) mutant background, which lacks air-2 catalytic activity, restores normal mitosis and thus embryonic viability (PubMed:18854144). Belongs to the AAA ATPase family. AFG2 subfamily. +The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-amino acid + H(+) Monomer. Belongs to the PTH family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Repressed under conditions of excess protein secretion capacity and derepressed when protein secretion becomes limiting. This is regulated by SecM. Belongs to the SecA family. +The 26S proteasome is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex (By similarity). Belongs to the AAA ATPase family. +Probable transporter. Belongs to the mitochondrial carrier (TC 2.A.29) family. +Catalyzes the synthesis of beta-nicotinate D-ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP. 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H2O + nicotinate = ADP + diphosphate + nicotinate beta-D-ribonucleotide + phosphate Cofactor biosynthesis; NAD(+) biosynthesis; nicotinate D-ribonucleotide from nicotinate: step 1/1. Transiently phosphorylated on a His residue during the reaction cycle. Phosphorylation strongly increases the affinity for substrates and increases the rate of nicotinate D-ribonucleotide production. Dephosphorylation regenerates the low-affinity form of the enzyme, leading to product release. Belongs to the NAPRTase family. +Truncated N-terminus. Truncated N-terminus. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 2 family. +Involved in calcium binding and microtubule stabilization. Belongs to the TCTP family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase epsilon chain family. +Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). H(+) + orotidine 5'-phosphate = CO2 + UMP Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. Homodimer. Belongs to the OMP decarboxylase family. Type 1 subfamily. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Involved in responses to osmotic stress and abscisic acid (ABA). May act as a positive regulator of ABA signaling during germination and seedling development under stress. Expressed in the root elongation zone, stele, root cap, embryo vascular system, leaf axilar buds, silique abscission zone and guard cells. By salt and ABA treatments. No visible phenotype under normal growth conditions, but mutant seedlings show reduced root elongation under salt stress and increased germination rates under osmotic stress and exogenous ABA treatments. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP). isopentenyl diphosphate = dimethylallyl diphosphate Binds 1 Mg(2+) ion per subunit. The magnesium ion binds only when substrate is bound. Binds 1 Mn(2+) ion per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1. Belongs to the IPP isomerase type 1 family. +Required for pathogen-induced salicylic acid (SA) accumulation and SA-mediated resistance to virulent and avirulent pathogens (e.g. P.syringae). By pathogenic bacteria (e.g. P.syringae) and jasmonic acid (MeJA). Hypersusceptiblity to both virulent and avirulent strains of the bacterial pathogen P.syringae associated with impaired pathogen-mediated induction of salicylic acid (SA) and reduced pathogenesis-related (PR) genes induction. These phenotypes are reversed by SA treatment. In the cv. No-0 but not the cv. Columbia background, defects in SA accumulation or signaling enhances resistance to necrotrophic pathogens such as the fungi B.cinerea and A.brassicicola, leading to small necrotic spots and minor chlorosis, as well as reduced fungal growth. Belongs to the plant acyltransferase family. +Stabilizes the tail sheath structure and acts as a connector between the end of tail and the portal vertex of the capsid. Hexamer. Interacts with gp3 and gp18 on the bottom part of the hexamer. Interacts with gp13 and gp14 on the top part of the hexamer. +Probable transcription factor involved in stress response (By similarity). Binds to DNA-specific sequences of CLPD1 and OAT promoters in vitro (PubMed:18813954). Expressed in phloem. Predominantly expressed in developing vascular tissue of the leaves and roots, and in developing flowers. Induced by salt and cold stresses. The NAC domain includes a DNA binding domain and a dimerization domain. +It is involved in the activation of genes necessary for anaerobic respiration. It probably also activates genes involved in the production of virulence factors. Binds 1 [4Fe-4S] cluster per subunit. Homodimer. By anaerobiosis. The DNA coding for this protein is not found in the complete genome of strain ATCC 27872 / DSM 7271 / JCM 12966 / VPI 2845. +Hydrolyzes agarose and also neoagarotetraose to yield neoagarobiose. Hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose, giving the tetramer as the predominant product. Belongs to the glycosyl hydrolase 50 family. +Belongs to the bacterial ribosomal protein bL36 family. +Part of the ABC transporter complex NikABCDE (Opp2) involved in nickel import. Binds nickel and transfers it to the membrane-bound permease. Required for full urease activity and plays a significant role in the virulence of S.aureus during urinary tract infection (UTI) (PubMed:20662775). May bind nickel via a nickel-chelator (PubMed:25611161). The complex is composed of two ATP-binding proteins (NikD and NikE), two transmembrane proteins (NikB and NikC) and a solute-binding protein (NikA). Induced in response to decrease in pH and as a function of growth phase. Deletion of the gene strongly reduces nickel transport and urease activity. Mutant shows decreased virulence in a mouse model of ascending UTI. Nickel accumulation and urease activity are almost completely abolished in a nixA-nikA double mutant. Belongs to the bacterial solute-binding protein 5 family. Truncated N-terminus. +Deoxycytidyl transferase involved in DNA repair and translesion synthesis (TLS). Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. Mediates also the insertion of dTMP or dGMP when the opposite base is G, and, with a low efficiency, dGMP insertions opposite G, T, and C, dAMP insertions opposite G, A, and T, and dTMP insertion opposite A. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents (e.g. UV and gamma ray), mostly via G to T transversions, and of spontaneous mutations in somatic cells. Confers resistance to ultraviolet-B (UV-B) and various DNA cross-linkers (e.g. mitomycin C MMC and cisplatin). Promotes stem growth. Mn(2+) ions. Can also use Mg(2+) ions with a lower efficiency. Monomer. The C-terminal domain is necessary for protein interactions. Reduced UV light- and gamma ray-induced mutation frequency. Slightly sensitive to ultraviolet-B (UV-B) and DNA cross-linkers (e.g. mitomycin C MMC and cisplatin). Lower germination rate. Belongs to the DNA polymerase type-Y family. +May be due to a competing acceptor splice site. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Specifically promotes functional cell surface expression of olfactory receptors, but not of other GPCRs. Interacts with olfactory receptors. Effective cell surface expression depends upon interaction with olfactory receptors. Predominantly expressed in olfactory and vomeronasal organs, in mature olfactory sensory neurons. Belongs to the TMEM7 family. +Belongs to the UPF0374 family. +The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. Binds 1 lipoyl cofactor covalently. The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvH family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Involved in protein precursor import into chloroplasts. Part of the redox regulon consisting of TIC32, TIC 55 and TIC62 (PubMed:12426385). Acts as a membrane anchor of LFNR1 and LFNR2. Has a NADPH-dependent dehydrogenase activity, but only after preincubation with lipids (By similarity). Part of the Tic complex. Interacts with TIC110 and TIC55. Interacts with LFNR1 and LFNR2. Component of high molecular weight thylakoid LFNRs-containing protein complexes containing LIR1, LFNR1, LFNR2, TIC62 and TROL proteins. Shuttles between the membranes and the stroma, depending on the redox state of the plastidic NADP(+)/NADPH pool. Expressed in cotyledons and leaves, but not in roots. Expressed from day 3 of seedling development and continues throughout the development of photosynthetic tissues. No visible phenotype, but loss of membrane-bound LFNR1 or LFNR2. +Involved in the balancing of excitation energy between the two photosystems I (PSI) and II (PSII). Component of the photosystem I (PSI) complex. Interacts directly with PSAL. Prevalent in stroma lamellae with low amounts in grana. Reduction by 50 percent in state transitions due to a disturbed balancing of excitation energy between the two photosystems. Short flowering delay. Belongs to the PSAO family. +N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 3/5. Belongs to the TrpF family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. +The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and thereby links the glycolytic pathway to the tricarboxylic cycle. (R)-N(6)-lipoyl-L-lysyl-[dihydrolipoyllysine-residue acetyltransferase] + H(+) + pyruvate = (R)-N(6)-(S(8)-acetyldihydrolipoyl)-L-lysyl-[dihydrolipoyllysine-residue acetyltransferase] + CO2 Pyruvate dehydrogenase activity is inhibited by phosphorylation of PDHA1; it is reactivated by dephosphorylation. Heterotetramer of two PDHA1 and two PDHB subunits. The heterotetramer interacts with DLAT, and is part of the multimeric pyruvate dehydrogenase complex that contains multiple copies of pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (DLAT, E2) and lipoamide dehydrogenase (DLD, E3). These subunits are bound to an inner core composed of about 48 DLAT and 12 PDHX molecules (By similarity). Phosphorylation at Ser-231, Ser-292 and Ser-299 by PDK family kinases inactivates the enzyme; for this phosphorylation at a single site is sufficient. Phosphorylation at Ser-292 interferes with access to active site, and thereby inactivates the enzyme. Dephosphorylation at all three sites, i.e. at Ser-231, Ser-292 and Ser-299, is required for reactivation. Acetylation alters the phosphorylation pattern. Deacetylated by SIRT3 (By similarity). +Multifunctional regulator of fatty acid metabolism. Homodimer. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Acyl transferase is part of the fatty acid reductase system required for aldehyde biosynthesis; it produces fatty acids for the luminescent reaction. Lipid metabolism; fatty acid reduction for biolumincescence. Belongs to the LuxD family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Can be acetylated to form H2BK6ac, H2BK33ac and H2BK34ac. Monoubiquitinated to form H2BK143ub1; may give a specific tag for epigenetic transcriptional activation. Belongs to the histone H2B family. To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-36; H2BK34ac = acetylated Lys-37; H2BK143ub1 = monoubiquitinated Lys-144. +Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily. +Toxic component of a type II toxin-antitoxin (TA) system. An RNase. Belongs to the PINc/VapC protein family. +Regulates gene expression patterns in meristems and thus modulates organ development. Required for correct embryo patterning and cotyledon organogenesis. Modulates auxin signaling pathway in early embryos. Involved in the cytokinin signaling pathway that promotes shoot regeneration. Acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). Interacts with class 3 HD-ZIP proteins such as ATHB-8, CNA, PHB, PHV, and REV. Expressed in shoot apical and floral meristems, and in organ primordia. Transient expression during shoot regeneration. First observed in the embryo at four-cell stage. At the globular stage, localized in cotyledons primordia. Later confined to embryonic cotyledons tips. Expressed from embryogenesis onward in the central zone of the shoot apical and floral meristems, in organ anlagen, and (transiently) in the distal domains of organ primordia. By cytokinins. 'Dornroeschen' means 'Sleeping beauty' in German. Belongs to the AP2/ERF transcription factor family. ERF subfamily. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 2 subfamily. +Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Belongs to the peptidase C19 family. +Usually encoded in the trnK tRNA gene intron. Probably assists in splicing its own and other chloroplast group II introns. Belongs to the intron maturase 2 family. MatK subfamily. +ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl-tRNA(Gln) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Participates in the regulation of alternative splicing by modulating the activity of other splice facors. Inhibits the splicing activity of SFRS1, SFRS2 and SFRS6. Augments the splicing activity of SFRS3 (By similarity). Homodimer. Binds SFRS1, SFRS2, SFRS3 and SFRS6. Interacts with the spliceosome (By similarity). Interacts with SREK1IP1. Belongs to the splicing factor SR family. Contaminating sequence. Potential poly-A sequence. +Belongs to the thioredoxin family. +Inhibitor of protein-phosphatase 1 (PP1). Interacts with pppB. Expressed at all stage of development with an increase from 8 hours after starvation. Belongs to the protein phosphatase inhibitor 2 family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Has a weak inhibitory effect on voltage-gated sodium channel Nav1.2/SCN2A. Weakly inhibits acetylcholine esterase in vitro. Increases interleukin-6 secretion from macrophages in vitro. Has no antifungal, antiviral or cytotoxic activity. Expressed by the venom gland. No effect on voltage-gated potassium channels. No effect on voltage-gated sodium channels Nav1.3/SCN3A, Nav1.4/SCN4A, Nav1.5/SCN5A and a sodium channel from B.germanica. Belongs to the non-disulfide-bridged peptide (NDBP) superfamily. +Escorts unspliced or incompletely spliced viral pre-mRNAs (late transcripts) out of the nucleus of infected cells. These pre-mRNAs carry a recognition sequence called Rev responsive element (RRE) located in the env gene, that is not present in fully spliced viral mRNAs (early transcripts). This function is essential since most viral proteins are translated from unspliced or partially spliced pre-mRNAs which cannot exit the nucleus by the pathway used by fully processed cellular mRNAs (By similarity). Homomultimer; when bound to the RRE. Multimeric assembly is essential for activity (By similarity). The presence of both nuclear import and nuclear export signals leads to continuous shuttling between the nucleus and cytoplasm. The RNA-binding motif binds to the RRE, a stem-and-loop structure present in incompletely spliced viral pre-mRNAs. This region also contains the NLS which mediates nuclear localization. These overlapping functions prevent Rev bound to RRE from undesirable return to the nucleus. When Rev binds the RRE, the NLS becomes masked while the NES remains accessible (By similarity). +Extracellular matrix and cell adhesion protein that plays a role in nervous system development and in synaptic plasticity. Both soluble and membranous forms promote neurite outgrowth of cerebellar and hippocampal neurons and suppress neuronal cell death. Plays a role in neuronal positioning of pyramidal neurons and in regulation of both the number of interneurons and the efficacy of GABAergic synapses. May play a role in regulating cell migration in nerve regeneration and cortical development. Potentiates integrin-dependent cell migration towards extracellular matrix proteins. Recruits ANK3 to the plasma membrane (By similarity). May interact with L1CAM. May interact with ITGB1/ITGA1 heterodimer and ITGB1/ITGA2 heterodimer as well as with ANK3 (By similarity). Soluble forms produced by cleavage/shedding also exist. Expressed in the fetal and adult brain as well as in Schwann cell culture. Also detected in adult peripheral tissues. The FIG[AQ]Y motif seems to be an ankyrin recruitment region. The DGEA motif seems to be a recognition site for integrin. Cleavage by metalloprotease ADAM8 in the extracellular part generates 2 soluble forms (125 kDa and 165 kDa) in vitro and is inhibited by metalloprotease inhibitors (By similarity). Cleaved by BACE1 (By similarity). N-glycosylated. Contains N-linked oligosaccharides with a sulfated carbohydrate structure type HNK-1 (SO4-3-GlcUABeta1,3GalBeta1,4GlcNAc) (By similarity). O-glycosylated. Belongs to the immunoglobulin superfamily. L1/neurofascin/NgCAM family. Extended N-terminus. +Chaperone protein which promotes assembly of the 20S proteasome. May cooperate with psmg1-psmg2 heterodimers to orchestrate the correct assembly of proteasomes (By similarity). Belongs to the PSMG3 family. +Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP). [phosphate](n) + ATP = [phosphate](n+1) + ADP An intermediate of this reaction is the autophosphorylated ppk in which a phosphate is covalently linked to a histidine residue through a N-P bond. Belongs to the polyphosphate kinase 1 (PPK1) family. +Represses ulaG and the ulaABCDEF operon. +Is an aliphatic amidase with a restricted substrate specificity, as it only hydrolyzes formamide. Probably involved in the nitrogen metabolism of H.pylori. formamide + H2O = formate + NH4(+) Inhibited by iodoacetate. Appears to be regulated by the fur protein, but this effect is not mediated at the transcriptional level. Optimum pH is 6. Optimum temperature is 45 degrees Celsius. Homotetramer. Unlike the other amidase AmiE, expression of amiF is not repressed by iron. Asp-168 is probably not involved in the catalytic mechanism, but is probably involved instead in maintenance of the structural integrity of the amidase. Expression of the amiF gene is stimulated in a mutant deficient in arginase activity, suggesting that production of this enzyme is regulated to maintain intracellular nitrogen balance in H.pylori. Belongs to the carbon-nitrogen hydrolase superfamily. Aliphatic amidase family. +RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs. Homohexamer. Belongs to the Hfq family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity). a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 5 family. +Endonuclease that is involved in the suppression of homologous recombination and may therefore have a key role in the control of bacterial genetic diversity. Homodimer. Belongs to the DNA mismatch repair MutS family. MutS2 subfamily. +Essential for the progression of premeiotic mitosis and meiosis during sporogenesis. Regulates the cell division of premeiotic germ cells, the proper modification of meiotic chromosomes, and the faithful progression of meiosis, probably via small RNA-mediated gene silencing. May be involved in histone H3 'Lys-9' demethylation in the pericentromeric region. Expressed specifically in male and female archesporial cells and sporogenous cells (SC) before meiosis but not in the nursery cells supporting SC. Arrest of meiosis in male and female germ cells, causing seed sterility. Belongs to the argonaute family. Ago subfamily. +Required for high-fidelity chromosome segregation during the later part of each cell cycle. Acts in opposition to the phosphatase PP1. Has a role in attaching the kinetochores to the microtubules and ensuring that sister kinetochores connect to opposite poles. The promotion of bi-orientation is achieved by selectively detaching kinetochore-microtubule attachments that are not under tension (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Associates with the mitotic spindle and on elongated and disassembling spindles. Also associated with the kinetochore (By similarity). Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. Aurora subfamily. +Belongs to the UPF0178 family. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. +Cell wall-associated. Constitutively expressed during growth in culture. Belongs to the peptidase S8 family. +Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA (PubMed:23352267). Performs the decatenation events required during the replication of a circular DNA molecule. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+). Pyrrolopyrimidines inhibit both GyrB and its paralog in topoisomerase IV (parE) (PubMed:23352267). Heterotetramer composed of ParC and ParE. Belongs to the type II topoisomerase family. ParE type 1 subfamily. +Homohexamer. Assembles into a hexameric ring structure. Belongs to the AAA ATPase family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Belongs to the V-ATPase E subunit family. +Ribosomal protein P0 is the functional equivalent of E.coli protein L10. P0 forms a pentameric complex by interaction with dimers of P1 and P2. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with APEX1. Interacts with FMR1. Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Belongs to the universal ribosomal protein uL10 family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Belongs to the DMRL synthase family. +NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm. The first step is catalyzed by NqrF, which accepts electrons from NADH and reduces ubiquinone-1 to ubisemiquinone by a one-electron transfer pathway. a ubiquinone + H(+) + n Na(+)(in) + NADH = a ubiquinol + n Na(+)(out) + NAD(+) Binds 1 [2Fe-2S] cluster. Composed of six subunits; NqrA, NqrB, NqrC, NqrD, NqrE and NqrF. Belongs to the NqrF family. +Acts as a plasma-membrane magnesium transporter. Belongs to the SLC41A transporter family. +Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide. 6-carboxyhexanoyl-[ACP] + H(+) + L-alanine = (8S)-8-amino-7-oxononanoate + CO2 + holo-[ACP] Cofactor biosynthesis; biotin biosynthesis. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP). diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 1/2. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrE subfamily. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex (By similarity). Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Probably functions as a manganese efflux pump. Belongs to the MntP (TC 9.B.29) family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Probably deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs), playing an important role in chemotaxis. H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Belongs to the CheD family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Monoubiquitination at Lys-35 (H2BK34Ub) by the MSL1/MSL2 dimer is required for histone H3 'Lys-4' (H3K4me) and 'Lys-79' (H3K79me) methylation and transcription activation at specific gene loci, such as HOXA9 and MEIS1 loci. Similarly, monoubiquitination at Lys-121 (H2BK120Ub) by the RNF20/40 complex gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation. It also functions cooperatively with the FACT dimer to stimulate elongation by RNA polymerase II. H2BK120Ub also acts as a regulator of mRNA splicing: deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons (By similarity). Phosphorylated on Ser-15 (H2BS14ph) by STK4/MST1 during apoptosis; which facilitates apoptotic chromatin condensation. Also phosphorylated on Ser-15 in response to DNA double strand breaks (DSBs), and in correlation with somatic hypermutation and immunoglobulin class-switch recombination. Phosphorylation at Ser-37 (H2BS36ph) by AMPK in response to stress promotes transcription. GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes (By similarity). Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes. Hydroxybutyrylation of histones is induced by starvation. Lactylated in macrophages by EP300/P300 by using lactoyl-CoA directly derived from endogenous or exogenous lactate, leading to stimulates gene transcription. Belongs to the histone H2B family. +Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate. ATP + L-glutamate = ADP + L-glutamyl 5-phosphate Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 1/2. Belongs to the glutamate 5-kinase family. +Belongs to the herpesviridae UL91 family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB). (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 4/7. Quinol/quinone metabolism; menaquinone biosynthesis. Belongs to the mandelate racemase/muconate lactonizing enzyme family. MenC type 1 subfamily. +Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). diphosphate + N-(5-phospho-beta-D-ribosyl)anthranilate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate Binds 2 magnesium ions per monomer. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 2/5. Homodimer. Belongs to the anthranilate phosphoribosyltransferase family. +Catalyzes the reversible phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha-D-ribose 1-phosphate a purine 2'-deoxy-D-ribonucleoside + phosphate = 2-deoxy-alpha-D-ribose 1-phosphate + a purine nucleobase Homohexamer; trimer of homodimers. Belongs to the PNP/UDP phosphorylase family. +Catalyzes the 3'-O-methylation of the flavonoids luteolin and quercetin (PubMed:9514654). Catalyzes the 3- of 5-O-methylation of the phenylpropanoids caffeate and 5-hydroxyferulate (PubMed:9514654). Substrate preference is 5-hydroxyferulate > luteolin > quercetin > caffeate (PubMed:9514654). Apigenin, kempferol and 3,4-dimethylquercetin do not seem to be substrates for methylation (PubMed:9514654). (E)-5-hydroxyferulate + S-adenosyl-L-methionine = E-sinapate + H(+) + S-adenosyl-L-homocysteine luteolin + S-adenosyl-L-methionine = chrysoeriol + H(+) + S-adenosyl-L-homocysteine quercetin + S-adenosyl-L-methionine = H(+) + isorhamnetin + S-adenosyl-L-homocysteine (E)-caffeate + S-adenosyl-L-methionine = (E)-ferulate + H(+) + S-adenosyl-L-homocysteine a 3'-hydroxyflavone + S-adenosyl-L-methionine = a 3'-methoxyflavone + H(+) + S-adenosyl-L-homocysteine Flavonoid metabolism. Homodimer. Belongs to the class I-like SAM-binding methyltransferase superfamily. Cation-independent O-methyltransferase family. COMT subfamily. It is not sure whether OMT1 and OMT2 are really encoded by two different genes or if they represent cloning artifacts. +Common subunit for the receptors for a variety of interleukins (PubMed:7718508). Probably in association with IL15RA, involved in the stimulation of neutrophil phagocytosis by IL15 (By similarity). The gamma subunit is common to the IL2, IL4, IL7, IL15, IL21 and probably also the IL13 receptors. Interacts with SHB upon interleukin stimulation (By similarity). Interacts with IL9 (PubMed:7718508). The WSXWS motif appears to be necessary for proper protein folding and thereby efficient intracellular transport and cell-surface receptor binding. The box 1 motif is required for JAK interaction and/or activation. Belongs to the type I cytokine receptor family. Type 5 subfamily. +Seems to play a role in the dimerization of PSII. Belongs to the PsbT family. +Bacteriocin active against S.aureus, E.coli, Salmonella sp. and Streptococcus sp. +Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis. ATP + beta-D-fructose 6-phosphate = ADP + beta-D-fructose 1,6-bisphosphate + H(+) Allosterically activated by ADP and other diphosphonucleosides, and allosterically inhibited by phosphoenolpyruvate. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 3/4. Homotetramer. Belongs to the phosphofructokinase type A (PFKA) family. ATP-dependent PFK group I subfamily. Prokaryotic clade 'B1' sub-subfamily. +Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate. AH2 + GTP + S-adenosyl-L-methionine = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + A + H(+) + L-methionine Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate. Cofactor biosynthesis; molybdopterin biosynthesis. Monomer and homodimer. Belongs to the radical SAM superfamily. MoaA family. +Plays a role in mitochondrial cytochrome c maturation. Probable component of a heme lyase complex involved in the reduction of apocytochrome c. Belongs to the CcmH/CycL/Ccl2/NrfF family. +Involved in poly(A)+ RNA transport. Involved in nephrogenesis (PubMed:30179222). Forms part of the Nup160 subcomplex in the nuclear pore which is composed of NUP160, NUP133, NUP107 and Nup96. This complex plays a role in RNA export and in tethering Nup98 and NUP153 to the nucleus. Located on both the cytoplasmic and nuclear sides of the nuclear pore (PubMed:11564755). During mitosis, localizes to the kinetochores (PubMed:11564755). Widely expressed in fetal and adult tissues. Expressed in the brain and kidney. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the nucleoporin Nup133 family. +Involved in light-induced chloroplast development and growth. Involved in the plant response to abiotic and photooxidative stresses. May be involved in the suppression of photooxidative damage. A number of isoforms are produced. According to EST sequences. Belongs to the Y3IP1/CEST family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +Cell surface receptor that binds to the chondroitin sulfate moiety of glycosaminoglycan chains and promotes cell attachment. Promotes granulocyte chemotaxis, degranulation and adhesion. In macrophages, promotes the release of inflammatory cytokines, including IL8 and TNF. Signals probably through G-proteins. Is a regulator of mast cell degranulation (PubMed:26841242). Forms a heterodimer, consisting of a large extracellular region non-covalently linked to a seven-transmembrane moiety. Interacts with chondroitin sulfate; the interaction with chondroitin sulfate is calcium-dependent. Interacts with CD55. Localized at the leading edge of migrating cells. A number of isoforms are probably produced. A soluble form due to a frameshift which introduced a stop codon immediately before the first TM domain is also detected. Expression is restricted to myeloid cells. Highest expression was found in peripheral blood leukocytes, followed by spleen and lymph nodes, with intermediate to low levels in thymus, bone marrow, fetal liver, placenta, and lung, and no expression in heart, brain, skeletal muscle, kidney, or pancreas. Expression is also detected in monocyte/macrophage and Jurkat cell lines but not in other cell lines tested. High expression in mast cells (PubMed:26841242). The GPS domain is necessary, but not sufficient for receptor cleavage, which require the entire extracellular stalk. Binding to chondroitin sulfate is mediated by the fourth EGF domain. Autoproteolytically cleaved into 2 subunits, an extracellular alpha subunit and a seven-transmembrane beta subunit. The disease is caused by variants affecting the gene represented in this entry. Has no murine ortholog. Belongs to the G-protein coupled receptor 2 family. Adhesion G-protein coupled receptor (ADGR) subfamily. +Catalyzes the desulfonation of aliphatic sulfonates. an alkanesulfonate + FMNH2 + O2 = an aldehyde + FMN + 2 H(+) + H2O + sulfite Homotetramer. FMNH(2) which is absolutely required for this enzymatic reaction, is provided by SsuE. Belongs to the SsuD family. +Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide. 6-carboxyhexanoyl-[ACP] + H(+) + L-alanine = (8S)-8-amino-7-oxononanoate + CO2 + holo-[ACP] Cofactor biosynthesis; biotin biosynthesis. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily. +The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-amino acid + H(+) Monomer. Belongs to the PTH family. +Transcriptional activator that mediates FGF signaling during neural development (By similarity). Plays a role in the regulation of cell movement (PubMed:17980025). Does not bind DNA by itself (By similarity). Detected throughout embryogenesis. Up-regulated by FGF signaling in embryos at mid-gastrulation. Belongs to the Churchill family. +May help in the organization of the PsaL subunit. Belongs to the PsaI family. +ATPase subunit of a proteasome-like degradation complex; this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the ClpX chaperone family. HslU subfamily. +Tetranectin binds to plasminogen and to isolated kringle 4. May be involved in the packaging of molecules destined for exocytosis (By similarity). Homotrimer. +Required for anchoring dihydrolipoamide dehydrogenase (E3) to the dihydrolipoamide transacetylase (E2) core of the pyruvate dehydrogenase complexes of eukaryotes. This specific binding is essential for a functional PDH complex. Part of the inner core of the multimeric pyruvate dehydrogenase complex that is composed of about 48 DLAT and 12 PDHX molecules (PubMed:14638692, PubMed:20361979). This core binds multiple copies of pyruvate dehydrogenase (subunits PDH1A and PDHB, E1), dihydrolipoamide acetyltransferase (DLAT, E2) and lipoamide dehydrogenase (DLD, E3) (PubMed:14638692). Interacts with SIRT4 (PubMed:25525879). Interacts with DLD (PubMed:20385101, PubMed:16263718, PubMed:16442803, PubMed:20160912, PubMed:20361979). Delipoylated at Lys-97 by SIRT4, delipoylation decreases the PHD complex activity. The disease is caused by variants affecting the gene represented in this entry. Belongs to the 2-oxoacid dehydrogenase family. +Belongs to the FAM90 family. Could be the product of a pseudogene. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +May play an important role in the heart development by scaffolding PKC to the Z-disk region. May play a role in the regulation of cardiomyocyte expansion. Isoforms lacking the LIM domains may negatively modulate the scaffolding activity of isoform 1. Overexpression promotes the development of heart hypertrophy. Contributes to the regulation of dendritic spine morphogenesis in neurons. May be required to restrain postsynaptic growth of excitatory synapses. Isoform 1, but not isoform 2, expression favors spine thinning and elongation. Interacts with various PKC isoforms through the LIM domains. Interacts with actin and alpha-actinin through the PDZ domain. Interacts (via LIM domains) with SIPA1L1/SPAR; this interaction may occur preferentially with isoform 1. Detected both at presynaptic and postsynaptic sites, exclusively at excitatory synapses, but not inhibitory synapses, in hippocampal neurons. Heart and skeletal muscle specific. Expression is commonly increased in the brain of patients with bipolar disorder, schizophrenia, and major depression. +Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P). D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate from glycerone phosphate: step 1/1. Homotetramer; dimer of dimers. Belongs to the triosephosphate isomerase family. +This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a 'molecular matchmaker', a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex. Belongs to the DNA mismatch repair MutL/HexB family. +Involved in chemotaxis. Part of a chemotaxis signal transduction system that modulates chemotaxis in response to various stimuli. Catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins or MCP) by CheR. Also mediates the irreversible deamidation of specific glutamine residues to glutamic acid. [protein]-L-glutamate 5-O-methyl ester + H2O = H(+) + L-glutamyl-[protein] + methanol H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Contains a C-terminal catalytic domain, and an N-terminal region which modulates catalytic activity. Phosphorylated by CheA. Phosphorylation of the N-terminal regulatory domain activates the methylesterase activity. Belongs to the CheB family. +Major acute phase reactant. Apolipoprotein of the HDL complex. Expressed by the liver; secreted in plasma. Belongs to the SAA family. +Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). This peptide corresponds to allele E1j. Has not been merged with other alleles since they may differ due to geographic variation (see strain in PubMed:19606224). Belongs to the conotoxin O1 superfamily. +Modulates transcription in response to changes in cellular NADH/NAD(+) redox state. Homodimer. Belongs to the transcriptional regulatory Rex family. +Lysosomal membrane glycoprotein which plays an important role in lysosome biogenesis, autophagy, and cholesterol homeostasis (By similarity). Also plays an important role in NK-cells cytotoxicity. Mechanistically, participates in cytotoxic granule movement to the cell surface and perforin trafficking to the lytic granule. In addition, protects NK-cells from degranulation-associated damage induced by their own cytotoxic granule content. Presents carbohydrate ligands to selectins. Also implicated in tumor cell metastasis (By similarity). Interacts with ABCB9; this interaction strongly stabilizes ABCB9 and protects ABCB9 against lysosomal degradation. Interacts with FURIN. This protein shuttles between lysosomes, endosomes, and the plasma membrane (By similarity). Colocalizes with OSBPL1A at the late endosome (By similarity). O- and N-glycosylated; some of the N-glycans attached to LAMP-1 are polylactosaminoglycans. Belongs to the LAMP family. +Mediates resistance to pathogens which are sensitive to stilbenes. 4-coumaroyl-CoA + 3 H(+) + 3 malonyl-CoA = 4 CO2 + 4 CoA + trans-resveratrol Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene biosynthesis; 3,4',5-trihydroxystilbene from trans-4-coumarate: step 2/2. Homodimer. Belongs to the thiolase-like superfamily. Chalcone/stilbene synthases family. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single-stranded and double-stranded RNA (By similarity). an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]. an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]. Monomer. Interacts with and forms tight 1:1 complexes with RNH1. Dimerization of two such complexes may occur. Interaction with RNH1 inhibits this protein (By similarity). Pancreas. Belongs to the pancreatic ribonuclease family. +Binds 3 Zn(2+) ions per subunit. Belongs to the PHP family. +Partially overlaps PRP19. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Down-regulated by growth on bacteria. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 2 subfamily. +2 ATP + H2O + hydrogencarbonate + L-glutamine = 2 ADP + carbamoyl phosphate + 2 H(+) + L-glutamate + phosphate Amino-acid biosynthesis; L-arginine biosynthesis; carbamoyl phosphate from bicarbonate: step 1/1. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 1/3. Composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate. Belongs to the CarA family. +Belongs to the bacterial ribosomal protein bS16 family. +Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine. putrescine + S-adenosyl 3-(methylsulfanyl)propylamine = H(+) + S-methyl-5'-thioadenosine + spermidine Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1. Homodimer or homotetramer. Belongs to the spermidine/spermine synthase family. +Probably part of the PhnSTUV complex (TC 3.A.1.11.5) involved in 2-aminoethylphosphonate import. Probably responsible for the translocation of the substrate across the membrane (By similarity). Belongs to the binding-protein-dependent transport system permease family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Endonuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves mobile four-strand junctions by introducing symmetrical nicks in paired strands. Promotes annealing of linear ssDNA with homologous dsDNA. Required for DNA repair, homologous recombination and chromosome segregation. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RecU family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes forming pentameric protein-lipid pores that allow ion transport. Also plays a role in the induction of apoptosis. Homopentamer. Interacts with membrane protein M in the budding compartment of the host cell, which is located between endoplasmic reticulum and the Golgi complex. Interacts with Nucleoprotein. The cytoplasmic tail functions as a Golgi complex-targeting signal. Belongs to the betacoronaviruses E protein family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Involved in the biogenesis of the PMF fimbria. Belongs to the periplasmic pilus chaperone family. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Transport of potassium into the cell. Belongs to the HAK/KUP transporter (TC 2.A.72) family. +Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase. Belongs to the HypA/HybF family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) In cyanobacteria the RNAP catalytic core is composed of 2 alpha, 1 beta, 1 beta', 1 gamma and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Regulator of deubiquitinating complexes. Activates deubiquitination by increasing the catalytic turnover without increasing the affinity of deubiquitinating enzymes for the substrate (By similarity). Belongs to the WD repeat WDR48 family. +May be involved in protein traffic between late Golgi and early endosomes. Belongs to the dopey family. Truncated N-terminus. +Belongs to the UPF0231 family. +Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls. H2O + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-2,6-diaminoheptanedioate + succinate Binds 2 Zn(2+) or Co(2+) ions per subunit. Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route): step 3/3. Homodimer. Belongs to the peptidase M20A family. DapE subfamily. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +Interacts strongly with CDK4 and CDK6. Potent inhibitor. Potential effector of TGF-beta induced cell cycle arrest (By similarity). Heterodimer of CDKN2B with CDK4 or CDK6. Expression abundant in lung, less abundant in testis, barely detectable in liver, and not detectable in neonatal kidney, adult kidney, brain, heart, or spleen. Belongs to the CDKN2 cyclin-dependent kinase inhibitor family. +Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Binds 2 divalent ions per subunit. Binds 1 potassium ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Homotetramer; dimer of dimers. Belongs to the AdoMet synthase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Redox regulated molecular chaperone. Protects both thermally unfolding and oxidatively damaged proteins from irreversible aggregation. Plays an important role in the bacterial defense system toward oxidative stress. Under oxidizing conditions two disulfide bonds are formed involving the reactive cysteines. Under reducing conditions zinc is bound to the reactive cysteines and the protein is inactive. Belongs to the HSP33 family. +Catalyzes the phosphorolysis of diverse nucleosides, yielding D-ribose 1-phosphate and the respective free bases. Can use uridine, adenosine, guanosine, cytidine, thymidine, inosine and xanthosine as substrates. Also catalyzes the reverse reactions. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha-D-ribose 1-phosphate adenosine + phosphate = adenine + alpha-D-ribose 1-phosphate cytidine + phosphate = alpha-D-ribose 1-phosphate + cytosine guanosine + phosphate = alpha-D-ribose 1-phosphate + guanine inosine + phosphate = alpha-D-ribose 1-phosphate + hypoxanthine phosphate + thymidine = 2-deoxy-alpha-D-ribose 1-phosphate + thymine phosphate + uridine = alpha-D-ribose 1-phosphate + uracil phosphate + xanthosine = alpha-D-ribose 1-phosphate + xanthine Belongs to the nucleoside phosphorylase PpnP family. +The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. Binds 1 lipoyl cofactor covalently. The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvH family. +Blocks the elongation and depolymerization of the actin filaments at the pointed end. The Tmod/TM complex contributes to the formation of the short actin protofilament, which in turn defines the geometry of the membrane skeleton (By similarity). Binds to the N-terminus of tropomyosin and to actin. Ubiquitous. Belongs to the tropomodulin family. +Cell wall formation. NADP(+) + UDP-N-acetyl-alpha-D-muramate = H(+) + NADPH + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +Forms an efflux pump with AaeB. Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family. +Required for the proteolytic cleavage of the transcription factor RIM101 in response to alkaline ambient pH. May act as a scaffold protein that recruits the calpain-like protease RIM13 via VPS32 to its substrate RIM101 (By similarity). Interacts with RIM101 by binding to its two YPX[LI] motifs. Belongs to the palA/RIM20 family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS15 family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +ATP-specific succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. ATP + CoA + succinate = ADP + phosphate + succinyl-CoA Binds 1 Mg(2+) ion per subunit. Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. Heterodimer of an alpha and a beta subunit. The beta subunit determines specificity for ATP. Interacts with ALAS2 (By similarity). Belongs to the succinate/malate CoA ligase beta subunit family. ATP-specific subunit beta subfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +ATP-dependent transporter of the ATP-binding cassette (ABC) family that actively extrudes physiological compounds and xenobiotics from cells. Transports a range of endogenous molecules that have a key role in cellular communication and signaling, including cyclic nucleotides such as cyclic AMP (cAMP) and cyclic GMP (cGMP), bile acids, steroid conjugates, urate, and prostaglandins. Mediates also the ATP-dependent efflux of glutathione conjugates such as leukotriene C4 (LTC4) and leukotriene B4 (LTB4). The presence of GSH is necessary for the ATP-dependent transport of LTB4, whereas GSH is not required for the transport of LTC4. Mediates the cotransport of bile acids with reduced glutathione (GSH). Transports a wide range of drugs and their metabolites, including anticancer, antiviral and antibiotics molecules. ATP + H2O + xenobioticSide 1 = ADP + phosphate + xenobioticSide 2. an S-substituted glutathione(in) + ATP + H2O = ADP + an S-substituted glutathione(out) + H(+) + phosphate 17beta-estradiol 17-O-(beta-D-glucuronate)(in) + ATP + H2O = 17beta-estradiol 17-O-(beta-D-glucuronate)(out) + ADP + H(+) + phosphate ATP + dehydroepiandrosterone 3-sulfate(in) + H2O = ADP + dehydroepiandrosterone 3-sulfate(out) + H(+) + phosphate ATP + H2O + leukotriene C4(in) = ADP + H(+) + leukotriene C4(out) + phosphate ATP + H2O + leukotriene B4(in) = ADP + H(+) + leukotriene B4(out) + phosphate ATP + H2O + urate(in) = ADP + H(+) + phosphate + urate(out) 3',5'-cyclic GMP(in) + ATP + H2O = 3',5'-cyclic GMP(out) + ADP + H(+) + phosphate 3',5'-cyclic AMP(in) + ATP + H2O = 3',5'-cyclic AMP(out) + ADP + H(+) + phosphate ATP + H2O + prostaglandin E2(in) = ADP + H(+) + phosphate + prostaglandin E2(out) ATP + H2O + prostaglandin E1(in) = ADP + H(+) + phosphate + prostaglandin E1(out) ATP + glutathione(in) + glycodeoxycholate(in) + H2O = ADP + glutathione(out) + glycodeoxycholate(out) + H(+) + phosphate ATP + cholate(in) + glutathione(in) + H2O = ADP + cholate(out) + glutathione(out) + H(+) + phosphate ATP + glutathione(in) + glycocholate(in) + H2O = ADP + glutathione(out) + glycocholate(out) + H(+) + phosphate ATP + glutathione(in) + H2O + taurocholate(in) = ADP + glutathione(out) + H(+) + phosphate + taurocholate(out) ATP + glutathione(in) + glycochenodeoxycholate(in) + H2O = ADP + glutathione(out) + glycochenodeoxycholate(out) + H(+) + phosphate ATP + glutathione(in) + H2O + taurochenodeoxycholate(in) = ADP + glutathione(out) + H(+) + phosphate + taurochenodeoxycholate(out) ATP + glutathione(in) + glycoursodeoxycholate(in) + H2O = ADP + glutathione(out) + glycoursodeoxycholate(out) + H(+) + phosphate ATP + glutathione(in) + H2O + tauroursodeoxycholate(in) = ADP + glutathione(out) + H(+) + phosphate + tauroursodeoxycholate(out) Interacts (via PDZ-binding motif) with SNX27 (via PDZ domain); this interaction accelerates MRP4 internalization. Its localization to the basolateral or apical membranes is tissue-dependent. Ubiquitous with high levels in kidney. N-glycosylated; leading to substrate-selective effects on its transport activity. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. Interacts with UvrB in an incision complex. Belongs to the UvrC family. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I. di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 4 family. MraY subfamily. +Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls. H2O + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-2,6-diaminoheptanedioate + succinate Binds 2 Zn(2+) or Co(2+) ions per subunit. Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route): step 3/3. Homodimer. Belongs to the peptidase M20A family. DapE subfamily. +Catalytic subunit of the DNA primase complex and component of the DNA polymerase alpha complex (also known as the alpha DNA polymerase-primase complex - primosome/replisome) which play an essential role in the initiation of DNA synthesis (PubMed:8918794). The primase subunit of the polymerase alpha complex initiates DNA synthesis by oligomerising short RNA primers on both leading and lagging strands (PubMed:8918794). ssDNA + n dNTP = ssDNA/pppdN(pdN)n-1 hybrid + (n-1) diphosphate. The presence of the regulatory subunit accelerates the kinetics of initiation and primer extension. Optimum pH is 7.6. Heterodimer of a catalytic subunit and a regulatory subunit, also known as the DNA primase complex. The bound zinc ion is not a cofactor. It is bound to a zinc knuckle motif that may be involved in sequence recognition and the binding of ssDNA (By similarity). Belongs to the eukaryotic-type primase small subunit family. +Has a role in spermatogenesis and oogenesis. Belongs to the cueball family. +Forms a channel through the mitochondrial outer membrane that allows diffusion of small hydrophilic molecules. The channel adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective (By similarity). Interacts with KIN14F/KP1 (PubMed:21406623). Interacts with FBA6 AND GAPC1 (PubMed:23316205). Expressed in leaf tips, anthers and stigma. Induced during the hypersensitive response to X.campestris pv campestris and by the bacterial pathogen P.syringae pv. tomato. Consists mainly of membrane-spanning sided beta-sheets. No visible phenotype under normal growth conditions. Belongs to the eukaryotic mitochondrial porin (TC 1.B.8.1) family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Molecular chaperone required for SopB/SigD stabilization and secretion. Homodimer or higher-order oligomers. Transcriptionally regulated by InvF and SicA. Also regulated by SirA. Belongs to the IpgE/SigE chaperone family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Binds RpoD and negatively regulates RpoD-mediated transcription activation by preventing the interaction between the primary sigma factor RpoD with the catalytic core of the RNA polymerase and with promoter DNA. May be involved in replacement of the RNA polymerase sigma subunit from RpoD to RpoS during the transition from exponential growth to the stationary phase. Interacts with RpoD. Belongs to the Rsd/AlgQ family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +hexadecanoyl-CoA + L-cysteinyl-[protein] = CoA + S-hexadecanoyl-L-cysteinyl-[protein] The DHHC domain is required for palmitoyltransferase activity. Autopalmitoylated. Belongs to the DHHC palmitoyltransferase family. PFA5 subfamily. +Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX. coproporphyrinogen III + 2 H(+) + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; protoporphyrinogen-IX from coproporphyrinogen-III (O2 route): step 1/1. Homodimer. Belongs to the aerobic coproporphyrinogen-III oxidase family. +Part of the ABC transporter complex GsiABCD involved in glutathione import. Probably responsible for the translocation of the substrate across the membrane. The complex is composed of two ATP-binding proteins (GsiA), two transmembrane proteins (GsiC and GsiD) and a solute-binding protein (GsiB). Belongs to the binding-protein-dependent transport system permease family. +RNA-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The eIF-3 complex interacts with pix. Belongs to the eIF-3 subunit A family. +Thiolesterase that catalyzes the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid. an S-(2-hydroxyacyl)glutathione + H2O = a 2-hydroxy carboxylate + glutathione + H(+) Binds 1 Fe(3+) ion per subunit. Electron spin resonance clearly indicates the presence of Fe(3+) (PubMed:16227621). Binds 1 Fe(2+) or Zn(2+) ion per subunit. Electron spin resonance indicates the presence of either Fe(2+) or Zn(2+), while X-ray crystallography shows the presence of Zn(2+). Mn(2+) is not a cofactor (PubMed:16227621). Secondary metabolite metabolism; methylglyoxal degradation; (R)-lactate from methylglyoxal: step 2/2. Monomer. May be due to a competing acceptor splice site. Belongs to the metallo-beta-lactamase superfamily. Glyoxalase II family. +Catalyzes the transfer of the alpha-amino group from S-adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only aminotransferase known to utilize SAM as an amino donor. (8S)-8-amino-7-oxononanoate + S-adenosyl-L-methionine = (7R,8S)-7,8-diammoniononanoate + S-adenosyl-4-methylsulfanyl-2-oxobutanoate Cofactor biosynthesis; biotin biosynthesis; 7,8-diaminononanoate from 8-amino-7-oxononanoate (SAM route): step 1/1. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. BioA subfamily. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Contacts the emerging nascent chain on the ribosome. Homodimer. Interacts with the ribosome. Binds ribosomal RNA. Belongs to the NAC-alpha family. +Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ). 5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphooxyethyl)-thiazole + ADP + H(+) Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-methyl-5-(2-phosphoethyl)-thiazole from 5-(2-hydroxyethyl)-4-methylthiazole: step 1/1. Belongs to the Thz kinase family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-aspartyl-tRNA(Asx) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine. L-leucyl-tRNA(Leu) + N-terminal L-lysyl-[protein] = H(+) + N-terminal L-leucyl-L-lysyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-arginyl-[protein] = H(+) + N-terminal L-leucyl-L-arginyl-[protein] + tRNA(Leu) an N-terminal L-alpha-aminoacyl-[protein] + L-phenylalanyl-tRNA(Phe) = an N-terminal L-phenylalanyl-L-alpha-aminoacyl-[protein] + tRNA(Phe) Belongs to the L/F-transferase family. +Calmodulin mediates the control of a large number of enzymes, ion channels and other proteins by Ca(2+). Among the enzymes to be stimulated by the calmodulin-Ca(2+) complex are a number of protein kinases and phosphatases. Belongs to the calmodulin family. +The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpA family. +Catalyzes the specific phosphorylation of 1,6-anhydro-N-acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. Is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling. 1,6-anhydro-N-acetyl-beta-muramate + ATP + H2O = ADP + H(+) + N-acetyl-D-muramate 6-phosphate Amino-sugar metabolism; 1,6-anhydro-N-acetylmuramate degradation. Cell wall biogenesis; peptidoglycan recycling. Belongs to the anhydro-N-acetylmuramic acid kinase family. +Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Is also a component of the minor U12 spliceosome (PubMed:15146077). May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through non-specific electrostatic contacts with RNA (Probable). Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:19325628, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Most spliceosomal snRNPs contain a common set of Sm proteins, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP (PubMed:10025403, PubMed:19325628, PubMed:21113136, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of the U1 snRNP (PubMed:19325628, PubMed:21113136, PubMed:25555158). The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C (PubMed:19325628, PubMed:21113136, PubMed:25555158). Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:26912367). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077). Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly (PubMed:16314521). Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP. Interacts (via C-terminus) with SMN1 (via Tudor domain); the interaction is direct (PubMed:10500148, PubMed:11135666). Interacts with GEMIN2; the interaction is direct (PubMed:21816274). Interacts with SNRPD2; the interaction is direct (PubMed:21816274, PubMed:31799625). SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes. Methylated on arginine residues by PRMT5 and PRMT7; probable asymmetric dimethylation which is required for assembly and biogenesis of snRNPs. In the autoimmune disease systemic lupus erythematosus, antinuclear antibodies are developed with Sm specificity. Belongs to the snRNP core protein family. +Part of the tra gene cluster that produces terrestric acid (PubMed:30811183). The clavatol biosynthesis cluster cla and the terrestric acid cluster tra are both involved in the production of peniphenones and penilactones (PubMed:30811183). The non-reducing PKS claF is responsible for the formation of clavatol from successive condensations of 3 malonyl-CoA units, presumably with a simple acetyl-CoA starter unit, and 2 methylation steps (PubMed:30811183). The esterase claE probably collaborates with claF by catalyzing the hydrolysis of ACP-bound acyl intermediates to free the ACP from stalled intermediates (By similarity). The clavatol oxidase claD then converts clavatol to hydroxyclavatol (PubMed:30811183). Spontaneous dehydration of hydroxyclavatol leads to the accumulation of the highly active ortho-quinone methide (PubMed:30811183, PubMed:31860310). On the other hand, the PKS-NRPS hybrid traA is involved in the formation of crustosic acid, with the help of traB and traD (PubMed:30811183). The polyketide synthase module (PKS) of traA is responsible for the synthesis of the polyketide backbone via the condensation of an acetyl-CoA starter unit with 3 malonyl-CoA units (PubMed:30811183). The downstream nonribosomal peptide synthetase (NRPS) module then amidates the carboxyl end of the polyketide with L-malic acid (PubMed:30811183). Because traA lacks a designated enoylreductase (ER) domain, the required activity is provided the enoyl reductase traG (By similarity). Crustosic acid undergoes decarboxylation and isomerization to the terrestric acid, catalyzed by the 2-oxoglutarate-dependent dioxygenase traH (PubMed:30811183). Both acids are further converted to the 2 gamma-butyrolactones (R)-5-methyltetronic acid and (S)-5-carboxylmethyltetronic acid, with involvement of the cytochrome P450 monooxygenase claJ (PubMed:30811183). Spontaneous addition of the methide to these gamma-butyrolactones leads to peniphenone D and penilactone D, which undergo again stereospecific attacking by methide to give penilactones A and B (PubMed:30811183, PubMed:31860310). TraE seems not to be involved in the biosynthesis of peniphenones and penilactones in the conditioons used to study its function (PubMed:30811183). Secondary metabolite biosynthesis. Does not result in significant changes in sencondary metabolites production. +Could be involved in insertion of integral membrane proteins into the membrane. Belongs to the UPF0161 family. +Expressed in leaves (especially in midribs and trichomes), apical meristemic regions, stems, roots and flowers. By salt stress (e.g. NaCl) and cold. Induced by P.tabacina. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Regulates the fusion of phagosomes and lysosomes. Endosomal pathway and the contractile vacuole membrane system. Belongs to the small GTPase superfamily. Rab family. +Component of the large ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Component of the large ribosomal subunit. Belongs to the universal ribosomal protein uL14 family. +Has high L-gulonate 3-dehydrogenase activity. It also exhibits low dehydrogenase activity toward L-3-hydroxybutyrate (HBA) and L-threonate. L-gulonate + NAD(+) = 3-dehydro-L-gulonate + H(+) + NADH Inhibited by malonate. Homodimer. Widely expressed, with highest levels in liver. Undetectable in skeletal muscle. Belongs to the 3-hydroxyacyl-CoA dehydrogenase family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Catalyzes the acetylation of L-2,4-diaminobutyrate (DABA) to gamma-N-acetyl-alpha,gamma-diaminobutyric acid (ADABA) with acetyl coenzyme A. acetyl-CoA + L-2,4-diaminobutanoate = (2S)-4-acetamido-2-aminobutanoate + CoA + H(+) Amine and polyamine biosynthesis; ectoine biosynthesis; L-ectoine from L-aspartate 4-semialdehyde: step 2/3. Belongs to the acetyltransferase family. EctA subfamily. +Belongs to the LTV1 family. +Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. 3 H2O + hydrogen sulfide + 3 NADP(+) = 4 H(+) + 3 NADPH + sulfite Binds 1 siroheme per subunit. Binds 1 [4Fe-4S] cluster per subunit. Sulfur metabolism; hydrogen sulfide biosynthesis; hydrogen sulfide from sulfite (NADPH route): step 1/1. Alpha(8)-beta(8). The alpha component is a flavoprotein, the beta component is a hemoprotein. Belongs to the nitrite and sulfite reductase 4Fe-4S domain family. +Acts as a neurotoxin by inhibiting an ion channel. Expressed by the venom duct. The cysteine framework is C-C-C-C-C-C-C-C-C-C-CC. Contains 6 disulfide bonds. +Involved in the biosynthesis of the osmoprotectant glycine betaine. Catalyzes the oxidation of choline to betaine aldehyde and betaine aldehyde to glycine betaine at the same rate. A + choline = AH2 + betaine aldehyde betaine aldehyde + H2O + NAD(+) = glycine betaine + 2 H(+) + NADH Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway; betaine aldehyde from choline (cytochrome c reductase route): step 1/1. Belongs to the GMC oxidoreductase family. +Belongs to the AtxA/AcpA family. Could be the product of a pseudogene. This sequence is much shorter than orthologs. +Receptor that may play a role in the perception of bitterness and is gustducin-linked. May play a role in sensing the chemical composition of the gastrointestinal content. The activity of this receptor may stimulate alpha gustducin, mediate PLC-beta-2 activation and lead to the gating of TRPM5 (By similarity). Most taste cells may be activated by a limited number of bitter compounds; individual taste cells can discriminate among bitter stimuli. Belongs to the G-protein coupled receptor T2R family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Methyltransferase required for the conversion of demethylmenaquinol (DMKH2) to menaquinol (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2). a 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + H(+) + S-adenosyl-L-homocysteine a 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-methionine = a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + H(+) + S-adenosyl-L-homocysteine Quinol/quinone metabolism; menaquinone biosynthesis; menaquinol from 1,4-dihydroxy-2-naphthoate: step 2/2. Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. MenG/UbiE family. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +Belongs to the UPF0251 family. +Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein. Belongs to the DsbB family. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Inhibited by both FK506 and rapamycin. Belongs to the FKBP-type PPIase family. FKBP2 subfamily. +Essential cell division protein that stabilizes the FtsZ protofilaments by cross-linking them and that serves as a cytoplasmic membrane anchor for the Z ring. Also required for the recruitment to the septal ring of downstream cell division proteins. Interacts with FtsZ via their C-terminal domains. Localizes to the Z ring in an FtsZ-dependent manner. Belongs to the ZipA family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +Inhibitor of PPP1CA. Has over 1000-fold higher inhibitory activity when phosphorylated, creating a molecular switch for regulating the phosphorylation status of PPP1CA substrates and smooth muscle contraction (By similarity). Belongs to the PP1 inhibitor family. +It may be a cellular address molecule specific to Purkinje cells. It may represent a receptor or a subunit of a receptor complex. Interacts with NEGR1. Found on the dendrites, somata and axons of developing Purkinje cells. Undetectable on other neurons like Golgi or granule cells. Expressed by developing cerebellar Purkinje cells. Expression coincides with the growth of the dendritic tree, after Purkinje cells have finished their migration from the ventricular zone (from E15 until E21). Expressed in the adult. Belongs to the immunoglobulin superfamily. IgLON family. +Belongs to the aromatic acid exporter ArAE (TC 2.A.85) family. +One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. Binds multiple chlorophylls and provides some of the ligands for the Ca-4Mn-5O cluster of the oxygen-evolving complex. It may also provide a ligand for a Cl- that is required for oxygen evolution. PSII binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbB/PsbC family. PsbC subfamily. +Cooperates with LY96 and CD14 to mediate the innate immune response to bacterial lipopolysaccharide (LPS). Acts via MYD88, TIRAP and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response (By similarity). Also involved in LPS-independent inflammatory responses triggered by free fatty acids, such as palmitate. In complex with TLR6, promotes sterile inflammation in monocytes/macrophages in response to oxidized low-density lipoprotein (oxLDL) or amyloid-beta 42. In this context, the initial signal is provided by oxLDL- or amyloid-beta 42-binding to CD36. This event induces the formation of a heterodimer of TLR4 and TLR6, which is rapidly internalized and triggers inflammatory response, leading to the NF-kappa-B-dependent production of CXCL1, CXCL2 and CCL9 cytokines, via MYD88 signaling pathway, and CCL5 cytokine, via TICAM1 signaling pathway, as well as IL1B secretion. Binds electronegative LDL (LDL(-)) and mediates the cytokine release induced by LDL(-) (By similarity). Activated by the signaling pathway regulator NMI which acts as damage-associated molecular patterns (DAMPs) in response to cell injury or pathogen invasion, therefore promoting nuclear factor NF-kappa-B activation (By similarity). Belongs to the lipopolysaccharide (LPS) receptor, a multi-protein complex containing at least CD14, LY96 and TLR4. Binding to bacterial LPS leads to homodimerization. Interacts with LY96 via the extracellular domain. Interacts with MYD88 and TIRAP via their respective TIR domains. Interacts with TICAM2. Interacts with NOX4. Interacts with CNPY3 and HSP90B1; this interaction is required for proper folding in the endoplasmic reticulum. Interacts with MAP3K21; this interaction leads to negative regulation of TLR4 signaling. Interacts with CD36, following CD36 stimulation by oxLDL or amyloid-beta 42, and forms a heterodimer with TLR6. The trimeric complex is internalized and triggers inflammatory response. LYN kinase activity facilitates TLR4-TLR6 heterodimerization and signal initiation. Interacts with TICAM1 in response to LPS in a WDFY1-dependent manner. Interacts with WDFY1 in response to LPS. Interacts with SMPDL3B. Interacts with CEACAM1; upon lipopolysaccharide stimulation, forms a complex including TLR4 and the phosphorylated form of SYK and CEACAM1, which in turn, recruits PTPN6 that dephosphorylates SYK, reducing the production of reactive oxygen species (ROS) and lysosome disruption, which in turn, reduces the activity of the inflammasome. Interacts with RFTN1; the interaction occurs in response to lipopolysaccharide stimulation. Interacts with SCIMP; the interaction occurs in response to lipopolysaccharide stimulation and is enhanced by phosphorylation of SCIMP by LYN (By similarity). This interaction facilitates the phosphorylation of TLR4 by LYN which elicits a selective cytokine response in macrophages (By similarity). Interacts with TRAF3IP3 (By similarity). Interacts with TREM1; this interaction enhances TLR4-mediated inflammatory response (By similarity). Upon complex formation with CD36 and TLR6, internalized through dynamin-dependent endocytosis. Colocalizes with RFTN1 at cell membrane and then together with RFTN1 moves to endosomes, upon lipopolysaccharide stimulation. The TIR domain mediates interaction with NOX4. Phosphorylated on tyrosine residues by LYN after binding lipopolysaccharide. Belongs to the Toll-like receptor family. In some plant proteins and in human SARM1, the TIR domain has NAD(+) hydrolase (NADase) activity (By similarity). However, despite the presence of the catalytic Asp residue, the isolated TIR domain of human TLR4 lacks NADase activity (By similarity). Based on this, it is unlikely that Toll-like receptors have NADase activity. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). The sulfur atoms are provided by the cysteine/cysteine desulfurase (IscS) system. AH2 + ATP + cytidine(32) in tRNA + S-sulfanyl-L-cysteinyl-[cysteine desulfurase] = 2-thiocytidine(32) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[cysteine desulfurase] Binds 1 [4Fe-4S] cluster per subunit. The cluster is chelated by three Cys residues, the fourth Fe has a free coordination site that may bind a sulfur atom transferred from the persulfide of IscS. tRNA modification. Homodimer. The thiolation reaction likely consists of two steps: a first activation step by ATP to form an adenylated intermediate of the target base of tRNA, and a second nucleophilic substitution step of the sulfur (S) atom supplied by the hydrosulfide attached to the Fe-S cluster. Belongs to the TtcA family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +H2O + L-arginine = L-citrulline + NH4(+) Amino-acid degradation; L-arginine degradation via ADI pathway; carbamoyl phosphate from L-arginine: step 1/2. Belongs to the arginine deiminase family. +Catalyzes a cyclopropane ring-opening reaction, the irreversible conversion of 1-aminocyclopropane-1-carboxylate (ACC) to ammonia and alpha-ketobutyrate. Allows growth on ACC as a nitrogen source. 1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanoate + NH4(+) Homotrimer. Belongs to the ACC deaminase/D-cysteine desulfhydrase family. +Cell adhesion molecule that mediates homophilic cell-cell adhesion in a Ca(2+)-independent manner. Promotes neurite outgrowth in hippocampal neurons (By similarity). Can form heteromeric complexes with LRFN1, LRFN2, LRFN4 and LRFN5. Able to form homomeric complexes across cell junctions, between adjacent cells. Does not interact with DLG4 (By similarity). Lacks a cytoplasmic PDZ-binding domain, which has been implicated in function of related Lrfn proteins. N-glycosylated. Belongs to the LRFN family. +Catalyzes the reduction of methionine sulfoxide (MetSO) to methionine in proteins. Plays a protective role against oxidative stress by restoring activity to proteins that have been inactivated by methionine oxidation. MSRB family specifically reduces the MetSO R-enantiomer (By similarity). [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(R)-S-oxide-[protein] Binds 1 zinc ion per subunit. Belongs to the MsrB Met sulfoxide reductase family. +By DNA damage. Belongs to the multi antimicrobial extrusion (MATE) (TC 2.A.66.1) family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft (By similarity). Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. Ubiquitously expressed. Belongs to the archaeal Rpo11/eukaryotic RPB11/RPC19 RNA polymerase subunit family. +Plays a role in the initiation of viral DNA replication. A dimer of E2 interacts with a dimer of E1 in order to improve specificity of E1 DNA binding activity. Once the complex recognizes and binds DNA at specific sites, the E2 dimer is removed from DNA. E2 also regulates viral transcription through binding to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory regions of the viral genome. Activates or represses transcription depending on E2RE's position with regards to proximal promoter elements including the TATA-box. Repression occurs by sterically hindering the assembly of the transcription initiation complex. Binds DNA as homodimer. Interacts with protein E1; this interaction greatly increases E1 DNA-binding activity. Interacts with protein L1; this interaction enhances E2-dependent replication and transcription activation. Interacts with protein L2; this interaction inhibits E2 transcriptional activity but not DNA replication function E2. Interacts with protein E7; this interaction inhibits E7 oncogenic activity. Interacts with host TAF1; this interaction modulates E2-dependent transcriptional regulation. Interacts with host BRD4; this interaction mediates E2 transcriptional activation function. Additionally, the interaction with host BRD4 on mitotic chromosomes mediates tethering of the viral genome. Interacts with host TOPBP1; this interaction is required for optimal viral DNA replication. Phosphorylated. Sumoylation plays a regulatory role in E2 transcriptional activity. Belongs to the papillomaviridae E2 protein family. +Energy-dependent efflux pump responsible for decreased drug accumulation in multi-drug-resistant cells. Probably uses a transmembrane proton gradient as the energy source. Causes the efflux of a variety of toxic substances, including such structurally diverse compounds as ethidium bromide, rhodamine and acridine dyes, tetraphenylphosphonium, puromycin, chloramphenicol, doxorubicin, and fluoroquinolone antibiotics. Belongs to the major facilitator superfamily. TCR/Tet family. +In vitro, possesses glutathione S-transferase activity toward 1-chloro-2,4-dinitrobenzene (CDNB) and benzyl isothiocyanate (BITC). May be involved in the conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles and have a detoxification role against certain herbicides. glutathione + RX = a halide anion + an S-substituted glutathione + H(+) Interacts with BAK1. Expressed in roots, stems, floral buds, mature flowers and leaves. By dehydration stress, wounding, H(2)O(2) and jasmonate, but not by growth regulators. No visible phenotype, maybe due to the possible redundancy with GSTF9. Belongs to the GST superfamily. Phi family. +Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose. beta-D-ribopyranose = beta-D-ribofuranose Carbohydrate metabolism; D-ribose degradation; D-ribose 5-phosphate from beta-D-ribopyranose: step 1/2. Homodecamer. Belongs to the RbsD / FucU family. RbsD subfamily. +Expressed by the parotoid glands. Belongs to the frog skin active peptide (FSAP) family. Phylloseptin subfamily. +Probable ligand for integrin in the brain. This is a non-catalytic metalloprotease-like protein. Detected in testis and barely expressed in heart and muscle. Not detectable in liver. Could not be detected in embryos until neurulation. In developing embryos, the expression is restricted to neural crest derivatives. A conserved motif [AVN[ED]CD] within the disintegrin-like domain could be involved in the binding to the integrin receptor. The precursor is cleaved by a furin endopeptidase. +Bacteriocin active against species of Gram-positive bacterial genera Bacillus, Enterococcus, Lactobacillus, Lactococcus, Micrococcus, Staphylococcus and Streptococcus. Active against L.monocytogenes (MIC=0.53 mg/ml). Has no activity against various Gram-negative species. Has no activity against strains of fungi C.albicans and A.brasiliensis. Stable from pH 2 to 12. Thermostable. Retains 100% activity after incubaction at 100 degrees Celsius for 30 minutes. Retains 70% activity after incubation at 121 degrees Celsius at high pressure for 30 minutes. Antibacterial activity is lost upon treatment with pronase E and partially with trypsin but not when treated with lysozyme or proteinase K. +Secreted aspartic protease; part of the gene cluster that mediates the biosynthesis of the mycotoxin lucilactaene and the lucilactaene-related compound NG-391 that act as cell cycle inhibitors with potent growth inhibitory activity against malarial parasites, moderate growth inhibitory activity against cancer cells, and no activity against bacteria and fungi (PubMed:32043422). Within the cluster, LUC5, LUC6, LUC2 and LUC1 are sufficient for lucilactaene production (Probable). The roles of the other LUC members are yet undetermined (Probable). Belongs to the peptidase A1 family. +Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. ATP + CoA + succinate = ADP + phosphate + succinyl-CoA Binds 1 Mg(2+) ion per subunit. Carbohydrate metabolism; tricarboxylic acid cycle; succinate from succinyl-CoA (ligase route): step 1/1. Heterotetramer of two alpha and two beta subunits. Belongs to the succinate/malate CoA ligase beta subunit family. +Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro). D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O Binds 1 Mg(2+) ion per subunit. kcat is 2.0 sec(-1) with D-mannonate. Carbohydrate metabolism; pentose and glucuronate interconversion. Belongs to the mandelate racemase/muconate lactonizing enzyme family. GalD subfamily. +Belongs to the LCL3 family. +Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on both glycolipids and glycoproteins. Shows strict specificity for Gal-beta-1,3-Gal-beta-1,4-Xyl, exhibiting negligible incorporation into other galactoside substrates. 3-O-(beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl)-L-seryl-[protein] + UDP-alpha-D-glucuronate = 3-O-(beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + H(+) + UDP Protein modification; protein glycosylation. Expressed at low levels from early embryos to adults; maximal expression in third instar larvae. Belongs to the glycosyltransferase 43 family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Promotes cell proliferation, chemotaxis, angiogenesis and cell adhesion. Appears to play a role in wound healing by up-regulating, in skin fibroblasts, the expression of a number of genes involved in angiogenesis, inflammation and matrix remodeling including VEGA-A, VEGA-C, MMP1, MMP3, TIMP1, uPA, PAI-1 and integrins alpha-3 and alpha-5 (By similarity). CCN1-mediated gene regulation is dependent on heparin-binding (By similarity). Down-regulates the expression of alpha-1 and alpha-2 subunits of collagen type-1 (By similarity). Promotes cell adhesion and adhesive signaling through integrin alpha-6/beta-1, cell migration through integrin alpha-1/beta-5 and cell proliferation through integrin alpha-v/beta-3 (By similarity). Interaction with integrins is heparin- and cell-type-dependent and promotes cell adhesion. Belongs to the CCN family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Belongs to the SecA family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseB family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +Secreted effector that suppresses pattern-triggered immunity (PTI) in plant host. Expression is up-regulated in spores. The RxLR-dEER motif acts to carry the protein into the host cell cytoplasm through binding to cell surface phosphatidylinositol-3-phosphate. Belongs to the RxLR effector family. +Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. The formation of the proteasomal ATPase PAN-20S proteasome complex, via the docking of the C-termini of PAN into the intersubunit pockets in the alpha-rings, triggers opening of the gate for substrate entry. Interconversion between the open-gate and close-gate conformations leads to a dynamic regulation of the 20S proteasome proteolysis activity. The 20S proteasome core is composed of 14 alpha and 14 beta subunits that assemble into four stacked heptameric rings, resulting in a barrel-shaped structure. The two inner rings, each composed of seven catalytic beta subunits, are sandwiched by two outer rings, each composed of seven alpha subunits. The catalytic chamber with the active sites is on the inside of the barrel. Has a gated structure, the ends of the cylinder being occluded by the N-termini of the alpha-subunits. Is capped at one or both ends by the proteasome regulatory ATPase, PAN. Belongs to the peptidase T1A family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +Catalyzes the ATP- as well as probably the pyrophosphate-dependent phosphorylation of 'Ser-46' in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK/P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P-Ser-HPr). The two antagonistic activities of HprK/P are regulated by several intracellular metabolites, which change their concentration in response to the absence or presence of rapidly metabolisable carbon sources (glucose, fructose, etc.) in the growth medium. Therefore, by controlling the phosphorylation state of HPr, the bifunctional HPr kinase/phosphorylase is a sensor enzyme that plays a major role in the regulation of carbon metabolism and sugar transport: it probably mediates carbon catabolite repression (CCR), and regulates PTS-catalyzed carbohydrate uptake and inducer exclusion. [HPr protein]-L-serine + ATP = [HPr protein]-O-phospho-L-serine + ADP + H(+) [HPr protein]-O-phospho-L-serine + H(+) + phosphate = [HPr protein]-L-serine + diphosphate Kinase activity is slightly activated by fructose 1,6-bisphosphate (FBP) at low ATP concentrations, and is inhibited by inorganic phosphate (Pi). Moreover, FBP, phosphoenolpyruvate and 2-phosphoglycerate, but not fructose 1-P, fructose 6-P, and ribulose 1,5-bisphosphate protect kinase activity against inhibition by Pi. Dephosphorylation of P-Ser-HPr by S.salivarius HPrK/P is strictly dependent on the presence of Pi, and is inhibited by FBP. FBP seems to modulate HPrK/P activities by enhancing affinity of the active site for ATP and, conversely, lowering the affinity for Pi. Optimum pH is 7.5. Active from pH 5.5 to 9.5. At pH 5.5, exhibits less than 15% of its optimal activity. Homohexamer. The Walker A ATP-binding motif also binds Pi and PPi. Both phosphorylation and phosphorolysis are carried out by the same active site and suggest a common mechanism for both reactions. Belongs to the HPrK/P family. +Part of a heterotetrameric complex that catalyzes the two-step biosynthesis of anthranilate, an intermediate in the biosynthesis of L-tryptophan. In the first step, the glutamine-binding beta subunit (TrpG) of anthranilate synthase (AS) provides the glutamine amidotransferase activity which generates ammonia as a substrate that, along with chorismate, is used in the second step, catalyzed by the large alpha subunit of AS (TrpE) to produce anthranilate. In the absence of TrpG, TrpE can synthesize anthranilate directly from chorismate and high concentrations of ammonia (By similarity). chorismate + L-glutamine = anthranilate + H(+) + L-glutamate + pyruvate Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 1/5. Heterotetramer consisting of two non-identical subunits: a beta subunit (TrpG) and a large alpha subunit (TrpE). +Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr). AH2 + epoxyqueuosine(34) in tRNA = A + H2O + queuosine(34) in tRNA Binds 2 [4Fe-4S] clusters per monomer. tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueG family. +Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA. Involved in the biogenesis of rRNA. Interacts with NF-kappa-B p50/NFKB1 and NF-kappa-B p65/RELA. Wrong choice of frame. Contaminating sequence. Potential poly-A sequence. Contaminating sequence. Potential poly-A sequence. Contaminating sequence. Potential poly-A sequence. Contaminating sequence. Potential poly-A sequence. Extended N-terminus. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +Master enzyme that delivers sulfur to a number of partners involved in Fe-S cluster assembly, tRNA modification or cofactor biosynthesis. Catalyzes the removal of elemental sulfur atoms from cysteine to produce alanine. Functions as a sulfur delivery protein for Fe-S cluster synthesis onto IscU, an Fe-S scaffold assembly protein, as well as other S acceptor proteins. [sulfur carrier]-H + L-cysteine = [sulfur carrier]-SH + L-alanine Cofactor biosynthesis; iron-sulfur cluster biosynthesis. Homodimer. Forms a heterotetramer with IscU, interacts with other sulfur acceptors. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. NifS/IscS subfamily. +May function as a coactivator for aryl hydrocarbon and nuclear receptors. Detected in the cytoplasm at stages I- II. Detected in the nucleus and the cytoplasm, except for the germ plasm, of almost all cells in cleaving embryos,. Expressed in the germinal vesicle of oocytes at stages I-III. Expressed in ectodermal and mesodermal cells and their derivatives after stage 10. At stages later than 28, highly expressed in the myotome, spinal cord and notochord (at protein level). Belongs to the CALCOCO family. +Confers susceptibility to the fungus Cochliobolus victoriae by conditioning victorin-dependent (victorin is a toxin synthesized by C.victoriae) induction of defense-associated proteins. Repressed by silencing mediated by polycomb group (PcG) protein complex containing EMF1 and EMF2. The LRR repeats probably act as specificity determinant of pathogen recognition. Belongs to the disease resistance NB-LRR family. RPP8/HRT subfamily. Has been shown to be a pseudogene in cv. Columbia (AC O04093) due to a stop codon at position 117 and a naturally occurring frameshift at position 846 in this strain. The sequence shown is from strain cv. Cl-0. Functional and comparative genomics of disease resistance gene homologs +Required for nicotinamide riboside transport across the inner membrane. Repressed by NadR. Belongs to the nicotinamide ribonucleoside (NR) uptake permease (TC 4.B.1) family. +Component of the lid subcomplex of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. In the complex, psmd11a is required for proteasome assembly (By similarity). Component of the lid subcomplex of the 19S proteasome regulatory particle complex (also named PA700 complex). The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits (By similarity). Belongs to the proteasome subunit S9 family. +Belongs to the dUTPase family. Product of a dubious CDS prediction. Could be the remnant of an endogenous retroviral dUTPase. +Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and/or repair of Fe-S clusters in biosynthetic enzymes. Belongs to the Fe(2+)-trafficking protein family. +Mediates the calcium-dependent uptake of imino acids such as L-proline, N-methyl-L-proline and pipecolate as well as N-methylated amino acids. Involved in the transport of glycine. Located in the apical brush border membrane of kidney proximal tubule cells. Kidney and small intestine. Expressed in the S3 segment of the proximal tubule. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Haploinsufficiency of SLC6A20 combined with deficiency of the neutral amino acid transporter SLC6A19 or partially inactivating mutations in SLC36A2, is responsible for iminoglycinuria. Additional polymorphisms and mutations in SLC6A18 can contribute to the IG phenotype in some families. Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A20 subfamily. +Plasma membrane ceramidase that hydrolyzes sphingolipid ceramides into sphingosine and free fatty acids at neutral pH (PubMed:11328816, PubMed:10488143, PubMed:15217782). Ceramides, sphingosine, and its phosphorylated form sphingosine-1-phosphate are bioactive lipids that mediate cellular signaling pathways regulating several biological processes including cell proliferation, apoptosis and differentiation (PubMed:11328816). Also catalyzes the reverse reaction allowing the synthesis of ceramides from fatty acids and sphingosine (PubMed:15123644, PubMed:11278489). Together with sphingomyelinase, participates in the production of sphingosine and sphingosine-1-phosphate from the degradation of sphingomyelin, a sphingolipid enriched in the plasma membrane of cells (PubMed:15217782). Also participates in the hydrolysis of ceramides from the extracellular milieu allowing the production of sphingosine-1-phosphate inside and outside cells. This is the case for instance with the digestion of dietary sphingolipids in the intestinal tract (By similarity). an N-acylsphing-4-enine + H2O = a fatty acid + sphing-4-enine H2O + N-hexadecanoylsphing-4-enine = hexadecanoate + sphing-4-enine H2O + N-tetradecanoylsphing-4-enine = sphing-4-enine + tetradecanoate H2O + N-(9Z-octadecenoyl)-sphing-4-enine = (9Z)-octadecenoate + sphing-4-enine H2O + N-(15Z-tetracosenoyl)-sphing-4-enine = (15Z)-tetracosenoate + sphing-4-enine H2O + N-octanoylsphing-4-enine = octanoate + sphing-4-enine H2O + N-dodecanoylsphing-4-enine = dodecanoate + sphing-4-enine H2O + N-(hexanoyl)sphing-4-enine = hexanoate + sphing-4-enine H2O + N-octadecanoylsphing-4-enine = octadecanoate + sphing-4-enine hexadecanoate + sphinganine = H2O + N-hexadecanoylsphinganine H2O + N-(octadecanoyl)-sphinganine = octadecanoate + sphinganine Binds 1 zinc ion per subunit. The reverse reaction is inhibited by Zn(2+) and Cu(2+) (PubMed:11278489). Inhibited by cardiolipin and phosphatidic acid (PubMed:11278489). More efficiently hydrolyzes N-lauroylsphingosine/C12:0-ceramides compared to N-palmitoylsphingosine/C16:0-ceramides and N-stearoylsphingosine/C18:0-ceramides (PubMed:11328816). The catalytic efficiency towards dihydroceramides and phytoceramides is very low (PubMed:11328816, PubMed:10488143). For the reverse synthetic reaction exhibits a higher activity with D-erythro-sphing-4-enine and the fatty acid tetradecanoate as substrates (PubMed:11278489). Optimum pH is 6-7 for N-hexadecanoylsphing-4-enine hydrolysis (PubMed:11328816). Optimum pH is 7-10 for N-hexadecanoylsphing-4-enine hydrolysis (PubMed:10488143). Optimum pH is 6-8 for N-(octanoyl)-sphing-4-enine hydrolysis (PubMed:15217782). Optimum pH is 6.5-7 for hexadecanoate in the reverse reaction (PubMed:11278489). Lipid metabolism; sphingolipid metabolism. Enriched in exosomes upon stimulation by cytokine (By similarity). Enriched in caveolae and lipid rafts (By similarity). The localization to the mitochondrion could not be confirmed (By similarity). Highly expressed in brain, kidney and heart (PubMed:11328816). Expressed at lower level in other tissues such as liver (PubMed:11328816). Expressed in intestine, kidney and liver (at protein level) (PubMed:11328816, PubMed:11330410). Localizes in the epithelia of the jejunum and ileum (PubMed:11330410). By interleukin-1-beta in renal mesangial cells. Proteolytic cleavage of the N-terminus removes the signal-anchor and produces a soluble form of the protein. N-glycosylated (PubMed:11328816, PubMed:15123644). Required for enzyme activity (PubMed:11328816). O-glycosylated (PubMed:12499379). Required to retain it as a type II membrane protein at the cell surface (PubMed:12499379). Phosphorylated. May prevent ubiquitination and subsequent degradation. Ubiquitinated, leading to its degradation by the proteasome. Ubiquitination is triggered by nitric oxide. Belongs to the neutral ceramidase family. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. (2S,6S)-2,6-diaminoheptanedioate = meso-2,6-diaminoheptanedioate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. Homodimer. Belongs to the diaminopimelate epimerase family. +Protamines substitute for histones in the chromatin of sperm during the haploid phase of spermatogenesis. They compact sperm DNA into a highly condensed, stable and inactive complex. Testis. Belongs to the protamine P1 family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Involved in nucleolar processing of pre-18S ribosomal RNA. Component of the ribosomal small subunit (SSU) processome composed of at least 40 protein subunits and snoRNA U3. Interacts with snoRNA U3. Interacts with EBP2, FAF1, MPP10, RPS16A and RRP14. Belongs to the UTP11 family. +Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. Binds cooperatively to specific DNA consensus sequences that are separated from XerD binding sites by a short central region, forming the heterotetrameric XerC-XerD complex that recombines DNA substrates. The complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids. In the complex XerC specifically exchanges the top DNA strands. FtsK may regulate the catalytic switch between XerC and XerD in the heterotetrameric complex during the two steps of the recombination process. Forms a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD, in which XerC interacts with XerD via its C-terminal region, XerD interacts with XerC via its C-terminal region and so on. Belongs to the 'phage' integrase family. XerC subfamily. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate. L-leucyl-tRNA(Leu) + N-terminal L-glutamyl-[protein] = H(+) + N-terminal L-leucyl-L-glutamyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-aspartyl-[protein] = H(+) + N-terminal L-leucyl-L-aspartyl-[protein] + tRNA(Leu) Belongs to the R-transferase family. Bpt subfamily. +Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process. 6 Fe(III)-[cytochrome c] + 2 H2O + NH4(+) = 6 Fe(II)-[cytochrome c] + 8 H(+) + nitrite Binds 1 Ca(2+) ion per monomer. Binds 5 heme c groups covalently per monomer. Nitrogen metabolism; nitrate reduction (assimilation). Belongs to the cytochrome c-552 family. +Catalyzes the NADPH-dependent reduction of glyoxylate and hydroxypyruvate into glycolate and glycerate, respectively. glycolate + NADP(+) = glyoxylate + H(+) + NADPH (R)-glycerate + NAD(+) = 3-hydroxypyruvate + H(+) + NADH (R)-glycerate + NADP(+) = 3-hydroxypyruvate + H(+) + NADPH Homodimer. Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. GhrB subfamily. +Phosphotransfer between the C1 and C5 carbon atoms of pentose. alpha-D-ribose 1-phosphate = D-ribose 5-phosphate 2-deoxy-alpha-D-ribose 1-phosphate = 2-deoxy-D-ribose 5-phosphate Binds 1 or 2 manganese ions. Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route II): step 1/3. Belongs to the phosphopentomutase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Catalyzes the circularization of gamma-N-acetyl-alpha,gamma-diaminobutyric acid (ADABA) to ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid), which is an excellent osmoprotectant. (2S)-4-acetamido-2-aminobutanoate = H2O + L-ectoine Amine and polyamine biosynthesis; ectoine biosynthesis; L-ectoine from L-aspartate 4-semialdehyde: step 3/3. Belongs to the ectoine synthase family. +Inhibits the sodium currents (Nav) in an apparent irreversible manner. Produces small depolarization and induces repetitive firing in squid axons. Is specific for arthropods (crickets, triatomides, crabs and squids), but is non-toxic to mice (By similarity). Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). Belongs to the long (4 C-C) scorpion toxin superfamily. Sodium channel inhibitor family. Beta subfamily. +Plays a role in the regulation of inhibitory synapse formation and function by being involved in maintening gamma-aminobutyric acid receptors (GABAARs) clustering and their associated scaffold proteins at inhibitory synaptic sites. Acts in concert with NLGN2 to recruit or stabilize GABAARs. Interacts with GABA(A) receptor subunits (By similarity). Interacts with GABRB3 (By similarity). Interacts with GABRA2 (By similarity). Interacts with GABRG2 (By similarity). Identified in a complex of 720 kDa composed of LHFPL4, NLGN2, GABRA1, GABRB2, GABRG2 and GABRB3 (By similarity). Interacts with GABRA1 (By similarity). Interacts with NLGN2; leading to mutual regulation of protein level and synaptic clustering (By similarity). Specifically localizes to inhibitory postsynaptic sites (By similarity). Colocalizes with GPHN, GABRG2 and NLGN2 at inhibitory postsynaptic sites (By similarity). Belongs to the LHFP family. +Involved in the post-transcriptional modification of the uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Catalyzes the conversion of 2-thiouridine (S2U-RNA) to 2-selenouridine (Se2U-RNA). Acts in a two-step process involving geranylation of 2-thiouridine (S2U) to S-geranyl-2-thiouridine (geS2U) and subsequent selenation of the latter derivative to 2-selenouridine (Se2U) in the tRNA chain. (2E)-geranyl diphosphate + 5-methylaminomethyl-2-thiouridine(34) in tRNA + H(+) + H2O + selenophosphate = (2E)-thiogeraniol + 5-methylaminomethyl-2-selenouridine(34) in tRNA + diphosphate + phosphate (2E)-geranyl diphosphate + 5-methylaminomethyl-2-thiouridine(34) in tRNA = 5-methylaminomethyl-S-(2E)-geranyl-thiouridine(34) in tRNA + diphosphate 5-methylaminomethyl-S-(2E)-geranyl-thiouridine(34) in tRNA + H(+) + selenophosphate = (2E)-thiogeraniol + 5-methylaminomethyl-2-(Se-phospho)selenouridine(34) in tRNA 5-methylaminomethyl-2-(Se-phospho)selenouridine(34) in tRNA + H2O = 5-methylaminomethyl-2-selenouridine(34) in tRNA + phosphate Monomer. Belongs to the SelU family. +ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 2/3. Homotetramer. Belongs to the argininosuccinate synthase family. Type 1 subfamily. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +A cytochrome P450 monooxygenase involved in the metabolism of steroid hormones and vitamins (PubMed:2732228, PubMed:10681376, PubMed:11093772, PubMed:12865317). Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (NADPH--hemoprotein reductase). Catalyzes the hydroxylation of carbon-hydrogen bonds (PubMed:12865317, PubMed:2732228, PubMed:10681376, PubMed:11093772). Exhibits high catalytic activity for the formation of catechol estrogens from 17beta-estradiol (E2) and estrone (E1), namely 2-hydroxy E1 and E2 (PubMed:12865317). Catalyzes 6beta-hydroxylation of the steroid hormones testosterone, progesterone, and androstenedione (PubMed:2732228). Catalyzes the oxidative conversion of all-trans-retinol to all-trans-retinal, a rate-limiting step for the biosynthesis of all-trans-retinoic acid (atRA) (PubMed:10681376). Further metabolizes all trans-retinoic acid (atRA) to 4-hydroxyretinoate and may play a role in hepatic atRA clearance (PubMed:11093772). Also involved in the oxidative metabolism of xenobiotics, including calcium channel blocking drug nifedipine and immunosuppressive drug cyclosporine (PubMed:2732228). an organic molecule + O2 + reduced [NADPH--hemoprotein reductase] = an alcohol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] 17beta-estradiol + O2 + reduced [NADPH--hemoprotein reductase] = 2-hydroxy-17beta-estradiol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] 17beta-estradiol + O2 + reduced [NADPH--hemoprotein reductase] = 4-hydroxy-17beta-estradiol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] estrone + O2 + reduced [NADPH--hemoprotein reductase] = 2-hydroxyestrone + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] estrone + O2 + reduced [NADPH--hemoprotein reductase] = 4-hydroxyestrone + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] O2 + reduced [NADPH--hemoprotein reductase] + testosterone = 6beta,17beta-dihydroxyandrost-4-en-3-one + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] androst-4-ene-3,17-dione + O2 + reduced [NADPH--hemoprotein reductase] = 6beta-hydroxyandrost-4-ene-3,17-dione + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] O2 + progesterone + reduced [NADPH--hemoprotein reductase] = 6beta-hydroxyprogesterone + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] all-trans-retinol + O2 + reduced [NADPH--hemoprotein reductase] = all-trans-retinal + H(+) + 2 H2O + oxidized [NADPH--hemoprotein reductase] all-trans-retinoate + O2 + reduced [NADPH--hemoprotein reductase] = all-trans-4-hydroxyretinoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Steroid hormone biosynthesis. Cofactor metabolism; retinol metabolism. By glucocorticoids, such as dexamethesone. Chimeric transcripts, characterized by CYP3A43 exon 1 joined at canonical splice sites to distinct sets of CYP3A5 exons, have been detected. All are possibly produced by trans-splicing. The chimeric transcripts exist in 2 different combinations: CYP3A43 exon 1 joined in frame to CYP3A5 exon 11-13 and CYP3A43 exon 1 joined in frame to CYP3A5 exon 12-13. All chimeric transcripts are expressed at very low levels in the liver (PubMed:11726664). Belongs to the cytochrome P450 family. CYP3A5 alleles +Belongs to the thioredoxin family. +This protein specifically catalyzes the removal of signal peptides from prolipoproteins. Release of signal peptides from bacterial membrane prolipoproteins. Hydrolyzes -Xaa-Yaa-Zaa-|-(S,diacylglyceryl)Cys-, in which Xaa is hydrophobic (preferably Leu), and Yaa (Ala or Ser) and Zaa (Gly or Ala) have small, neutral side chains. Protein modification; lipoprotein biosynthesis (signal peptide cleavage). Belongs to the peptidase A8 family. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin. di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available. Belongs to the UppP family. +Cell wall formation. ATP + L-alanine + UDP-N-acetyl-alpha-D-muramate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Involved in the catabolism of oxalate and in the adapatation to low pH. ACOCT serves to prime the oxalate-induced acid tolerance response (ATR) cycle by producing substrate for oxalyl-CoA decarboxylase (OXC) and formyl-coenzyme A transferase (FCOCT). Catalyzes the reversible conversion of acetyl-CoA and oxalate to oxalyl-CoA and acetate. It can also use formyl-CoA and oxalate to produce oxalyl-CoA and formate with significantly reduced specific activity. acetyl-CoA + oxalate = acetate + oxalyl-CoA kcat is 1.8 sec(-1) for the CoA-transferase activity with oxalate as substrate (at pH 6.7 and 25 degrees Celsius). kcat is 2 sec(-1) for the CoA-transferase activity with acetyl-CoA as substrate (at pH 6.7 and 25 degrees Celsius). Homodimer. Belongs to the CoA-transferase III family. +Catalyzes a trans-dehydration via an enolate intermediate. 3-dehydroquinate = 3-dehydroshikimate + H2O Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 3/7. Homododecamer. Belongs to the type-II 3-dehydroquinase family. +Involved in glucose metabolism. Heterodimer of a B chain or a B chain' and an A chain probably linked by three disulfide bonds. Expressed in the central region of the cerebral ganglia mostly within the F and C clusters. Insulin A chain. Insulin B chain. Insulin B chain'. Insulin (AI) with the disulfide bonds. The measured ranges are 32-76, 105-139. Insulin (AI') with the disulfide bonds. The measured ranges are 32-72, 105-139. Belongs to the insulin family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. Belongs to the phosphatidylserine decarboxylase family. PSD-A subfamily. +Methylates ribosomal protein L11. L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. PrmA family. +Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain. +Probable neurotoxin with unknown target. Possibly targets ion channels. Expressed by the venom duct. The mature peptide does not contain cysteine residue. Belongs to the conotoxin NSf-1 superfamily. +Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose. beta-D-ribopyranose = beta-D-ribofuranose Carbohydrate metabolism; D-ribose degradation; D-ribose 5-phosphate from beta-D-ribopyranose: step 1/2. Homodecamer. Belongs to the RbsD / FucU family. RbsD subfamily. +Belongs to the YiaX1 family. +Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner. ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) Monomer. ValRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated threonine is translocated from the active site to the editing site. The C-terminal coiled-coil domain is crucial for aminoacylation activity. Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily. +Involved in the biogenesis of rRNA. Required for the formation of 18S and 5.8S rRNA (By similarity). Component of the ribosomal small subunit (SSU) processome. +Hydrolyzes lysophosphatidic acid (LPA) containing a medium length fatty acid chain to the corresponding monoacylglycerol. Has highest activity with lysophosphatidic acid containing myristate (C14:0), monounsaturated oleate (C18:1) or palmitate (C16:0), and lower activity with C18:0 and C6:0 lysophosphatidic acid. a phosphate monoester + H2O = an alcohol + phosphate 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O = 1-(9Z-octadecenoyl)-sn-glycerol + phosphate Monomer. Detected in brain (at protein level). Belongs to the histidine acid phosphatase family. It is uncertain whether Met-1 or Met-10 is the initiator. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Calmodulin mediates the control of a large number of enzymes, ion channels and other proteins by Ca(2+). Among the enzymes to be stimulated by the calmodulin-Ca(2+) complex are a number of protein kinases and phosphatases. This protein has four functional calcium-binding sites. Belongs to the calmodulin family. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Homodimer. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Archaeal CCA-adding enzyme subfamily. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 3 family. +Highly glycosylated atypical beta-defensin involved in several aspects of sperm function. Facilitates sperm transport in the female reproductive tract and contributes to sperm protection against immunodetection; both functions are probably implicating the negative surface charge provided by its O-linked oligosaccharides in the sperm glycocalyx. Involved in binding of sperm to oviductal epithelial cells to form a sperm reservoir until ovulation. Release from the sperm surface during capacitation and ovaluation by an elevation of oviductal fluid pH is unmasking other surface components and allows sperm to penetrate the cumulus matrix and bind to the zona pellucida of the oocyte (By similarity). In vitro has antimicrobial activity and may inhibit LPS-mediated inflammation (PubMed:19373462, PubMed:23229569). Homodimer or homooligomer; disulfide-linked. Secreted by epididymal cells and is absorbed to the surface of sperm during transit through the epididymis (By similarity). Mainly located on the sperm acrosome. High-level and epididymis-specific expression. Expression is down-regulated in infertile men. O-glycosylated; glycans contain alpha(2,3)-linked sialic acids. May be involved in infertility. Homozygosity for frameshift truncating mutations are associated with reduced sperm O-linked glycan content, impaired sperm mobility and a reduced live birth rate (PubMed:21775668, PubMed:25721098). However, for one common mutation the change in sperm sialic acid levels has been challenged (PubMed:26832966). Belongs to the beta-defensin family. +Sesquiterpene synthase involved in the biosynthesis of volatile compounds (PubMed:21813655, PubMed:20431087, PubMed:21818683). Mediates the conversion of (2E,6E)-farnesyl diphosphate (FPP) into (1E,4E,8E)-alpha-humulene and (-)-(E)-beta-caryophyllene, and of (2Z,6Z)-farnesyl diphosphate ((ZZ)-FPP) into beta-bisabolene, gamma-curcumene and (Z)-gamma-bisabolene (PubMed:21813655, PubMed:20431087, PubMed:21818683). Can act with a low efficiency as a monoterpene synthase with geranyl diphosphate (GPP) as substrate, thus producing beta-myrcene, (E)-beta-ocimene, limonene and terpinolene (PubMed:21818683). (2E,6E)-farnesyl diphosphate = alpha-humulene + diphosphate (2E,6E)-farnesyl diphosphate = (-)-(E)-beta-caryophyllene + diphosphate (2Z,6Z)-farnesyl diphosphate = beta-bisabolene + diphosphate (2E)-geranyl diphosphate = diphosphate + terpinolene (2E)-geranyl diphosphate = diphosphate + limonene (2E)-geranyl diphosphate = beta-myrcene + diphosphate (2E)-geranyl diphosphate = (E)-beta-ocimene + diphosphate (2Z,6Z)-farnesyl diphosphate = diphosphate + gamma-curcumene (2Z,6Z)-farnesyl diphosphate = (Z)-gamma-bisabolene + diphosphate Binds 3 Mg(2+) or Mn(2+) ions per subunit. Secondary metabolite biosynthesis; terpenoid biosynthesis. Mostly expressed in leaves, to a lower extent in stems, trichomes, flowers and roots and, at low levels, in fruits. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg(2+). Belongs to the terpene synthase family. Tpsa subfamily. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. This function is generally fulfilled by the C-terminal part of HisG, which is missing in some bacteria such as this one. Belongs to the class-II aminoacyl-tRNA synthetase family. HisZ subfamily. +H(+) + L-arginine = agmatine + CO2 Binds 1 pyruvoyl group covalently per subunit. Belongs to the PdaD family. +Hypodermis, cuticle and uterus. Belongs to the phosphatidylethanolamine-binding protein family. +Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate. adenosylcob(III)inamide-GDP + alpha-ribazole = adenosylcob(III)alamin + GMP + H(+) adenosylcob(III)inamide-GDP + alpha-ribazole 5'-phosphate = adenosylcob(III)alamin 5'-phosphate + GMP + H(+) Cofactor biosynthesis; adenosylcobalamin biosynthesis; adenosylcobalamin from cob(II)yrinate a,c-diamide: step 7/7. Belongs to the CobS family. +Modulates the activity of the host recBCD nuclease. And thus protects linear double-stranded DNA from exonuclease degradation. +This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a 'molecular matchmaker', a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex. Belongs to the DNA mismatch repair MutL/HexB family. +Involved in ds DNA break repair. Has a role in non-homologous integration (NHI) pathways where it is required in the final step of non-homologous end-joining. ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate. Belongs to the ATP-dependent DNA ligase family. +Expressed in the late phase of the viral replicative cycle. Belongs to the asfivirus E146L family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase epsilon chain family. +Probable ATP-binding RNA helicase which plays a central role during spermatogenesis and oogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi and govern the methylation and subsequent repression of transposons. Involved in the repression of LTR retrotransposon copia. Also involved in telomere regulation by repressing specialized telomeric retroelements HeT-A, TAHRE, and TART; Drosophila telomeres being maintained by transposition of specialized telomeric retroelements. Involved in telomeric trans-silencing, a repression mechanism by which a transposon or a transgene inserted in subtelomeric heterochromatin has the capacity to repress in trans in the female germline, a homologous transposon, or transgene located in euchromatin. Involved in the repression of testis-expressed Stellate genes by the homologous Su(Ste) repeats. Required for anteroposterior and dorsoventral axis formation during oogenesis (By similarity). ATP + H2O = ADP + H(+) + phosphate Component of the nuage, also named P granule, a germ-cell-specific organelle required to repress transposon during meiosis. Belongs to the DEAD box helicase family. DEAH subfamily. +ATP + L-glutamate + NH4(+) = ADP + H(+) + L-glutamine + phosphate Homooctamer. Belongs to the glutamine synthetase family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +High affinity, high specificity proton-dependent sulfate transporter, which mediates sulfate uptake. Provides the sulfur source for the cysteine synthesis pathway. Belongs to the CysZ family. +Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. H2O + IMP + NAD(+) = H(+) + NADH + XMP Mycophenolic acid (MPA) is a non-competitive inhibitor that prevents formation of the closed enzyme conformation by binding to the same site as the amobile flap. In contrast, mizoribine monophosphate (MZP) is a competitive inhibitor that induces the closed conformation. MPA is a potent inhibitor of mammalian IMPDHs but a poor inhibitor of the bacterial enzymes. MZP is a more potent inhibitor of bacterial IMPDH. Purine metabolism; XMP biosynthesis via de novo pathway; XMP from IMP: step 1/1. Homotetramer. Belongs to the IMPDH/GMPR family. +D-serine = NH4(+) + pyruvate Belongs to the serine/threonine dehydratase family. DsdA subfamily. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA. a fatty acyl-[ACP] + phosphate = an acyl phosphate + holo-[ACP] Lipid metabolism; phospholipid metabolism. Homodimer. Probably interacts with PlsY. Associated with the membrane possibly through PlsY. Belongs to the PlsX family. +2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + ADP + H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole from N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide: step 2/2. Belongs to the AIR synthase family. +The small GTPases Rab are key regulators in vesicle trafficking (By similarity). Essential for maintaining the integrity of endosome-trans-Golgi network structure (By similarity). Together with LRRK2, plays a role in the retrograde trafficking pathway for recycling proteins, such as mannose 6 phosphate receptor (M6PR), between lysosomes and the Golgi apparatus in a retromer-dependent manner (By similarity). Recruits LRRK2 to the Golgi apparatus and stimulates LRRK2 kinase activity (By similarity). Regulates also neuronal process morphology in the intact central nervous system (CNS) (By similarity). Interacts with LRRK2. Colocalizes with GM130 at the Golgi apparatus (By similarity). Colocalizes with LRRK2 at dynamic tubules emerging from and retracting to the Golgi apparatus (By similarity). Colocalizes with TGN46 at the trans-Golgi network (TGN) (By similarity). Belongs to the small GTPase superfamily. Rab family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Endonuclease that resolves Holliday junction intermediates made during homologous genetic recombination and DNA repair. Exhibits sequence and structure-selective cleavage of four-way DNA junctions, where it introduces symmetrical nicks in two strands of the same polarity at the 5' side of CC dinucleotides. Corrects the defects in genetic recombination and DNA repair associated with inactivation of RuvAB or RuvC (By similarity). Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Homodimer. Belongs to the RusA family. +The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpA family. +Purine salvage pathway enzyme that catalyzes the transfer of the ribosyl-5-phosphate group from 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to the N9 position of the 6-oxopurines guanine and xanthine to form the corresponding ribonucleotides GMP (guanosine 5'-monophosphate) and XMP (xanthosine 5'-monophosphate), with the release of PPi. To a lesser extent, also acts on hypoxanthine. diphosphate + GMP = 5-phospho-alpha-D-ribose 1-diphosphate + guanine diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine diphosphate + IMP = 5-phospho-alpha-D-ribose 1-diphosphate + hypoxanthine Purine metabolism; GMP biosynthesis via salvage pathway; GMP from guanine: step 1/1. Purine metabolism; XMP biosynthesis via salvage pathway; XMP from xanthine: step 1/1. Homotetramer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. XGPT subfamily. +Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import. Cofactor biosynthesis; adenosylcobalamin biosynthesis. Forms an energy-coupling factor (ECF) transporter complex composed of an ATP-binding protein (A component, CbiO), a transmembrane protein (T component, CbiQ) and 2 possible substrate-capture proteins (S components, CbiM and CbiN) of unknown stoichimetry. Belongs to the CbiN family. +ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. Catalyzes an ATP-dependent conformational change of U2 snRNP. Bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA (By similarity). ATP + H2O = ADP + H(+) + phosphate The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis. Belongs to the DEAD box helicase family. DDX46/PRP5 subfamily. +Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis. (R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) A monovalent cation. Ammonium or potassium. Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Homodimer. Belongs to the type III pantothenate kinase family. +ATP + L-aspartate + NH4(+) = AMP + diphosphate + H(+) + L-asparagine Amino-acid biosynthesis; L-asparagine biosynthesis; L-asparagine from L-aspartate (ammonia route): step 1/1. Belongs to the class-II aminoacyl-tRNA synthetase family. AsnA subfamily. +Catalyzes the attachment of tryptophan to tRNA(Trp). ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + H(+) + L-tryptophanyl-tRNA(Trp) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity and assembly of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 1 family. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +Belongs to the universal ribosomal protein uS2 family. +Belongs to the glycosyltransferase 8 family. +Cytochrome P450 monooxygenase; part of the gene cluster that mediates the biosynthesis of oxaleimides, cytotoxic compounds containing an unusual disubstituted succinimide moiety (PubMed:28365998). The first step of the pathway is provided by the HR-PKS poxF that serves in a new mode of collaborative biosynthesis with the PKS-NRPS poxE, by providing the olefin containing amino acid substrate via the synthesis of an ACP-bound dec-4-enoate (PubMed:28365998). The cytochrome P450 monooxygenase poxM-catalyzed oxidation at the alpha-position creates the enzyme-bound 2-hydroxydec-4-enoyl-ACP thioester, which may be prone to spontaneous hydrolysis to yield 2-hydroxydec-4-enoic acid due to increased electrophilicity of the carbonyl (PubMed:28365998). 2-hydroxydec-4-enoic acid can then be further oxidized by poxM to yield the alpha-ketoacid 2-oxodec-4-enoicacid, which is reductively aminated by the aminotransferase poxL to yield (S,E)-2-aminodec-4-enoic acid (PubMed:28365998). The Hybrid PKS-NRPS synthetase poxE then performs condensation between the octaketide product of its PKS modules and the amino group of (S,E)-2-aminodec-4-enoic acid which is activated and incorporated by the adenylation domain (PubMed:28365998). The resulting aminoacyl product can be cyclized by the Diels-Alderase PoxQ and reductively released by the reductive (R) domain of poxE to yield an aldehyde intermediate (PubMed:28365998) (Probable). The released aldehyde is then substrate for a Knoevenagel condensation by the hydrolyase poxO followed by an oxidation at the 5-position of the pyrrolidone ring (PubMed:28365998). The presence of the olefin from the amino acid building block allows for migration of the substituted allyl group to occur (PubMed:28365998). This allylic transposition reaction takes place in a conjugate addition, semipinacol-like fashion to yield a succinimide intermediate (PubMed:28365998). Iterative two-electron oxidations of the C7 methyl of the succinimide intermediate to the carboxylic acid can be catalyzed by one of two remaining cytochrome P450 monooxygenasess poxC or poxD to yield oxaleimide A (PubMed:28365998). Subsequent oxidation yields the maleimide scaffold oxaleimide I (PubMed:28365998). Both oxaleimide A and oxaleimide I can undergo oxidative modifications in the decalin ring to yield the series of products oxaleimides B to H (PubMed:28365998). Secondary metabolite biosynthesis. Expression is positively regulated by the oxaleimides biosynthesis cluster-specific transcription factor poxB. Belongs to the cytochrome P450 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + H2O + oxidized [flavodoxin] = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + reduced [flavodoxin] Binds 1 [4Fe-4S] cluster. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 5/6. Belongs to the IspG family. +Regulatory subunit of the cAMP-dependent protein kinases involved in cAMP signaling in cells. The inactive holoenzyme is composed of two regulatory chains and two catalytic chains. Activation by cAMP releases the two active catalytic monomers and the regulatory dimer. Interacts with PRKX; regulates this cAMP-dependent protein kinase (By similarity). Interacts with smAKAP; this interaction may target PRKAR1B to the plasma membrane (By similarity). Abundant in brain and testis. No expression in lung, heart, liver, spleen, kidney and skeletal muscle. The pseudophosphorylation site binds to the substrate-binding region of the catalytic chain, resulting in the inhibition of its activity. Belongs to the cAMP-dependent kinase regulatory chain family. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +Belongs to the TCEANC2 family. +Probable catalytic subunit of a GTPase activating protein that has specificity for Rab3 subfamily (RAB3A, RAB3B, RAB3C and RAB3D). Rab3 proteins are involved in regulated exocytosis of neurotransmitters and hormones. Specifically converts active Rab3-GTP to the inactive form Rab3-GDP. Required for normal eye and brain development. May participate in neurodevelopmental processes such as proliferation, migration and differentiation before synapse formation, and non-synaptic vesicular release of neurotransmitters. The Rab3 GTPase-activating complex is a heterodimer composed of RAB3GAP and RAB3-GAP150. The Rab3 GTPase-activating complex interacts with DMXL2 (PubMed:11809763, PubMed:9733780). Interacts with LMAN1 (By similarity). In neurons, it is enriched in the synaptic soluble fraction. Belongs to the Rab3-GAP catalytic subunit family. +May affect the movement of lipids in the cytoplasm or allow the binding of lipids to organelles. Widely expressed; the highest levels are in prostate, lung and placenta; also detected in kidney, bone marrow, spleen, thymus, spinal cord, adrenal gland, salivary gland, trachea and mammary gland; levels are low in brain, heart, fetal liver, pancreas and testis. In vitro, is responsive to TNF. Belongs to the apolipoprotein L family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds a dinuclear copper A center per subunit. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome (By similarity). The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (PubMed:27654913). Found in a complex with TMEM177, COA6, COX18, COX20, SCO1 and SCO2. Interacts with TMEM177 in a COX20-dependent manner. Interacts with COX20. Interacts with COX16 (By similarity). Belongs to the cytochrome c oxidase subunit 2 family. +Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline. carbamoyl phosphate + L-ornithine = H(+) + L-citrulline + phosphate Amino-acid degradation; L-arginine degradation via ADI pathway; carbamoyl phosphate from L-arginine: step 2/2. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. OTCase family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. This function is generally fulfilled by the C-terminal part of HisG, which is missing in some bacteria such as this one. Belongs to the class-II aminoacyl-tRNA synthetase family. HisZ subfamily. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Participates in the translocation of lipoproteins from the inner membrane to the outer membrane. Only forms a complex with a lipoprotein if the residue after the N-terminal Cys is not an aspartate (The Asp acts as a targeting signal to indicate that the lipoprotein should stay in the inner membrane). Monomer. Belongs to the LolA family. +Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Binds 1 potassium ion per subunit. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln), leading to the formation of s(2)U34, the first step of tRNA-mnm(5)s(2)U34 synthesis. Sulfur is provided by IscS, via a sulfur-relay system. Binds ATP and its substrate tRNAs. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Interacts with TusE. Belongs to the MnmA/TRMU family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Homodimer. Belongs to the UPF0210 family. +Receptor that may play a role in the perception of bitterness and is gustducin-linked. May play a role in sensing the chemical composition of the gastrointestinal content. The activity of this receptor may stimulate alpha gustducin, mediate PLC-beta-2 activation and lead to the gating of TRPM5. Expressed in subsets of taste receptor cells of the tongue and palate epithelium and exclusively in gustducin-positive cells. Most taste cells may be activated by a limited number of bitter compounds; individual taste cells can discriminate among bitter stimuli. Belongs to the G-protein coupled receptor T2R family. +May play a role in apoptosis. Isoform 1 seems to be the main initiator. Interacts with MCL1, BCL2, BCL2L1/BCL-Xl, BCL2A1 and BCL2L2/BCL-w. Interacts with the myosin V actin motor complex through its binding to DLC2 (By similarity). Isoform 1 is mainly expressed in B-lymphoid cells. Isoform 2 and isoform 3 are mainly expressed in B-CLL and normal B-cells. Belongs to the Bcl-2 family. +The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. Binds 1 lipoyl cofactor covalently. The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvH family. +Belongs to the UPF0344 family. +Involved in meiotic DNA-break repair. Required for the recruitment of DCM1 to meiosis recombination hot spots. Forms a ternary complex with DMC1 and MEI5. Localizes at chromosomal foci at leptotene and zigotene. During meiosis. Belongs to the SWI5/SAE3 family. +The C-terminal part of the hedgehog protein precursor displays an autoproteolysis activity that results in the cleavage of the full-length protein into two parts (N-product and C-product) (By similarity). In addition, the C-terminal part displays a cholesterol transferase activity that results by the covalent attachment of a cholesterol moiety to the C-terminal of the newly generated N-product (By similarity). Once cleaved, the C-product has no signaling activity and diffuses from the cell (By similarity). The dually lipidated hedgehog protein N-product is a morphogen which is essential for a variety of patterning events during development. Establishes the anterior-posterior axis of the embryonic segments and patterns the larval imaginal disks. Binds to the patched (ptc) receptor, which functions in association with smoothened (smo), to activate the transcription of target genes wingless (wg), decapentaplegic (dpp) and ptc. In the absence of hh, ptc represses the constitutive signaling activity of smo through fused (fu). Essential component of a signaling pathway which regulates the Duox-dependent gut immune response to bacterial uracil; required to activate Cad99C-dependent endosome formation, norpA-dependent Ca2+ mobilization and p38 MAPK, which are essential steps in the Duox-dependent production of reactive oxygen species (ROS) in response to intestinal bacterial infection. During photoreceptor differentiation, it up-regulates transcription of Ubr3, which in turn promotes the hh-signaling pathway by mediating the ubiquitination and degradation of cos. cholesterol + glycyl-L-cysteinyl-[protein] + H(+) = [protein]-C-terminal glycyl cholesterol ester + N-terminal L-cysteinyl-[protein] Interacts with shf. Nuclear up to embryonic stage 10 and then at stage 11 shifts to the cytoplasm. Also secreted in either cleaved or uncleaved form to mediate signaling to other cells. The N-terminal peptide remains associated with the cell surface. Heparan sulfate proteoglycans of the extracellular matrix play an essential role in diffusion. Lipophorin is required for diffusion, probably by acting as vehicle for its movement, explaining how it can spread over long distances despite its lipidation. The C-terminal part of the hedgehog protein precursor displays an autoproteolysis activity that results in the cleavage of the full-length protein into two parts (N-product and C-product) (By similarity). In addition, the C-terminal part displays a cholesterol transferase activity that results by the covalent attachment of a cholesterol moiety to the C-terminal of the newly generated N-product (By similarity). The N-product is the active species in both local and long-range signaling, whereas the C-product has no signaling activity (By similarity). Cholesterylation is required for N-product targeting to lipid rafts and multimerization. N-palmitoylation by Rasp of the hedgehog N-product, within the secretory pathway, is required for the embryonic and larval patterning activities of the hedgehog signal. Belongs to the hedgehog family. +Shows a strict specificity for N-acetyl arylalkylamines but not acetanilide derivatives. an N-acetylarylalkylamine + H2O = acetate + an aralkylamine Activated by divalent metal ions. Inhibited by certain thiol reagents. Homotetramer. +Dimethylates a single guanine residue at position 26 of a number of tRNAs using S-adenosyl-L-methionine as donor of the methyl groups. guanosine(26) in tRNA + 2 S-adenosyl-L-methionine = 2 H(+) + N(2)-dimethylguanosine(26) in tRNA + 2 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. Trm1 family. +E3 ubiquitin-protein ligase that acts in the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, which targets misfolded proteins that accumulate in the endoplasmic reticulum (ER) for ubiquitination and subsequent proteasome-mediated degradation. Protects cells from ER stress-induced apoptosis. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Predominantly expressed in testis. Expression in testis already detected at postnatal day 1 (P1), progressively increases with adult levels reached at P20. +Important for reducing fluoride concentration in the cell, thus reducing its toxicity. Belongs to the CrcB (TC 9.B.71) family. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +GTPase-activating protein for ADP ribosylation factor family members, including ARF1. May form heterooligomers with GIT1 (Probable). Directly interacts with protein Piccolo/PCLO (PubMed:12473661). Interacts with PPFIA1 and PPFIA2 (PubMed:12629171). Interacts with ARHGEF7 (By similarity). Identified in a complex with ARHGEF6 and BIN2 (By similarity). Interacts with PAK3 (By similarity). Interacts with PXN/paxillin (By similarity). Interacts with TGFB1I1 (By similarity). Forms a complex with EFNB1 and GRB4/NCK2 (By similarity). +Cell division inhibitor that blocks the formation of polar Z ring septums. Rapidly oscillates between the poles of the cell to destabilize FtsZ filaments that have formed before they mature into polar Z rings. Prevents FtsZ polymerization. Interacts with MinD and FtsZ. Belongs to the MinC family. Extended N-terminus. +Soluble frizzled-related proteins (sFRPS) function as modulators of Wnt signaling through direct interaction with Wnts. They have a role in regulating cell growth and differentiation in specific cell types. SFRP5 may be involved in determining the polarity of photoreceptor, and perhaps, other cells in the retina. The FZ domain is involved in binding with Wnt ligands. Belongs to the secreted frizzled-related protein (sFRP) family. +Demethylates proteins that have been reversibly carboxymethylated. Demethylates PPP2CB (in vitro) and PPP2CA. Binding to PPP2CA displaces the manganese ion and inactivates the enzyme (By similarity). [phosphatase 2A protein]-C-terminal L-leucine methyl ester + H2O = [phosphatase 2A protein]-C-terminal L-leucine + H(+) + methanol Binds PPP2CA and PPP2CB. Ubiquitous. Highly expressed in testis and brain. Phosphorylated by SIK1 following increases in intracellular sodium, leading to dissociation from the protein phosphatase 2A (PP2A) complex and subsequent dephosphorylation of sodium/potassium-transporting ATPase ATP1A1. Belongs to the AB hydrolase superfamily. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +May be involved in metal transport. Belongs to the CbiM family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate from the periplasm across the membrane. Belongs to the dicarboxylate/amino acid:cation symporter (DAACS) (TC 2.A.23) family. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. This subunit is found at the monomer-monomer interface. Cyanobacterial PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins PsbO, PsbU, PsbV and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbM family. +Phosphatase involved in the regulation of protein synthesis. Affects translational accuracy. H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 manganese ions per subunit. Present with 319 molecules/cell in log phase SD medium. Belongs to the PPP phosphatase family. PP-Z subfamily. +During host cell infection by tachyzoites, does not play a role in tethering the parasitophorous vacuole to the host mitochondria, probably because it does not bind host mitochondrial import protein TOMM70. Interacts with host SAMM50. Expressed in tachyzoites (at protein level). The MAF1 locus encodes multiple tandemly duplicated paralogs that vary in expression, sequence and copy number across T.gondii strains (PubMed:26920761). For instance, type I strain GT1 has 6 copies, type I strain RH has 4 copies, type II strains ME49 and PRU have 4 copies, type III strain VEG has 4 copies and type III strain CTG has only 2 copies (PubMed:26920761). The paralogs are classified into two groups, a and b and have probably arisen from the neofunctionalization of an ancestral MAF1 a gene (PubMed:26920761). They are characterized by the presence or absence of a repetitive stretch of 4 to 7 prolines followed by a serine (P(4:7)S), as well as differences in the amino acids surrounding the proline motif (PubMed:26920761). This motif is either completely missing (a and b0 paralogs) or repeated up to six times (b paralogs) (PubMed:26920761). Across the strains, transcript levels for the a paralogs are similar, however, in type II strain ME49, transcript levels for the b paralogs are low and no paralog MAF1 b1 protein is produced (PubMed:26920761). Paralogs differ in their ability to mediate host mitochondrial association (HMA), but also in their ability to confer a selective advantage during infection in a mouse model (PubMed:26920761, PubMed:29505111). Tachyzoites from type I and III strains associate with host mitochondria (HMA(+)), while tachyzoites from type II strains, such as ME49, do not associate with host mitochondria (HMA(-)) due to a lack of MAF1 b1 expression (PubMed:26920761). +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 4L family. +Negative regulator of amyloid-beta peptide production. May inhibit the processing of APP by blocking its access to alpha- and beta-secretase. Binding to the beta-secretase-cleaved APP C-terminal fragment is negligible, suggesting that ITM2C is a poor gamma-secretase cleavage inhibitor. May play a role in TNF-induced cell death and neuronal differentiation (By similarity). Interacts with BACE1. Interacts with APP. Interacts with STMN2. High levels in the brain, specifically in the cerebral cortex, medulla, amygdala, hippocampus, thalamus, caudate nucleus, cerebellum, olfactory lobe and spinal cord. Very low levels in other organs. Type I membrane-bound, as well as soluble, furin has a pre-eminent role in ITM2C proteolytic processing. PCSK7 and PCSK5 may also be involved although to a lesser extent. The soluble form of PCSK7 is incapable of processing ITM2C. Fails to undergo shedding by ADAM10 and intramembrane cleavage by SPPL2B. Belongs to the ITM2 family. +Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. adenosine + H(+) + H2O = inosine + NH4(+) 2'-deoxyadenosine + H(+) + H2O = 2'-deoxyinosine + NH4(+) Binds 1 zinc ion per subunit. Belongs to the metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. Adenosine deaminase subfamily. +Component of the cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery. Required for the maturation of extramitochondrial Fe-S proteins. Part of an electron transfer chain functioning in an early step of cytosolic Fe-S biogenesis, facilitating the de novo assembly of a [4Fe-4S] cluster on the cytosolic Fe-S scaffold complex. Electrons are transferred from NADPH via FAD- and FMN-containing diflavin oxidoreductase TAH18/ATR3 (PubMed:23754812). Together with the diflavin oxidoreductase, also required for the assembly of the diferric tyrosyl radical cofactor of ribonucleotide reductase (RNR), probably by providing electrons for reduction during radical cofactor maturation in the catalytic small subunit (By similarity). Required for embryo development (PubMed:23754812). Monomer (By similarity). Interacts with ATR3 (PubMed:20406405). The C-terminal domain binds 2 Fe-S clusters but is otherwise mostly in an intrinsically disordered conformation. The N-terminal domain has structural similarity with S-adenosyl-L-methionine-dependent methyltransferases, but does not bind S-adenosyl-L-methionine. It is required for correct assembly of the 2 Fe-S clusters. The twin Cx2C motifs are involved in the recognition by the mitochondrial MIA40-ERV1 disulfide relay system. The formation of 2 disulfide bonds in the Cx2C motifs through dithiol/disulfide exchange reactions effectively traps the protein in the mitochondrial intermembrane space. Belongs to the anamorsin family. +First expressed in developing facial cartilage in early tailbud embryos, with expression localized to the basihyobranchial, palatoquadrate and possibly Meckel's cartilages. Shortly after, a second area of expression is seen in the musculature of the anterior gut. During late embryogenesis, gut expression extends into hindgut tissues. In adults, expressed at a high level in the kidney, pancreas, spleen and stomach and at a slightly lower level in the intestine, skeletal muscle and tongue. Adult heart, liver and lung show little or no expression. First expressed during late neurula stage (stage 18). Levels increase slowly up to the tailbud stage (stage 28), then increase sharply before remaining approximately constant through the remaining tailbud and tadpole stages (stages 30-44). By foxf1-B. Belongs to the NK-3 homeobox family. +Belongs to the bacterial ribosomal protein bL27 family. +Ceramide synthase that catalyzes formation of ceramide from sphinganine and acyl-CoA substrates, with high selectivity toward long and very-long chains (C18:0-C22:0) as acyl donor. octadecanoyl-CoA + sphinganine = CoA + H(+) + N-(octadecanoyl)-sphinganine eicosanoyl-CoA + sphinganine = CoA + H(+) + N-eicosanoylsphinganine docosanoyl-CoA + sphinganine = CoA + H(+) + N-docosanoylsphinganine sphinganine + tetracosanoyl-CoA = CoA + H(+) + N-tetracosanoylsphinganine hexacosanoyl-CoA + sphinganine = CoA + H(+) + N-hexacosanoylsphinganine a fatty acyl-CoA + sphing-4-enine = an N-acylsphing-4-enine + CoA + H(+) octadecanoyl-CoA + sphing-4-enine = CoA + H(+) + N-octadecanoylsphing-4-enine hexadecasphinganine + octadecanoyl-CoA = CoA + H(+) + N-octadecanoylhexadecasphinganine Lipid metabolism; sphingolipid metabolism. The last loop motif confers selectivity toward stearoyl-CoA (octadecanoyl-CoA; C18:0-CoA) to behenoyl-CoA (docosanoyl-CoA; C22:0-CoA) as acyl donors. Phosphorylated at the C-terminus by CK2. Some prediction bioinformatics tools predict the presence of a homeobox domain (By similarity). However, the domain is degenerate and residues that are important for DNA-binding are absent (By similarity). +Required for pre-18S rRNA processing. May bind microtubules (By similarity). Belongs to the NOP5/NOP56 family. +Catalyzes the dehydration of D-mannonate. D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O Carbohydrate metabolism; pentose and glucuronate interconversion. Belongs to the mannonate dehydratase family. +Secreted protein that plays an essential role in immune innate response inhibition by interacting with and inhibiting host TLR2. In turn, bacteria recognition by immune cells is impaired and cytokine production is inhibited. Mechanistically, by interacting with TLR2, blocks ligand binding and thus inhibits activation. Second, by interacting with an already formed TLR2-lipopeptide complex, prevents TLR heterodimerization and downstream signaling. The interaction with host TLR2 does not involve sialyl Lewis X interactions. Interacts with host TLR2 (via its extracellular domain). The C-terminal domain contains a V-shape binding site for sialyl Lewis X. Belongs to the staphylococcal/streptococcal toxin family. +Light-harvesting photosynthetic bile pigment-protein from the phycobiliprotein complex (phycobilisome, PBS). Phycocyanin is the major phycobiliprotein in the PBS rod. Heterodimer of an alpha and a beta subunit (PubMed:8168545). Dimers further assemble into trimers and the trimers into hexamers. The basic functional unit of phycobiliproteins is a ring-shaped hexamer formed from two back-to-back trimers contacting via the alpha chain subunits. The trimers are composed of alpha/beta subunit heterodimers arranged around a three-fold axis of symmetry. The phycoerythrins also contain a gamma subunit which is located in the center of the hexamer (By similarity). Part of the phycobilisome rod. Contains one covalently linked phycocyanobilin chromophore. Belongs to the phycobiliprotein family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Required for maturation of ribosomal RNAs and formation of the large ribosomal subunit. Belongs to the WD repeat BOP1/ERB1 family. +Alkaline phosphatase that metabolizes various phosphate compounds and plays a key role in skeletal mineralization and adaptive thermogenesis (By similarity). Has broad substrate specificity and can hydrolyze a considerable variety of compounds: however, only a few substrates, such as diphosphate (inorganic pyrophosphate; PPi), pyridoxal 5'-phosphate (PLP) and N-phosphocreatine are natural substrates (By similarity). Plays an essential role in skeletal and dental mineralization via its ability to hydrolyze extracellular diphosphate, a potent mineralization inhibitor, to phosphate: it thereby promotes hydroxyapatite crystal formation and increases inorganic phosphate concentration (PubMed:19098289). Acts in a non-redundant manner with PHOSPHO1 in skeletal mineralization: while PHOSPHO1 mediates the initiation of hydroxyapatite crystallization in the matrix vesicles (MVs), ALPL/TNAP catalyzes the spread of hydroxyapatite crystallization in the extracellular matrix (By similarity). Also promotes dephosphorylation of osteopontin (SSP1), an inhibitor of hydroxyapatite crystallization in its phosphorylated state; it is however unclear whether ALPL/TNAP mediates SSP1 dephosphorylation via a direct or indirect manner (By similarity). Catalyzes dephosphorylation of PLP to pyridoxal (PL), the transportable form of vitamin B6, in order to provide a sufficient amount of PLP in the brain, an essential cofactor for enzymes catalyzing the synthesis of diverse neurotransmitters (By similarity). Additionally, also able to mediate ATP degradation in a stepwise manner to adenosine, thereby regulating the availability of ligands for purinergic receptors (By similarity). Also capable of dephosphorylating microbial products, such as lipopolysaccharides (LPS) as well as other phosphorylated small-molecules, such as poly-inosine:cytosine (poly I:C) (By similarity). Acts as a key regulator of adaptive thermogenesis as part of the futile creatine cycle: localizes to the mitochondria of thermogenic fat cells and acts by mediating hydrolysis of N-phosphocreatine to initiate a futile cycle of creatine dephosphorylation and phosphorylation (By similarity). During the futile creatine cycle, creatine and N-phosphocreatine are in a futile cycle, which dissipates the high energy charge of N-phosphocreatine as heat without performing any mechanical or chemical work (By similarity). a phosphate monoester + H2O = an alcohol + phosphate diphosphate + H2O = H(+) + 2 phosphate H2O + pyridoxal 5'-phosphate = phosphate + pyridoxal H2O + phosphoethanolamine = ethanolamine + phosphate H2O + N-phosphocreatine = creatine + phosphate ATP + H2O = ADP + H(+) + phosphate ADP + H2O = AMP + H(+) + phosphate AMP + H2O = adenosine + phosphate Binds 1 Mg(2+) ion. Binds 2 Zn(2+) ions. Phosphatase activity is specifically inhibited by 5-((5-chloro-2-methoxyphenyl)sulfonamido)nicotinamide (SBI-425). Homodimer. Localizes to special class of extracellular vesicles, named matrix vesicles (MVs), which are released by osteogenic cells. Localizes to the mitochondria of thermogenic fat cells: tethered to mitochondrial membranes via a GPI-anchor and probably resides in the mitochondrion intermembrane space. Calcium-binding is structural and does not influence the alkaline phosphatase activity. At very high concentrations, calcium can however substitute for zinc at zinc-binding sites, leading to strongly reduced enzyme activity. N-glycosylated. Belongs to the alkaline phosphatase family. +Belongs to the bacterial ribosomal protein bS16 family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Phosphotransfer between the C1 and C5 carbon atoms of pentose. alpha-D-ribose 1-phosphate = D-ribose 5-phosphate 2-deoxy-alpha-D-ribose 1-phosphate = 2-deoxy-D-ribose 5-phosphate Binds 1 or 2 manganese ions. Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route II): step 1/3. Belongs to the phosphopentomutase family. +Binds DNA and activates transcription of CYP11A1. Interaction with CREBBP and EP300 results in a synergistic transcriptional activation of CYP11A1. Interacts with CREBBP and EP300. Interacts with DNTTIP1 and DNTT. Highly expressed in kidney, lung and brain. In the brain, expression was seen in the basal ganglia, hippocampus, piriform cortex, cerebral cortex, ventromedial nucleus of the hypothalamus and the dorsal and superior central nuclei of the raphe. At 15.5 dpc, highly expressed in brain, lung, adrenal, thymus and kidney. Expression was also seen in spinal cord, retina and snout. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. Homodimer. Belongs to the transketolase family. DXPS subfamily. +Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells. CDH23 is required for establishing and/or maintaining the proper organization of the stereocilia bundle of hair cells in the cochlea and the vestibule during late embryonic/early postnatal development. It is part of the functional network formed by USH1C, USH1G, CDH23 and MYO7A that mediates mechanotransduction in cochlear hair cells. Required for normal hearing. antiparallel heterodimer with PCDH15 (By similarity). Interacts with USH1C and USH1G (PubMed:19297620, PubMed:21436032). Additional isoforms seem to exist. Particularly strong expression in the retina (PubMed:11138009). Found also in the cochlea. Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain. Cadherin repeats 1 and 2 mediate calcium-dependent heterophilic interaction with PCDH15. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting distinct genetic loci, including the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Disease susceptibility is associated with variants affecting the gene represented in this entry. Retina International's Scientific Newsletter +Elementary body. Belongs to the PMP outer membrane protein family. +Interconversion of serine and glycine. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Homotetramer. Identified in complex with ABRAXAS2 and the other subunits of the BRISC complex, at least composed of ABRAXAS2, BRCC3/BRCC36, BABAM2 and BABAM1/NBA1. In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one. Belongs to the SHMT family. +RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit. Belongs to the RnpA family. +Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate. (R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA + diphosphate Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 4/5. Homohexamer. Belongs to the bacterial CoaD family. +Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Binds 1 potassium ion per subunit. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. +Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +May play an important role in hippocampus-dependent long-lasting memory. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +A cytochrome P450 monooxygenase involved in the metabolism of various endogenous substrates, including fatty acids, steroid hormones and vitamins. Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (NADPH--hemoprotein reductase). Catalyzes the hydroxylation of carbon-hydrogen bonds. Exhibits high catalytic activity for the formation of hydroxyestrogens from estrone (E1) and 17beta-estradiol (E2), namely 2-hydroxy E1 and E2. Metabolizes cholesterol toward 25-hydroxycholesterol, a physiological regulator of cellular cholesterol homeostasis. May act as a major enzyme for all-trans retinoic acid biosynthesis in the liver. Catalyzes two successive oxidative transformation of all-trans retinol to all-trans retinal and then to the active form all-trans retinoic acid. Primarily catalyzes stereoselective epoxidation of the last double bond of polyunsaturated fatty acids (PUFA), displaying a strong preference for the (R,S) stereoisomer. Catalyzes bisallylic hydroxylation and omega-1 hydroxylation of PUFA. May also participate in eicosanoids metabolism by converting hydroperoxide species into oxo metabolites (lipoxygenase-like reaction, NADPH-independent). Plays a role in the oxidative metabolism of xenobiotics. Catalyzes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin. Metabolizes caffeine via N3-demethylation. an organic molecule + O2 + reduced [NADPH--hemoprotein reductase] = an alcohol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] 17beta-estradiol + O2 + reduced [NADPH--hemoprotein reductase] = 2-hydroxy-17beta-estradiol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] 17beta-estradiol + O2 + reduced [NADPH--hemoprotein reductase] = 4-hydroxy-17beta-estradiol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] estrone + O2 + reduced [NADPH--hemoprotein reductase] = 2-hydroxyestrone + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] estrone + O2 + reduced [NADPH--hemoprotein reductase] = 4-hydroxyestrone + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] cholesterol + O2 + reduced [NADPH--hemoprotein reductase] = 25-hydroxycholesterol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] all-trans-retinol + O2 + reduced [NADPH--hemoprotein reductase] = all-trans-retinal + H(+) + 2 H2O + oxidized [NADPH--hemoprotein reductase] all-trans-retinal + O2 + reduced [NADPH--hemoprotein reductase] = all-trans-retinoate + 2 H(+) + H2O + oxidized [NADPH--hemoprotein reductase] (5Z,8Z,11Z,14Z)-eicosatetraenoate + O2 + reduced [NADPH--hemoprotein reductase] = (14R,15S)-epoxy-(5Z,8Z,11Z)-eicosatrienoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] (5Z,8Z,11Z,14Z)-eicosatetraenoate + O2 + reduced [NADPH--hemoprotein reductase] = (14S,15R)-epoxy-(5Z,8Z,11Z)-eicosatrienoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate + O2 + reduced [NADPH--hemoprotein reductase] = (17R,18S)-epoxy-(5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate + O2 + reduced [NADPH--hemoprotein reductase] = (19R,20S)-epoxy-(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] (5S)-hydroperoxy-(6E,8Z,11Z,14Z)-eicosatetraenoate = 5-oxo-(6E,8Z,11Z,14Z)-eicosatetraenoate + H2O (12S)-hydroperoxy-(5Z,8Z,10E,14Z)-eicosatetraenoate = 12-oxo-(5Z,8Z,10E,14Z)-eicosatetraenoate + H2O (15S)-hydroperoxy-(5Z,8Z,11Z,13E)-eicosatetraenoate = 15-oxo-(5Z,8Z,11Z,13E)-eicosatetraenoate + H2O (13S)-hydroperoxy-(9Z,11E)-octadecadienoate = 13-oxo-(9Z,11E)-octadecadienoate + H2O (5Z,8Z,11Z,14Z)-eicosatetraenoate + O2 + reduced [NADPH--hemoprotein reductase] = 13-hydroxy-(5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] (5Z,8Z,11Z,14Z)-eicosatetraenoate + O2 + reduced [NADPH--hemoprotein reductase] = 19-hydroxy-(5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] (9Z,12Z)-octadecadienoate + O2 + reduced [NADPH--hemoprotein reductase] = 11-hydroxy-(9Z,12Z)-octadecadienoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Cofactor metabolism; retinol metabolism. Steroid metabolism; cholesterol metabolism. Lipid metabolism; arachidonate metabolism. Interacts with PGRMC1; the interaction requires PGRMC1 homodimerization. Belongs to the cytochrome P450 family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles. Belongs to the globin family. +Uses inorganic polyphosphate (polyP) as a donor to convert both AMP to ADP and ADP to ATP. Can also use GMP, CMP, UMP, GDP, CDP and UDP. [phosphate](n) + ADP = [phosphate](n+1) + AMP [phosphate](n) + ATP = [phosphate](n+1) + ADP Optimum temperature is 60-70 degrees Celsius. Belongs to the polyphosphate kinase 2 (PPK2) family. Class III subfamily. +Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate. (R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA + diphosphate Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 4/5. Homohexamer. Belongs to the bacterial CoaD family. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NAD(+) (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + H(+) + NADPH + uridine(54) in tRNA = (6S)-5,6,7,8-tetrahydrofolate + 5-methyluridine(54) in tRNA + NADP(+) Belongs to the MnmG family. TrmFO subfamily. +CD2 interacts with lymphocyte function-associated antigen CD58 (LFA-3) and CD48/BCM1 to mediate adhesion between T-cells and other cell types. CD2 is implicated in the triggering of T-cells, the cytoplasmic domain is implicated in the signaling function (By similarity). Interacts with CD48 (By similarity). Interacts with CD58 (LFA-3) (By similarity). Interacts with CD2AP (By similarity). Interacts with PSTPIP1 (By similarity). Interacts with FCGR3A; this interaction modulates NK cell activation and cytotoxicity. +Forms a channel through the mitochondrial outer membrane that allows diffusion of small hydrophilic molecules. The channel adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective (By similarity). Expressed in roots, stems, leaves, palea, lemma and pollen. Highly expressed during the first days following germination and then decreases with time. Not induced by osmotic stress. Consists mainly of membrane-spanning sided beta-sheets. Belongs to the eukaryotic mitochondrial porin (TC 1.B.8.1) family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 1 subfamily. +Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides. [thioredoxin]-dithiol + a hydroperoxide = [thioredoxin]-disulfide + an alcohol + H2O Homodimer. The active site is a conserved redox-active cysteine residue, the peroxidatic cysteine (C(P)), which makes the nucleophilic attack on the peroxide substrate. The peroxide oxidizes the C(P)-SH to cysteine sulfenic acid (C(P)-SOH), which then reacts with another cysteine residue, the resolving cysteine (C(R)), to form a disulfide bridge. The disulfide is subsequently reduced by an appropriate electron donor to complete the catalytic cycle. In this atypical 2-Cys peroxiredoxin, C(R) is present in the same subunit to form an intramolecular disulfide. The disulfide is subsequently reduced by thioredoxin. Belongs to the peroxiredoxin family. Tpx subfamily. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Cleaves the N-terminal amino acid of tripeptides. Release of the N-terminal residue from a tripeptide. Binds 2 Zn(2+) ions per subunit. Belongs to the peptidase M20B family. +Myotropic peptide. Belongs to the gastrin/cholecystokinin family. +ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 2/3. Homotetramer. Belongs to the argininosuccinate synthase family. Type 1 subfamily. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the PetM family. +The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-amino acid + H(+) Monomer. Belongs to the PTH family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The L component serves as a unique electron donor to the NB-component of the complex, and binds Mg-ATP. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per dimer. Porphyrin-containing compound metabolism; bacteriochlorophyll biosynthesis (light-independent). Homodimer. Protochlorophyllide reductase is composed of three subunits; BchL, BchN and BchB. Belongs to the NifH/BchL/ChlL family. +a 2-oxocarboxylate + H(+) = an aldehyde + CO2 Binds 1 metal ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Homotetramer. Expressed in shoots and at lowe levels in roots, flowers and siliques. By abscisic acid (ABA), salt and osmotic stress. Not induced by anoxia. Belongs to the TPP enzyme family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Converts internalized glutamate to GABA and increases the internal pH. Involved in glutamate-dependent acid resistance in gastric fluid. H(+) + L-glutamate = 4-aminobutanoate + CO2 Belongs to the group II decarboxylase family. +Provides oxygen to the bacteroids. This role is essential for symbiotic nitrogen fixation. Root nodules. Belongs to the plant globin family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS8 family. +May act as a transcriptional coregulator during muscle development through its interaction with SNW1. Has lost its ancestral function as a Na,K-ATPase beta-subunit. Associates with a SMAD7-transcriptional complex. Interacts with SNW1 and TOR1AIP1 (By similarity). According to PubMed:17592128, does not associate with known Na,K-ATPase alpha-subunits. Detected in nuclear envelops. Highly expressed in skeletal muscle and at a lower level in heart. Belongs to the X(+)/potassium ATPases subunit beta family. +Catalyzes the hydrolysis of esters. a carboxylic ester + H2O = a carboxylate + an alcohol + H(+) Belongs to the FrsA family. +Cell cycle associated protein capable of promoting cell proliferation through the activation of CDK2 at the G1/S phase transition. Interacts with CDK2. Belongs to the cullin family. +Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. In transcription, TFIIH has an essential role in transcription initiation. When the pre-initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module CAK controls the initiation of transcription. Part of a TFIID-containing RNA polymerase II pre-initiation complex that is composed of TBP and at least GTF2A1, GTF2A2, GTF2E1, GTF2E2, GTF2F1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, GTF2B, TCEA1, ERCC2, ERCC3, TAF1, TAF2, TAF3, TAF4, TAF5, TAF6, TAF7, TAF8, TAF9, TAF10, TAF11, TAF12 and TAF13. Component of the 7-subunit TFIIH core complex composed of XPB/ERCC3, XPD/ERCC2, GTF2H1, GTF2H2, GTF2H3, GTF2H4 and GTF2H5, which is active in NER. The core complex associates with the 3-subunit CDK-activating kinase (CAK) module composed of CCNH/cyclin H, CDK7 and MNAT1 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription (By similarity). Interacts with RARA; the interaction requires prior phosphorylation of RARA on 'Ser-369' which then enhances interaction of RARA with CDK7 (By similarity). Belongs to the TFB4 family. +Cell wall formation. NADP(+) + UDP-N-acetyl-alpha-D-muramate = H(+) + NADPH + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurB family. +Binds to 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29. Belongs to the universal ribosomal protein uL23 family. +Metallothioneins have a high content of cysteine residues that bind various heavy metals. Class I metallothioneins contain 2 metal-binding domains: four divalent ions are chelated within cluster A of the alpha domain and are coordinated via cysteinyl thiolate bridges to 11 cysteine ligands. Cluster B, the corresponding region within the beta domain, can ligate three divalent ions to 9 cysteines. Belongs to the metallothionein superfamily. Type 1 family. +Catalyzes the hydrolysis of N(4)-acetylcytidine (ac4C). H2O + N(4)-acetylcytidine = acetate + cytidine + H(+) H2O + N(4)-acetyl-2'-deoxycytidine = 2'-deoxycytidine + acetate + H(+) H2O + N(4)-acetylcytosine = acetate + cytosine + H(+) Belongs to the N(4)-acetylcytidine amidohydrolase family. +Snake venom endo-hyaluronidase that degrades hyaluronan to smaller oligosaccharide fragments. In venom, it is not toxic by itself, but increases the diffusion of other venom proteins by degrading the extracellular matrix. In addition, it displays antiedematogenic activity (By similarity). Random hydrolysis of (1->4)-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate. Monomer. Expressed by the venom gland. Belongs to the glycosyl hydrolase 56 family. +Involved in heme d1 biosynthesis. Catalyzes the decarboxylation of siroheme into didecarboxysiroheme. Siroheme is probably decarboxylated to monodecarboxysiroheme, which is in turn decarboxylated to didecarboxysiroheme. 2 H(+) + siroheme = 12,18-didecarboxysiroheme + 2 CO2 Porphyrin-containing compound metabolism. H.thermophilus possesses the fused nirDL gene but lacks the genes encoding NirG and NirH. Belongs to the Ahb/Nir family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Involved in concentration and sorting of cargo proteins of the multivesicular body (MVB) for incorporation into intralumenal vesicles. Belongs to the BRO1 family. +Involved in the pathway that organizes the shaping and sizing of the prospore membrane (PSM) during sporulation. May provide a meiosis-specific scaffold for the assembly of other proteins on spindle pole bodies (SPBs), and may be a limiting component for SPB formation. Interacts directly with MPC54, NUD1 and SPC42. Interacts with ADY3. Interacts with ADY4. Probable component of a SPB complex composed of ADY3, SSP1, DON1, MPC54, SPO21/MPC70, NUD1 and CNM67. Localizes to the ends of spindle microtubules in cells in meiosis. Meiosis-specific. Expressed during meiosis II, from 3 to 9 hours after induction of sporulation. Not expressed during mitosis. Belongs to the MPC70 family. +Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 magnesium ions per subunit. Monomer. Belongs to the DNA polymerase type-Y family. +Associates loosely with the viral DNA to form an outer shell around the nucleoprotein-DNA complex and links it with the capsid by binding the endosome lysis protein. Dissociates from the viral genome during entry. Might be involved in nuclear capsid assembly of the viral particles through its association with NPM1/nucleophosmin. Monomer. Homodimer. Exists in equilibrium between monomers and dimers in solution. Interacts with the histone-like nucleoprotein; this interactions bridge the virus core to the capsid. Interacts with core protein X; this interactions bridge the virus core to the capsid. Interacts with the endosome lysis protein VI; this interactions bridge the virus core to the capsid. Interacts with the peripentonal hexons. Interacts with host NPM1; this interaction might play a role in virus assembly. Located inside the capsid (core). Present in 157 copies per virion. Localizes in the nucleoli during infection, then translocates from the nucleoli to the nucleoplasm as the infection progresses and is finally incorporated into the viral particles. Expressed in the late phase of the viral replicative cycle. All late proteins expressed from the major late promoter are produced by alternative splicing and alternative polyadenylation of the same gene giving rise to non-overlapping ORFs. A leader sequence is present in the N-terminus of all these mRNAs and is recognized by the viral shutoff protein to provide expression although conventional translation via ribosome scanning from the cap has been shut off in the host cell. This protein is only encoded by mastadenoviruses, and may therefore play a role in mammals tropism. Belongs to the adenoviridae core-capsid bridging protein family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Catalyzes the dehydration of D-mannonate. D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O Carbohydrate metabolism; pentose and glucuronate interconversion. Belongs to the mannonate dehydratase family. +PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) Binds 1 Ca(2+) ion. Expressed by the venom gland. Belongs to the phospholipase A2 family. Group I subfamily. D49 sub-subfamily. +May participate in lipoprotein metabolism. Belongs to the apolipoprotein C4 family. Wrong choice of frame. +Secreted effector that activates ROS-mediated cell death in plant host and is essential for virulence (PubMed:30703564, PubMed:29029698). Plays a role in the transition from the biotrophic to necrotrophic stage (PubMed:30703564). Associates with and promotes the degradation of Nicotiana benthamiana BPA1, BPL1, BPL2, and BPL4 to disrupt ACD11 stabilization in a 26S proteasome-dependent manner (PubMed:30703564). Interacts with Nicotiana benthamiana ACD11, BPA1 (binding partner of ACD11), as well as BPA-like proteins BPL1, BPL2, BPL3 and BPL4. Expression is induced at 9-18 hours post-infiltration (hpi). The RxLR-dEER motif acts to carry the protein into the host cell cytoplasm through binding to cell surface phosphatidylinositol-3-phosphate. The disordered structure between residues 82 and 99 contributes to the effector function in cell death activation. Exhibits significantly reduced virulence with smaller lesions on Nicotiana benthamiana infected leaves. Belongs to the RxLR effector family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a, b, b' and c. Belongs to the ATPase A chain family. +Cell wall formation. ATP + L-alanine + UDP-N-acetyl-alpha-D-muramate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +MFS transporter; part of the gene cluster that mediates the biosynthesis of dihydroxynaphthalene (DHN)-melanin, a bluish-green pigment forming a dark layer in the conidial wall that protects the conidia from UV radiations. Expression is positively regulazed by the cluster-specific transcription factor pfmaF. Does not affect the production of scytalone. Belongs to the major facilitator superfamily. Allantoate permease family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +May play a role in the development of the nervous system such as in neurite outgrowth and elongation. May be involved in motor axon growth and guidance. Interacts with RABGGTB. Found in spleen, testis, prostate and fetal liver. Expression limited to vascular muscle of testis, smooth muscle of prostate stroma, heart muscle, skeletal muscle, crypts of small intestine, and red pulp of spleen. B lymphocytes express isoform 2 only; peripheral blood T lymphocytes express isoform 3 only; granulocytes and monocytes express neither isoform 2 nor isoform 3. During development of T lymphocytes, bone marrow progenitor cells express isoform 2 only; thymocytes at different stages of maturation express predominantly isoform 2 and weakly isoform 3, and mature thymocytes express only isoform 2. N-glycosylated. A protein of the expected size has been detected by antibody binding and Western blot in at least one of the analyzed tissues or cells. Produced by alternative promoter usage. Produced by alternative promoter usage. Produced by alternative splicing of isoform 2. Produced by alternative splicing of isoform 1. Chondrolectin +Degrades acharan sulfate and, to a lesser extent, heparin and heparan sulfate. Inhibited by Cu(2+) ion, nitrogen and cobalt. Activated by reducing agents, such as DL-dithiothreitol and 2-mercaptoethanol. Optimum pH is 7.2. Optimum temperature 45 degrees Celsius. Monomer. The N-terminus is blocked. +(S)-2,3,4,5-tetrahydrodipicolinate + H2O + succinyl-CoA = (S)-2-succinylamino-6-oxoheptanedioate + CoA Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route): step 1/3. Homotrimer. Belongs to the transferase hexapeptide repeat family. +Probable mitochondrial mRNA stabilization factor. Belongs to the ATP25 family. +Has a role in meiosis. Belongs to the UPF0300 family. +May function as a neurotransmitter or modulator. Belongs to the FARP (FMRFamide related peptide) family. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. This subunit is found at the monomer-monomer interface and is required for correct PSII assembly and/or dimerization. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbL family. +Cell division protein that is part of the divisome complex and is recruited early to the Z-ring. Probably stimulates Z-ring formation, perhaps through the cross-linking of FtsZ protofilaments. Its function overlaps with FtsA. Homodimer. Interacts with FtsZ. Localizes to the division site, in a FtsZ-dependent manner. Belongs to the SepF family. +In vitro, phosphorylates various substrates such as EmbR, PepE, MmaA4, Pyk, LldD and GroEL2. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by certain divalent metal cations, such as cobalt, manganese, nickel or magnesium. Zinc or iron ions do not affect activity. Homodimer. Autophosphorylated. Dephosphorylated by PstP. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins. Homomultimer. Interacts with envelope E protein in the budding compartment of the host cell, which is located between endoplasmic reticulum and the Golgi complex. Forms a complex with HE and S proteins. Interacts with nucleocapsid N protein. This interaction probably participates in RNA packaging into the virus. Largely embedded in the lipid bilayer. Belongs to the betacoronaviruses M protein family. +Together with LptE, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Component of the lipopolysaccharide transport and assembly complex. Interacts with LptE and LptA. Belongs to the LptD family. +Belongs to the DoxX family. +Essential for sperm motility and male fertility but is not required for the completion of spermatogenesis. (2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls. H2O + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-2,6-diaminoheptanedioate + succinate Binds 2 Zn(2+) or Co(2+) ions per subunit. Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route): step 3/3. Homodimer. Belongs to the peptidase M20A family. DapE subfamily. +Involved in the transcriptional regulation of genes required for mesoderm differentiation. In the developing embryo, expressed in the mesenchyme founder cells, vegetal plate of the mesenchyme blastula, extending tip of the invaginating archenteron and, later, in the secondary mesenchyme cells. First detected in the swimming blastula, maximally expressed in the gastrula. Levels decrease in the prism larval stage and are barely detectable by the pluteus larval stage. +Transport of potassium into the cell. Belongs to the HAK/KUP transporter (TC 2.A.72) family. +May transfer electrons to the iron-sulfur centers of SerB. A + H2O + selenite = AH2 + selenate Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit. Heterotrimer of alpha, beta and gamma subunits. Has potential use in bioremediation of waste sites contaminated with selenate, such as agricultural drainage waters. +Belongs to the SfsA family. +Belongs to the UPF0435 family. +Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. NUP84 is involved in nuclear poly(A)+ RNA export, in NPC assembly and distribution, as well as in nuclear envelope organization. Component of the nuclear pore complex (NPC). NPC constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. Due to its 8-fold rotational symmetry, all subunits are present with 8 copies or multiples thereof. Symmetric distribution. Belongs to the Nup84/Nup107 nucleoporin family. +Prevents the establishment of the cellular antiviral state by inhibiting TRIM25-mediated DDX58 ubiquitination, which normally triggers the antiviral transduction signal that leads to the activation of type I IFN genes by transcription factors IRF3 and IRF7. Prevents human EIF2AK2/PKR activation, either by binding double-strand RNA, or by interacting directly with EIF2AK2/PKR. This function may be important at the very beginning of the infection, when NS1 is mainly present in the cytoplasm. Also binds poly(A) and U6 snRNA. Inhibits post-transcriptional processing of cellular pre-mRNA, by binding and inhibiting two cellular proteins that are required for the 3'-end processing of cellular pre-mRNAs: the 30 kDa cleavage and polyadenylation specificity factor/CPSF4 and the poly(A)-binding protein 2/PABPN1. In turn, unprocessed 3' end pre-mRNAs accumulate in the host nucleus and are no longer exported to the cytoplasm. Cellular protein synthesis is thereby shut off very early after virus infection. Viral protein synthesis is not affected by the inhibition of the cellular 3' end processing machinery because the poly(A) tails of viral mRNAs are produced by the viral polymerase through a stuttering mechanism. Homodimer. Interacts with host TRIM25 (via coiled coil); this interaction specifically inhibits TRIM25 multimerization and TRIM25-mediated DDX58 CARD ubiquitination. Interacts with human EIF2AK2/PKR, CPSF4, IVNS1ABP and PABPN1. In uninfected, transfected cells, NS1 is localized in the nucleus. Only in virus infected cells, the nuclear export signal is unveiled, presumably by a viral protein, and a fraction of NS1 is exported in the cytoplasm. The dsRNA-binding region is required for suppression of RNA silencing. Upon interferon induction, ISGylated via host HERC5; this results in the impairment of NS1 interaction with RNA targets due to its inability to form homodimers and to interact with host EIF2AK2/PKR. Belongs to the influenza A viruses NS1 family. +Hydrolyzes glucose-6-phosphate to glucose in the endoplasmic reticulum. May form with the glucose-6-phosphate transporter (SLC37A4/G6PT) a ubiquitously expressed complex responsible for glucose production through glycogenolysis and gluconeogenesis. Probably required for normal neutrophil function (By similarity). D-glucose 6-phosphate + H2O = D-glucose + phosphate Inhibited by vanadate. Carbohydrate biosynthesis; gluconeogenesis. Expressed in liver and kidney. It is the major glucose-6-phosphatase expressed in the small intestine. Up-regulated upon fasting. Belongs to the glucose-6-phosphatase family. +Nucleolar protein that acts as a regulator of RNA polymerase I by connecting RNA polymerase I with enzymes responsible for ribosomal processing and modification. Required for neural crest specification: following monoubiquitination by the BCR(KBTBD8) complex, associates with NOLC1 and acts as a platform to connect RNA polymerase I with enzymes responsible for ribosomal processing and modification, leading to remodel the translational program of differentiating cells in favor of neural crest specification. Heterodimer; heterodimerizes with NOLC1 following monoubiquitination. Part of a large pre-ribosomal ribonucleoprotein (RNP) complex, that consists of at least 62 ribosomal proteins, 45 nonribosomal proteins and both pre-rRNA and mature rRNA species. Within this complex directly interacts with NOP56 in an RNA-independent manner. Ubiquitous in adult and embryonic tissues. Expression elevated at 11 dpc when the branchial arches and facial swellings are present. Pyrophosphorylated by 5-diphosphoinositol pentakisphosphate (5-IP7) (PubMed:17873058). Serine pyrophosphorylation is achieved by Mg(2+)-dependent, but enzyme independent transfer of a beta-phosphate from a inositol pyrophosphate to a pre-phosphorylated serine residue (PubMed:17873058). Ubiquitinated. Monoubiquitination by the BCR(KBTBD8) complex promotes the formation of a NOLC1-TCOF1 complex that acts as a platform to connect RNA polymerase I with enzymes responsible for ribosomal processing and modification, leading to remodel the translational program of differentiating cells in favor of neural crest specification. +Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). 5,6-dimethylbenzimidazole + nicotinate beta-D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate Nucleoside biosynthesis; alpha-ribazole biosynthesis; alpha-ribazole from 5,6-dimethylbenzimidazole: step 1/2. Belongs to the CobT family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has four main subunits: a(1), b(1), b'(1) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta, b and b' chains. In plastids the F-type ATPase is also known as CF(1)CF(0). Belongs to the ATPase C chain family. +Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion. alpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + NH4(+) Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 5/5. Belongs to the glucosamine/galactosamine-6-phosphate isomerase family. NagB subfamily. +Connects the signal transduction between the two-component systems EvgS/EvgA and PhoQ/PhoP, by directly interacting with PhoQ and thus activating the PhoQ/PhoP system, in response to acid stress conditions. Interacts with PhoQ. By acid stress, via the EvgS/EvgA system. Belongs to the SafA family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine. H(+) + S-adenosyl-L-methionine = CO2 + S-adenosyl 3-(methylsulfanyl)propylamine Binds 1 pyruvoyl group covalently per subunit. Amine and polyamine biosynthesis; S-adenosylmethioninamine biosynthesis; S-adenosylmethioninamine from S-adenosyl-L-methionine: step 1/1. Heterotetramer of two alpha and two beta chains arranged as a dimer of alpha/beta heterodimers. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl group blocking the N-terminus of the alpha chain. Belongs to the prokaryotic AdoMetDC family. Type 1 subfamily. +Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate. (2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate + CO2 + NADH Binds 1 Mg(2+) or Mn(2+) ion per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4. Homodimer. Belongs to the isocitrate and isopropylmalate dehydrogenases family. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Ornithine decarboxylase (ODC) antizyme protein that negatively regulates ODC activity and intracellular polyamine biosynthesis and uptake in response to increased intracellular polyamine levels. Binds to ODC monomers, inhibiting the assembly of the functional ODC homodimer, and targets the monomers for ubiquitin-independent proteolytic destruction by the 26S proteasome. Interacts with ODC1 and thereby sterically blocks ODC homodimerization. A ribosomal frameshift occurs between the codons for Ser-61 and Asp-62. An autoregulatory mechanism enables modulation of frameshifting according to the cellular concentration of polyamines. Preferentially expressed in adult female midguts. Belongs to the ODC antizyme family. +Component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis. Component of the SEA complex composed of at least IML1/SEA1, RTC1/SEA2, MTC5/SEA3, NPR2, NPR3, SEA4, SEC13 and SEH1. Present with 279 molecules/cell in log phase SD medium. Belongs to the IML1 family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Transcription factor involved in the regulation of the insulin signaling pathway. Consistently activates both the downstream target Thor\d4EBP and the feedback control target InR. Involved in negative regulation of the cell cycle, modulating cell growth and proliferation. In response to cellular stresses, such as nutrient deprivation or increased levels of reactive oxygen species, foxo is activated and inhibits growth through the action of target genes such as Thor. Foxo activated in the adult fat body can regulate lifespan in adults; an insulin peptide itself may function as one secondary messenger of insulin-regulated aging. Also regulates Lip4, homolog of human acid lipases, thereby acting as a key modulator of lipid metabolism by insulin signaling and integrates insulin responses to glucose and lipid homeostasis (By similarity). Interacts with melt. When phosphorylated, translocated from nucleus to cytoplasm. Dephosphorylation triggers nuclear translocation (By similarity). +Probably functions as component of the Arp2/3 complex which is involved in regulation of actin polymerization and together with an activating nucleation-promoting factor (NPF) mediates the formation of branched actin networks (By similarity). In addition to its role in the cytoplasmic cytoskeleton, the Arp2/3 complex also promotes actin polymerization in the nucleus, thereby regulating gene transcription and repair of damaged DNA (By similarity). Probable component of the Arp2/3 complex in which it may replace ARPC1B. Belongs to the WD repeat ARPC1 family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Homodimer. Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily. +Inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. Acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase. Binds 1 zinc ion. Interacts with GyrB. Belongs to the DNA gyrase inhibitor YacG family. +(4aS,6R)-4a-hydroxy-L-erythro-5,6,7,8-tetrahydrobiopterin = (6R)-L-erythro-6,7-dihydrobiopterin + H2O Belongs to the pterin-4-alpha-carbinolamine dehydratase family. +Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. [protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family. +D-glucuronate = D-fructuronate aldehydo-D-galacturonate = keto-D-tagaturonate Carbohydrate metabolism; pentose and glucuronate interconversion. Belongs to the metallo-dependent hydrolases superfamily. Uronate isomerase family. +Belongs to the CbbQ/NirQ/NorQ/GpvN family. +Belongs to the SlyX family. +Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids. acetyl-CoA + H(+) + malonyl-[ACP] = 3-oxobutanoyl-[ACP] + CO2 + CoA Lipid metabolism; fatty acid biosynthesis. Homodimer. The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH. Belongs to the thiolase-like superfamily. FabH family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. 2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl 1-phosphate + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine = H(+) + lipid A disaccharide (E. coli) + UDP a lipid X + a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a lipid A disaccharide + H(+) + UDP Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 5/6. Belongs to the LpxB family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system. The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. Belongs to the TatA/E family. +Putative Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. May be involved in spermatogenesis during sexual maturation (By similarity). Belongs to the SCM family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +This protein may play a role in the biosynthesis of the prosthetic group of nitrogenase (FeMo cofactor). Cofactor biosynthesis; Fe-Mo cofactor biosynthesis. Belongs to the NifD/NifK/NifE/NifN family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Belongs to the UPF0182 family. +Nitrilase that hydrolyzes preferentially phenylacetonitrile, but also (R,S)-mandelonitrile, and 2-phenylpropionitrile. a nitrile + 2 H2O = a carboxylate + NH4(+) 4-chlorophenylacetonitrile + 2 H2O = 4-chlorophenylacetate + NH4(+) Optimum pH is 8.0-8.5. Optimum temperature is 38 degrees Celsius. Belongs to the carbon-nitrogen hydrolase superfamily. Nitrilase family. +Signaling peptide (root growth factor) that regulates the pattern of root growth and lateral root development by modulating the length and the number of cortical cells in the root apical meristem (RAM), and the anticlinal asymmetric cell divisions in lateral root initiation cells (PubMed:22307643, PubMed:23370719). Also involved in the regulation of hypocotyl bending and root gravitropism in a PIN2-traffic dependent manner, thus influencing the formation of auxin gradients (PubMed:22421050). Maintains the postembryonic root stem cell niche (PubMed:20798316). Binds to LRR receptor-like serine/threonine-protein kinases to trigger their dimerization with SERK proteins and subsequent signaling. The precursor is detected in the endoplasmic reticulum probably during its processing. Expressed in stems, hypocotyls, cotyledons, leaves, flowers, shoot apex, siliques, stamens and petals. Absent from the primary root (PubMed:23370719). Expressed irregularly throughout the cotyledon and accumulates at the base of the organ (PubMed:23370719). In leaves, present at a high level in the basal part, close to the main veins, irregularly in the lamina joining these veins, and in separate segments of the leaf margin (PubMed:23370719). Observed in the stem, the rachis of the inflorescence, and the lower portion of the flower pedicel, especially at its upper side (PubMed:23370719). In flowers, detected throughout its development at the base of the sepals, in the petals, the filament of the stamens and the gynoecium, and later in siliques (PubMed:23370719). During seedling gravitropic response, restricted to the epidermis and cortex and enhanced at the lower side of the reoriented hypocotyl (PubMed:22421050). Rapidly induced by auxin. Reduced hypocotyl bending and dose-dependent altered root gravitropism associated with an altered PIN2 traffic that impairs the formation of auxin gradients, thus leading to an irregular waves root shape. 'Golven' means irregular waves in Dutch. Belongs to the RGF family. +May be a general steroid carrier protein. Causes an allergic reaction in human. Is a cause of type I allergic reactions in Europe, North America and USSR. Belongs to the BetVI family. +Contains ten tandem EGF-like repeats strikingly similar to those found in the cysteine rich 'stalk-like' structure of integrin beta-subunits. +Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein. Monomer. Belongs to the LolB family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Belongs to the UPF0246 family. +Substrate recognition and binding subunit of the essential mitochondrial processing protease (MPP), which cleaves the mitochondrial sequence off newly imported precursors proteins. Heterodimer of mas2 (alpha) and mas1 (beta) subunits, forming the mitochondrial processing protease (MPP) in which mas2 is involved in substrate recognition and binding and mas1 is the catalytic subunit. Belongs to the peptidase M16 family. Does not seem to have a protease activity as it lack the zinc-binding site. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. +Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Binds 1 zinc ion per subunit. Consists of a catalytic RNA component and at least 4-5 protein subunits. Belongs to the eukaryotic/archaeal RNase P protein component 4 family. Extended N-terminus. +Serine/threonine-protein kinase that plays an essential role in the regulation of actin filament dynamics. Acts downstream of several Rho family GTPase signal transduction pathways (PubMed:10436159, PubMed:11832213, PubMed:12807904, PubMed:15660133, PubMed:16230460, PubMed:18028908, PubMed:22328514, PubMed:23633677). Activated by upstream kinases including ROCK1, PAK1 and PAK4, which phosphorylate LIMK1 on a threonine residue located in its activation loop (PubMed:10436159). LIMK1 subsequently phosphorylates and inactivates the actin binding/depolymerizing factors cofilin-1/CFL1, cofilin-2/CFL2 and destrin/DSTN, thereby preventing the cleavage of filamentous actin (F-actin), and stabilizing the actin cytoskeleton (PubMed:11832213, PubMed:15660133, PubMed:16230460, PubMed:23633677). In this way LIMK1 regulates several actin-dependent biological processes including cell motility, cell cycle progression, and differentiation (PubMed:11832213, PubMed:15660133, PubMed:16230460, PubMed:23633677). Phosphorylates TPPP on serine residues, thereby promoting microtubule disassembly (PubMed:18028908). Stimulates axonal outgrowth and may be involved in brain development (PubMed:18028908). Has a dominant negative effect on actin cytoskeletal changes. Required for atypical chemokine receptor ACKR2-induced phosphorylation of cofilin (CFL1). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts (via LIM domain) with the cytoplasmic domain of NRG1. Interacts with NISCH. Interacts with RLIM and RNF6 (By similarity). Self-associates to form homodimers (PubMed:10196227). Interacts with HSP90AA1; this interaction promotes LIMK1 dimerization and subsequent transphosphorylation (PubMed:16641196). Interacts with CDKN1C (PubMed:14530263). Interacts with SSH1 (PubMed:15660133). Interacts with ROCK1 (PubMed:10436159, PubMed:10652353). Interacts (via LIM zinc-binding domains) with FAM89B/LRAP25 (via LRR repeat). Forms a tripartite complex with CDC42BPA, CDC42BPB and FAM89B/LRAP25 (By similarity). Predominantly found in the cytoplasm. Localizes in the lamellipodium in a CDC42BPA, CDC42BPB and FAM89B/LRAP25-dependent manner. Highest expression in both adult and fetal nervous system. Detected ubiquitously throughout the different regions of adult brain, with highest levels in the cerebral cortex. Expressed to a lesser extent in heart and skeletal muscle. Autophosphorylated. Phosphorylated on Thr-508 by ROCK1 and PAK1, resulting in activation. Phosphorylated by PAK4 which increases the ability of LIMK1 to phosphorylate cofilin. Phosphorylated at Ser-323 by MAPKAPK2 during activation of VEGFA-induced signaling, which results in activation of LIMK1 and promotion of actin reorganization, cell migration, and tubule formation of endothelial cells. Dephosphorylated and inactivated by SSH1. Phosphorylated by CDC42BP. Ubiquitinated. 'Lys-48'-linked polyubiquitination by RNF6 leads to proteasomal degradation through the 26S proteasome, modulating LIMK1 levels in the growth cone and its effect on axonal outgrowth. Also polyubiquitinated by RLIM (By similarity). LIMK1 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. +Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA). NADP(+) + shikimate = 3-dehydroshikimate + H(+) + NADPH Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 4/7. Homodimer. Belongs to the shikimate dehydrogenase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA. ATP + oxaloacetate = ADP + CO2 + phosphoenolpyruvate Binds 1 Mn(2+) ion per subunit. Carbohydrate biosynthesis; gluconeogenesis. Monomer. Belongs to the phosphoenolpyruvate carboxykinase (ATP) family. +May play a role in intracellular membrane fusion. Belongs to the SVAP1 family. +PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) Binds 1 Ca(2+) ion. Expressed by the venom gland. Belongs to the phospholipase A2 family. Group II subfamily. D49 sub-subfamily. +Belongs to the UPF0756 family. +May have dioxygenase activity. Binds 1 Fe cation per subunit. Belongs to the 4HPPD family. +Required for nucleoid occlusion (NO) phenomenon, which prevents Z-ring formation and cell division over the nucleoid. Acts as a DNA-associated cell division inhibitor that binds simultaneously chromosomal DNA and FtsZ, and disrupts the assembly of FtsZ polymers. SlmA-DNA-binding sequences (SBS) are dispersed on non-Ter regions of the chromosome, preventing FtsZ polymerization at these regions. Homodimer. Interacts with FtsZ. Belongs to the nucleoid occlusion factor SlmA family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity). a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Catalyzes the cleavage of L-kynurenine (L-Kyn) and L-3-hydroxykynurenine (L-3OHKyn) into anthranilic acid (AA) and 3-hydroxyanthranilic acid (3-OHAA), respectively. H2O + L-kynurenine = anthranilate + H(+) + L-alanine 3-hydroxy-L-kynurenine + H2O = 3-hydroxyanthranilate + H(+) + L-alanine Amino-acid degradation; L-kynurenine degradation; L-alanine and anthranilate from L-kynurenine: step 1/1. Cofactor biosynthesis; NAD(+) biosynthesis; quinolinate from L-kynurenine: step 2/3. Homodimer. Belongs to the kynureninase family. +Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides. Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low. Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids. Binds 2 manganese ions per subunit. Belongs to the peptidase M17 family. +The phosphorylation of phosphatidylinositol (PI) to PI4P is the first committed step in the generation of phosphatidylinositol 4,5-bisphosphate (PIP2), a precursor of the second messenger inositol 1,4,5-trisphosphate (InsP3). a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + ATP = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate) + ADP + H(+) By salt. Belongs to the PI3/PI4-kinase family. Type II PI4K subfamily. +Plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis. Belongs to the YciB family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Controls the copy number in gene replication. +Plays an essential role virus particle assembly and budding. Acts by interacting with viral ribonucleocapsid and host members of the ESCRT (endosomal sorting complex required for transport) system such as host VPS4, PDCD6IP/ALIX, NEDD4 or TGS101. The interaction with host E3 ubiquitin ligase SMURF2 also facilitates virus budding. May play a role in immune cell dysfunction by being packaged into exosomes that can decrease the viability of recipient cells (via RNAi suppression and exosome-bystander apoptosis). Homodimer. Homohexamer. Homooctamer. Exists as a dimer until it reorganizes at the plasma membrane into a hexameric form using phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). Hexamers are critical for budding. Octamers function in genome replication and RNA binding. Interacts with host TSG101. As a homohexamer, interacts with the WW domain 3 of host NEDD4. Interacts with the nucleoprotein/NP. Interacts (via YPx(n)L/I motif) with host PDCD6IP/ALIX; this interaction supports efficient egress of viral particles. Interacts with VP35. Interacts with host ITCH; this interaction is required for efficient egress. Interacts (via PPXY motif) with host SMURF2 (via WW domains); the interaction positively regulates virus budding. In virion, localizes on the intravirional side of the membrane. In the host cell, it is found associated with virus-induced membrane proliferation foci and probably also in multivesicular bodies. These VP40-enriched membrane clusters are then redistributed to the plasma membrane where budding takes place. Late-budding domains (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. VP40 contains two overlapping L domains: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101 and a PPXY motif which interacts with the WW domain 3 of NEDD4 E3 ubiquitin ligase and the three WW domains of SMURF2 E3 ubiquitin ligase. Most abundant protein in the virion. Belongs to the filoviridae matrix protein VP40 family. +Involved in mitochondrial tRNA methylation (By similarity). Specifically methylates the N1 position of guanosine-37 in various tRNAs. Methylation is not dependent on the nature of the nucleoside 5' of the target nucleoside. This is the first step in the biosynthesis of wybutosine (yW), a modified base adjacent to the anticodon of tRNAs and required for accurate decoding. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Monomer. Predominantly in the mitochondria and in the nucleus. Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM5/TYW2 family. +Seems to be involved in cell adhesion through trans-homophilic and -heterophilic interactions, the latter including specifically interactions with NECTIN1. Does not act as receptor for alpha-herpesvirus entry into cells. (Microbial infection) Acts as a receptor for measles virus. Self-associates. Interacts via its Ig-like V-type domain with NECTIN1 Ig-like V-type domain. Interacts via its C-terminus with AFDN. (Microbial infection) Interacts with measles virus Hemagglutinin protein (PubMed:22048310, PubMed:23202587). Colocalizes with AFDN at cadherin-based adherens junctions (PubMed:11544254). The secreted form is found in breast tumor patients (PubMed:15784625). Predominantly expressed in placenta. Not detected in normal breast epithelium but expressed in breast carcinoma. The soluble form is produced by proteolytic cleavage at the cell surface (shedding), probably by ADAM17/TACE. The disease is caused by variants affecting the gene represented in this entry. Belongs to the nectin family. +Probably part of the ABC transporter complex RfuABCD involved in riboflavin import. Binds riboflavin. Monomer in solution (PubMed:23404400). The complex is probably composed of two ATP-binding proteins (RfuB), two transmembrane proteins (RfuC and RfuD) and a solute-binding protein (RfuA) (Probable). Belongs to the BMP lipoprotein family. +Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression (By similarity). Binds 1 zinc ion per subunit. Binds DNA as a homotetramer. Belongs to the p53 family. +Binds to the Fc region of immunoglobulins gamma. Low affinity receptor. By binding to IgG it initiates cellular responses against pathogens and soluble antigens. Interacts with FGR and LYN. Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases. Phosphorylated by SRC-type Tyr-kinases such as LYN, BLK, FYN and SYK. +Interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. May be required in mitosis for the processing of stalled or collapsed replication forks. May self-associate. Interacts with MUS81. Recruited to regions of DNA damage in S-phase cells. Belongs to the EME1/MMS4 family. +May function to confer stability and plasticity to neuronal membrane via multiple interactions, including the spectrin-actin-based cytoskeleton, integral membrane channels and membrane-associated guanylate kinases. Interacts with AGAP2. Additional isoforms seem to exist. Highest expression in brain, lower in heart and kidney. Within the brain, highest expression in cerebellum. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the trimethylation of the amino group of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine. The three successive methylation reactions represent the second step of diphthamide biosynthesis. 2-[(3S)-amino-3-carboxypropyl]-L-histidyl-[translation elongation factor 2] + 3 S-adenosyl-L-methionine = diphthine-[translation elongation factor 2] + 3 H(+) + 3 S-adenosyl-L-homocysteine Protein modification; peptidyl-diphthamide biosynthesis. Homodimer. Belongs to the diphthine synthase family. +Isoform 1, but not isoform 3, exhibits some choline transporter activity. Interacts with COCH. Present in supporting cells of the inner ear (at protein level). Only isoform 3 is expressed in inner ear vestibular tissue. Produced by alternative promoter usage. Belongs to the CTL (choline transporter-like) family. Truncated N-terminus. +Catalyzes quinol oxidation with the concomitant reduction of oxygen to water. 2 a quinol + O2 = 2 a quinone + 2 H2O Binds a copper B center. Heme A3. Energy metabolism; oxidative phosphorylation. Belongs to the heme-copper respiratory oxidase family. +Usually encoded in the trnK tRNA gene intron. Probably assists in splicing its own and other chloroplast group II introns. Belongs to the intron maturase 2 family. MatK subfamily. +Mediates, with Gag-Pol polyprotein, the essential events in virion assembly, including binding the plasma membrane, making the protein-protein interactions necessary to create spherical particles, recruiting the viral Env proteins, and packaging the genomic RNA via direct interactions with the RNA packaging sequence (Psi). Targets the polyprotein to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus (By similarity). Matrix protein is part of the pre-integration complex. Implicated in the release from host cell mediated by Vpu. Binds to RNA (By similarity). Forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Most core are conical, with only 7% tubular. The core is constituted by capsid protein hexamer subunits. The core is disassembled soon after virion entry (By similarity). The capsid promotes immune invasion by cloaking viral DNA from CGAS detection (By similarity). Host restriction factors such as TRIM5-alpha or TRIMCyp bind retroviral capsids and cause premature capsid disassembly, leading to blocks in reverse transcription. Capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species. Host PIN1 apparently facilitates the virion uncoating (By similarity). On the other hand, interactions with PDZD8 or CYPA stabilize the capsid (By similarity). Encapsulates and protects viral dimeric unspliced genomic RNA (gRNA). Binds these RNAs through its zinc fingers. Acts as a nucleic acid chaperone which is involved in rearangement of nucleic acid secondary structure during gRNA retrotranscription. Also facilitates template switch leading to recombination. As part of the polyprotein, participates in gRNA dimerization, packaging, tRNA incorporation and virion assembly. Plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1. Homotrimer; further assembles as hexamers of trimers. Oligomerization possibly creates a central hole into which the cytoplasmic tail of the gp41 envelope protein may be inserted. Interacts with host TRIM22; this interaction seems to disrupt proper trafficking of Gag polyprotein and may interfere with budding. Interacts with host PDZD8. When ubiquitinated, interacts (via p6-gag domain) with host PACSIN2; this interaction allows PACSIN2 recruitment to viral assembly sites and its subsequent incorporation into virions. Interacts with MOV10 (By similarity). Homotrimer; further assembles as hexamers of trimers. Interacts with gp41 (via C-terminus). Interacts with host CALM1; this interaction induces a conformational change in the Matrix protein, triggering exposure of the myristate group. Interacts with host AP3D1; this interaction allows the polyprotein trafficking to multivesicular bodies during virus assembly. Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase. Homodimer; the homodimer further multimerizes as homohexamers or homopentamers (By similarity). Interacts with host NUP98 (By similarity). Interacts with host PPIA/CYPA; this interaction stabilizes the capsid (By similarity). Interacts with host NUP153 (By similarity). Interacts with host PDZD8; this interaction stabilizes the capsid. Interacts with host TRIM5; this interaction destabilizes the capsid (By similarity). Interacts with host CPSF6 (By similarity). Interacts with host NONO; the interaction is weak (By similarity). Interacts with host NUP98. Interacts with Vpr; this interaction allows Vpr incorporation into the virion. Interacts with host TSG101. p6-gag interacts with host PDCD6IP/AIP1. These locations are probably linked to virus assembly sites. The main location is the cell membrane, but under some circumstances, late endosomal compartments can serve as productive sites for virion assembly. Translation results in the formation of the Gag polyprotein most of the time. Ribosomal frameshifting at the gag-pol genes boundary occurs at low frequency and produces the Gag-Pol polyprotein. This strategy of translation probably allows the virus to modulate the quantity of each viral protein. Maintenance of a correct Gag to Gag-Pol ratio is essential for RNA dimerization and viral infectivity. Late-budding domains (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. p6-gag contains two L domains: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101 and a LYPX(n)L motif which interacts with PDCD6IP/AIP1. Gag-Pol polyprotein: Specific enzymatic cleavages by the viral protease yield mature proteins. Tyrosine phosphorylated presumably in the virion by a host kinase. Phosphorylation is apparently not a major regulator of membrane association. Capsid protein p24 is phosphorylated possibly by host MAPK1; this phosphorylation is necessary for Pin1-mediated virion uncoating. Nucleocapsid protein p7 is methylated by host PRMT6, impairing its function by reducing RNA annealing and the initiation of reverse transcription. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Produced by conventional translation. Belongs to the primate lentivirus group gag polyprotein family. +Putative component of some signal peptidase complex which removes signal peptides from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum. Cleavage of hydrophobic, N-terminal signal or leader sequences from secreted and periplasmic proteins. Belongs to the peptidase S26B family. Could be the product of a pseudogene. +Might be involved in DNA-binding; the protein binds DNA in gel-shift assays and immunogold electron microscopy shows labelling of condensed chromatin. Only detected in the small cell variant (SCV) stage (at protein level). LCVs are more metabolically active than SCVs. The protein is present in SCVs from Nine Mile phase I strains, but its distribution in phase II strains was not examined (PubMed:8899704). The protein sequence was determined from Nine Mile phase II cells. +Belongs to the UPF0337 (CsbD) family. +Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12. [sulfur carrier]-SH + AH2 + L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 2 S-adenosyl-L-methionine = 3-methylsulfanyl-L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Belongs to the methylthiotransferase family. RimO subfamily. +Almost completely overlaps YLR364C-A. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. The gene for this protein is duplicated in strains AX3 and AX4. These strains contain a duplication of a segment of 750 kb of chromosome 2 compared to the corresponding sequence in strain AX2. +May be involved in transcriptional regulation. Belongs to the krueppel C2H2-type zinc-finger protein family. +Tyrosine-protein phosphatase which acts as a regulator of endoplasmic reticulum unfolded protein response. Mediates dephosphorylation of EIF2AK3/PERK; inactivating the protein kinase activity of EIF2AK3/PERK. May play an important role in CKII- and p60c-src-induced signal transduction cascades. May regulate the EFNA5-EPHA3 signaling pathway which modulates cell reorganization and cell-cell repulsion. May also regulate the hepatocyte growth factor receptor signaling pathway through dephosphorylation of MET (By similarity). H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate Interacts with EPHA3 (phosphorylated); dephosphorylates EPHA3 and may regulate its trafficking and function. Interacts with MET. Interacts with EPHA3 at the cell membrane. Most abundant in testis. Also found in kidney, spleen, muscle, liver, heart and brain. Ser-50 is the major site of phosphorylation as compared to Ser-242 and Ser-243. Activated by phosphorylation at Ser-50 (By similarity). S-nitrosylation of Cys-215 inactivates the enzyme activity. Sulfhydration at Cys-215 following endoplasmic reticulum stress inactivates the enzyme activity, promoting EIF2AK3/PERK activity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class 1 subfamily. +Involved in allosteric regulation of aspartate carbamoyltransferase. Binds 1 zinc ion per subunit. Contains catalytic and regulatory chains. Belongs to the PyrI family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose. Belongs to the glycosyl hydrolase 1 family. +Catalyzes the reduction of the double bond of an array of alpha,beta-unsaturated aldehydes and ketones. It also reduces the nitro group of nitroester and nitroaromatic compounds. It could have a role in detoxification processes. A + H(+) + NADPH = AH2 + NADP(+) Homotetramer. Belongs to the NADH:flavin oxidoreductase/NADH oxidase family. NamA subfamily. +May be involved in head or eye development; development of the clypeolabrum and several head sensory organs. Expressed during early development of the head. First expressed in a band around the anterior end of stage 5 blastoderm embryo, at 93% to 85% egg length. By gastrula stage, site of expression shifts to the dorsal-anterior region. At stage 12, expression is found in the clypeolabrum, the stomodaeum, and in ectoderm dorsal to the future supraesophageal ganglion. Expressed during embryonic development. Belongs to the SIX/Sine oculis homeobox family. +Rho GTPase-activating protein involved in the signal transduction pathway. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +Divisome component that associates with the complex late in its assembly, after the Z-ring is formed, and is dependent on DivIC and PBP2B for its recruitment to the divisome. Together with EzrA, is a key component of the system that regulates PBP1 localization during cell cycle progression. Its main role could be the removal of PBP1 from the cell pole after pole maturation is completed. Also contributes to the recruitment of PBP1 to the division complex. Not essential for septum formation. Forms polymers through the coiled coil domains. Interacts with PBP1, MreC and EzrA. Shuttles between the lateral wall and the division site in a cell cycle-dependent manner. Belongs to the GpsB family. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Serine protease inhibitor. Expressed by the venom gland. Belongs to the venom Kunitz-type family. +Transforms avian and murine macrophages and fibroblasts as well as murine B-lymphoid cells. Efficient DNA binding requires dimerization with another bHLH protein. This protein is synthesized as a Gag-vMyc chimeric protein. The sequence shown here corresponds to the Myc homolog fragment of the chimera. +(6R)-L-erythro-5,6,7,8-tetrahydrobiopterin + L-tryptophan + O2 = (4aS,6R)-4a-hydroxy-L-erythro-5,6,7,8-tetrahydrobiopterin + 5-hydroxy-L-tryptophan Aromatic compound metabolism; serotonin biosynthesis; serotonin from L-tryptophan: step 1/2. Belongs to the biopterin-dependent aromatic amino acid hydroxylase family. +Belongs to the UPF0145 family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +H(+) + NADP(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADPH + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Homodimer. Belongs to the ferredoxin--NADP reductase type 2 family. +Participates in ABA-regulated gene expression during seed development and subsequent vegetative stage by acting as the major mediator of ABA repression of growth. Binds to the embryo specification element and the ABA-responsive element (ABRE) of the Dc3 gene promoter and to the ABRE of the Em1 and Em6 genes promoters. Can also trans-activate its own promoter, suggesting that it is autoregulated. Plays a role in sugar-mediated senescence. DNA-binding homodimer. DNA-binding heterodimer with AREB3/DPBF3 or EEL/DPBF4. Interacts with ABI3, KEG, the mediator subunit MED25, and the AFP proteins AFP1, AFP2, AFP3 and AFP4. Interacts with TAP46. Interacts with the 36 kDa catalytic subunit (subunit C) of PP2A (PubMed:11489176, PubMed:12569131, PubMed:16247556, PubMed:17194765, PubMed:18484180, PubMed:22822206, PubMed:24357600). Interacts with FYPP1 and FYPP3 (PubMed:22715043). Interacts with FREE1 (via C-terminus) (PubMed:30962512). Predominantly expressed in seeds. Expressed in embryo during the latest stages of seed maturation. Up-regulated by drought, salt, abscisic acid (ABA) and glucose or 2-deoxy-glucose (2DG). Autoregulated. Positively regulated by the light-signaling component HY5. Phosphorylated by SRK2D and SRK2I in vitro. Ubiquitinated. AFP1, KEG and RPN10 mediate its proteasome-dependent degradation. Its stability or degradation plays a central role in abscisic acid response. Sumoylated at Lys-391 by SIZ1. Sumoylation protects ABI5 from proteasome degradation, attenuating ABA signaling and sensitivity to ABA. Exhibits abscisic acid (ABA) insensitivity. Belongs to the bZIP family. ABI5 subfamily. +Adapter protein required for efficient degradation of Spx by ClpXP under non-stress conditions. Interaction with Spx stabilizes Spx and exposes the C-terminus of Spx for recognition and proteolysis by ClpXP. Interacts with Spx. Belongs to the SpxH family. +A + a 2,3-saturated acyl-CoA = a 2,3-dehydroacyl-CoA + AH2 Belongs to the acyl-CoA dehydrogenase family. Truncated N-terminus. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +Belongs to the UPF0473 family. +Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP). [phosphate](n) + ATP = [phosphate](n+1) + ADP An intermediate of this reaction is the autophosphorylated ppk in which a phosphate is covalently linked to a histidine residue through a N-P bond. Belongs to the polyphosphate kinase 1 (PPK1) family. +Belongs to the eukaryotic ribosomal protein eS1 family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Feedback inhibited by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Belongs to the ATP phosphoribosyltransferase family. Long subfamily. +Component of the cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery. Required for the maturation of extramitochondrial Fe-S proteins. Part of an electron transfer chain functioning in an early step of cytosolic Fe-S biogenesis, facilitating the de novo assembly of a [4Fe-4S] cluster on the cytosolic Fe-S scaffold complex. Electrons are transferred from NADPH via a FAD- and FMN-containing diflavin oxidoreductase. Together with the diflavin oxidoreductase, also required for the assembly of the diferric tyrosyl radical cofactor of ribonucleotide reductase (RNR), probably by providing electrons for reduction during radical cofactor maturation in the catalytic small subunit. Monomer. The C-terminal domain binds 2 Fe-S clusters but is otherwise mostly in an intrinsically disordered conformation. The N-terminal domain has structural similarity with S-adenosyl-L-methionine-dependent methyltransferases, but does not bind S-adenosyl-L-methionine. It is required for correct assembly of the 2 Fe-S clusters. The twin Cx2C motifs are involved in the recognition by the mitochondrial MIA40-ERV1 disulfide relay system. The formation of 2 disulfide bonds in the Cx2C motifs through dithiol/disulfide exchange reactions effectively traps the protein in the mitochondrial intermembrane space. Belongs to the anamorsin family. +Binds 1 Fe(2+) ion per subunit. +Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P). an N-acyl-D-glucosamine 6-phosphate = an N-acyl-D-mannosamine 6-phosphate Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 3/5. Belongs to the NanE family. +Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is transferred onto alpha-ketoisovalerate to form ketopantoate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = (6S)-5,6,7,8-tetrahydrofolate + 2-dehydropantoate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantoate from 3-methyl-2-oxobutanoate: step 1/2. Homodecamer; pentamer of dimers. Belongs to the PanB family. +Part of the ABC transporter complex RbsABC involved in ribose import. Responsible for energy coupling to the transport system. ATP + D-ribose(out) + H2O = ADP + D-ribose(in) + H(+) + phosphate The complex is composed of an ATP-binding protein (RbsA), two transmembrane proteins (RbsC) and a solute-binding protein (RbsB). Belongs to the ABC transporter superfamily. Ribose importer (TC 3.A.1.2.1) family. +hydrolysis of (1->4)-alpha-D-glucosidic linkage in 4-alpha-D-[(1->4)-alpha-D-glucanosyl]n trehalose to yield trehalose and (1->4)-alpha-D-glucan. Optimum pH is 5.0. Optimum temperature is 85 degrees Celsius. Glycan biosynthesis; trehalose biosynthesis. Homodimer. Belongs to the glycosyl hydrolase 13 family. +(6S)-10-formyltetrahydrofolate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide = (6S)-5,6,7,8-tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide H2O + IMP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide Purine metabolism; IMP biosynthesis via de novo pathway; 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide (10-formyl THF route): step 1/1. Purine metabolism; IMP biosynthesis via de novo pathway; IMP from 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide: step 1/1. The IMP cyclohydrolase activity resides in the N-terminal region. Belongs to the PurH family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation (By similarity). Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). The b'-subunit is a diverged and duplicated form of b found in plants and photosynthetic bacteria (By similarity). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains (By similarity). Belongs to the ATPase B chain family. +Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFL1, triggers the GTP-dependent release of EIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating EIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. Required for normal levels of protein synthesis. May play a role in cellular stress resistance. May play a role in cellular response to DNA damage. May play a role in cell proliferation (By similarity). Associates with the 60S ribosomal subunit. Interacts with NPM1, RPA1 and PRKDC. May interact with NIP7. Found in a complex consisting of the 60S ribosomal subunit, SBDS and EFL1. Interacts with CLN3 (By similarity). Primarily detected in the cytoplasm, and at low levels in nucleus. Detected in the nucleolus during G1 and G2 phase of the cell cycle, and diffusely distributed in the nucleus during S phase. Detected at the mitotic spindle. Colocalizes with the microtubule organizing center during interphase (By similarity). Belongs to the SDO1/SBDS family. +Receptor for a number of inflammatory CC-chemokines including CCL3/MIP-1-alpha, CCL4/MIP-1-beta and RANTES and subsequently transduces a signal by increasing the intracellular calcium ion level. May play a role in the control of granulocytic lineage proliferation or differentiation. Participates in T-lymphocyte migration to the infection site by acting as a chemotactic receptor. Interacts with PRAF2. Efficient ligand binding to CCL3/MIP-1alpha and CCL4/MIP-1beta requires sulfation, O-glycosylation and sialic acid modifications. Glycosylation on Ser-6 is required for efficient binding of CCL4. Interacts with GRK2. Interacts with ARRB1 and ARRB2. Interacts with CNIH4. Interacts with S100A4; this interaction stimulates T-lymphocyte chemotaxis. Sulfated on at least 2 of the N-terminal tyrosines. Sulfation is required for efficient binding of the chemokines, CCL3 and CCL4 (By similarity). Palmitoylation in the C-terminal is important for cell surface expression. Phosphorylation on serine residues in the C-terminal is stimulated by binding CC chemokines especially by APO-RANTES. O-glycosylated, but not N-glycosylated. Ser-6 appears to be the major site even if Ser-7 may be also O-glycosylated. Also sialylated glycans present which contribute to chemokine binding. Thr-16 and Ser-17 may also be glycosylated and, if so, with small moieties such as a T-antigen. Belongs to the G-protein coupled receptor 1 family. +Microtubule binding protein that promotes the stabilization of dynamic microtubules. Required for mitotic spindle formation (By similarity). Interacts with microtubules. Belongs to the CLASP family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Required for high affinity copper (probably reduced Cu I) transport into the cell. Oligomer. Expressed in limited copper conditions. Expression is positively controlled by MAC1 and TYE7. Induced during biofilm formation and contact with macrophages as well as by alkaline pH via RIM101. Expression is down-regulated by 17-beta-estradiol. Impairs growth on solid low-copper and low-iron medium and displays altered morphology in response to copper-depleted conditions. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Involved in DNA repair and RecF pathway recombination. Belongs to the RecO family. +Catalyzes the formation of CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol (CDP-archaeol) from 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate (DGGGP) and CTP. This reaction is the third ether-bond-formation step in the biosynthesis of archaeal membrane lipids. 2,3-bis-O-(geranylgeranyl)-sn-glycerol 1-phosphate + CTP + H(+) = CDP-2,3-bis-O-(geranylgeranyl)-sn-glycerol + diphosphate Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the CDP-archaeol synthase family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. Belongs to the phosphatidylserine decarboxylase family. PSD-A subfamily. +a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) Belongs to the complex I subunit 4 family. +Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. May lack catalytic activity. AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine Purine metabolism; AMP biosynthesis via salvage pathway; AMP from adenine: step 1/1. Present with 937 molecules/cell in log phase SD medium. Belongs to the purine/pyrimidine phosphoribosyltransferase family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Calcium-dependent lectin that mediates cell adhesion by binding to glycoproteins on neighboring cells. Mediates the adherence of lymphocytes to endothelial cells of high endothelial venules in peripheral lymph nodes. Promotes initial tethering and rolling of leukocytes in endothelia. Interaction with SELPLG/PSGL1 and PODXL2 is required for promoting recruitment and rolling of leukocytes. This interaction is dependent on the sialyl Lewis X glycan modification of SELPLG and PODXL2, and tyrosine sulfation modifications of SELPLG. Sulfation on 'Tyr-51' of SELPLG is important for L-selectin binding. Highly expressed in lymphocytes from peripheral lymph nodes. Low in lymphocytes isolated from Peyer patches. N-glycosylated. Belongs to the selectin/LECAM family. +Serine kinase that plays an essential role in the NF-kappa-B signaling pathway which is activated by multiple stimuli such as inflammatory cytokines, bacterial or viral products, DNA damages or other cellular stresses. Acts as part of the canonical IKK complex in the conventional pathway of NF-kappa-B activation and phosphorylates inhibitors of NF-kappa-B on 2 critical serine residues. These modifications allow polyubiquitination of the inhibitors and subsequent degradation by the proteasome. In turn, free NF-kappa-B is translocated into the nucleus and activates the transcription of hundreds of genes involved in immune response, growth control, or protection against apoptosis. In addition to the NF-kappa-B inhibitors, phosphorylates several other components of the signaling pathway including NEMO/IKBKG, NF-kappa-B subunits RELA and NFKB1, as well as IKK-related kinases TBK1 and IKBKE. IKK-related kinase phosphorylations may prevent the overproduction of inflammatory mediators since they exert a negative regulation on canonical IKKs. Phosphorylates FOXO3, mediating the TNF-dependent inactivation of this pro-apoptotic transcription factor. Also phosphorylates other substrates including NCOA3, BCL10 and IRS1. Within the nucleus, acts as an adapter protein for NFKBIA degradation in UV-induced NF-kappa-B activation (By similarity). Phosphorylates RIPK1 at 'Ser-25' which represses its kinase activity and consequently prevents TNF-mediated RIPK1-dependent cell death (By similarity). Phosphorylates the C-terminus of IRF5, stimulating IRF5 homodimerization and translocation into the nucleus (By similarity). ATP + L-seryl-[I-kappa-B protein] = ADP + H(+) + O-phospho-L-seryl-[I-kappa-B protein] ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Component of the I-kappa-B-kinase (IKK) core complex consisting of CHUK, IKBKB and IKBKG; probably four alpha/CHUK-beta/IKBKB dimers are associated with four gamma/IKBKG subunits. The IKK core complex seems to associate with regulatory or adapter proteins to form a IKK-signalosome holo-complex. The IKK complex associates with TERF2IP/RAP1, leading to promote IKK-mediated phosphorylation of RELA/p65. Part of a complex composed of NCOA2, NCOA3, CHUK/IKKA, IKBKB, IKBKG and CREBBP. Part of a 70-90 kDa complex at least consisting of CHUK/IKKA, IKBKB, NFKBIA, RELA, ELP1 and MAP3K14. Found in a membrane raft complex, at least composed of BCL10, CARD11, DPP4 and IKBKB. Interacts with SQSTM1 through PRKCZ or PRKCI. Forms an NGF-induced complex with IKBKB, PRKCI and TRAF6. May interact with MAVS/IPS1. Interacts with NALP2. Interacts with TICAM1. Interacts with FAF1; the interaction disrupts the IKK complex formation. Interacts with ATM. Part of a ternary complex consisting of TANK, IKBKB and IKBKG. Interacts with NIBP; the interaction is direct. Interacts with ARRB1 and ARRB2. Interacts with TRIM21. Interacts with NLRC5; prevents IKBKB phosphorylation and kinase activity. Interacts with PDPK1. Interacts with EIF2AK2/PKR. The phosphorylated form interacts with PPM1A and PPM1B. Interacts with ZNF268; the interaction is further increased in a TNF-alpha-dependent manner. Interacts with IKBKE. Interacts with NAA10, leading to NAA10 degradation. Interacts with FOXO3. Interacts with ZC3H12A. Interacts with AKAP13 (By similarity). Interacts with IFIT5; the interaction synergizes the recruitment of IKK to MAP3K7 and enhances IKK phosphorylation (By similarity). Interacts with LRRC14; disrupts IKBKB-IKBKG interaction preventing I-kappa-B-kinase (IKK) core complex formation and leading to a decrease of IKBKB phosphorylation and NF-kappaB activation (By similarity). Interacts with SASH1 (By similarity). Interacts with ARFIP2 (By similarity). Interacts with FKBP5 (By similarity). Colocalized with DPP4 in membrane rafts. The kinase domain is located in the N-terminal region. The leucine zipper is important to allow homo- and hetero-dimerization. At the C-terminal region is located the region responsible for the interaction with NEMO/IKBKG (By similarity). Upon cytokine stimulation, phosphorylated on Ser-177 and Ser-181 by MEKK1 and/or MAP3K14/NIK as well as TBK1 and PRKCZ; which enhances activity. Once activated, autophosphorylates on the C-terminal serine cluster; which decreases activity and prevents prolonged activation of the inflammatory response. Phosphorylated by the IKK-related kinases TBK1 and IKBKE, which is associated with reduced CHUK/IKKA and IKBKB activity and NF-kappa-B-dependent gene transcription. Dephosphorylated at Ser-177 and Ser-181 by PPM1A and PPM1B. Ubiquitinated. Monoubiquitination involves TRIM21 that leads to inhibition of Tax-induced NF-kappa-B signaling. 'Ser-163' may not serve as a monoubiquitination site. Ubiquitination on 'Ser-163' may modulate phosphorylation on C-terminal serine residues. Hydroxylated by PHD1/EGLN2, loss of hydroxylation under hypoxic conditions results in activation of NF-kappa-B. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. I-kappa-B kinase subfamily. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. By heat shock. Belongs to the chaperonin (HSP60) family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Catalyzes the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH 5,10-methenyltetrahydrofolate + H2O = (6S)-10-formyltetrahydrofolate + H(+) One-carbon metabolism; tetrahydrofolate interconversion. Homodimer. Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family. +Catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG. D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5. Homotetramer. Binds human plasminogen. Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. +Catalyzes the condensation of ribulose 5-phosphate with formaldehyde to form 3-hexulose 6-phosphate. D-ribulose 5-phosphate + formaldehyde = D-arabino-hex-3-ulose 6-phosphate One-carbon metabolism; formaldehyde assimilation via RuMP pathway; D-fructose 6-phosphate from D-ribulose 5-phosphate and formaldehyde: step 1/2. Belongs to the HPS/KGPDC family. HPS subfamily. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. Interacts with UvrB in an incision complex. Belongs to the UvrC family. +Essential tubulin-folding protein involved in the final step of the tubulin folding pathway. Required for continuous microtubule cytoskeleton organization, mitotic division, cytokinesis, and to couple cell cycle progression to cell division in embryos and endosperms. Not essential for cell viability. Binds probably to the multimeric supercomplex, stimulating GTP hydrolysis by the bound beta-tubulin and the release of the alpha-/beta-tubulin heterodimer. Supercomplex made of cofactors A to E. Cofactors A and D function by capturing and stabilizing tubulin in a quasi-native conformation. Cofactor E binds to the cofactor D-tubulin complex; interaction with cofactor C then causes the release of tubulin polypeptides that are committed to the native state. Not associated with microtubular arrays. Ubiquitously expressed (at protein level). Present in leaves, roots, flowers, and stems. Disturbed microtubule organization. Lethal embryos that consist of one or a few grossly enlarged cells that lack microtubules but not actin filaments. Failure to localize KNOLLE in mitotic cells. Cortical microtubules-free interphase cells and mitotic nuclei missing spindles. Reduced trichome size with fewer branches. Belongs to the PILZ group of genes that disrupt, when mutated, the microtubule cytoskeleton and produce mushroom-shaped ('pilz' in German) embryos. Belongs to the TBCC family. +Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction: the enzyme is irreversibly inactivated. a 6-O-methyl-2'-deoxyguanosine in DNA + L-cysteinyl-[protein] = a 2'-deoxyguanosine in DNA + S-methyl-L-cysteinyl-[protein] a 4-O-methyl-thymidine in DNA + L-cysteinyl-[protein] = a thymidine in DNA + S-methyl-L-cysteinyl-[protein] Binds 1 zinc ion. This enzyme catalyzes only one turnover and therefore is not strictly catalytic. According to one definition, an enzyme is a biocatalyst that acts repeatedly and over many reaction cycles. Belongs to the MGMT family. +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Regulates the transcription of genes required for cell separation. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Probable thiol-disulfide oxidoreductase that may participate in various redox reactions. Belongs to the thioredoxin family. The active site contains a CGGC motif wich differs from the conserved CGPC motif. +Belongs to the bacterial ribosomal protein bL32 family. +Involved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. The regulation of gene expression in response to changes in cell density is called quorum sensing. Catalyzes the transformation of S-ribosylhomocysteine (RHC) to homocysteine (HC) and 4,5-dihydroxy-2,3-pentadione (DPD). S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine Binds 1 Fe cation per subunit. Homodimer. Belongs to the LuxS family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. In this organism, the P 'protein' is a heterodimer of two subunits. Belongs to the GcvP family. C-terminal subunit subfamily. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Part of a complex that catalyzes the reversible reduction of CoM-S-S-CoB to the thiol-coenzymes H-S-CoM (coenzyme M) and H-S-CoB (coenzyme B). Probably involved in methylotrophic methanogenesis but not in aceticlastic methanogenesis. coenzyme B + coenzyme M + 2 oxidized [2Fe-2S]-[ferredoxin] = coenzyme M-coenzyme B heterodisulfide + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 4 [4Fe-4S] cluster. Cofactor metabolism; coenzyme M-coenzyme B heterodisulfide reduction; coenzyme B and coenzyme M from coenzyme M-coenzyme B heterodisulfide: step 1/1. The ferredoxin:CoB-CoM heterodisulfide reductase is composed of three subunits; HdrA1, HdrB1 and HdrC1. Induced on trimethylamine or methanol, but not on acetate as the sole energy source. Triple hdrA1C1B1 deletion decreases methane production from methanol, but does not affect methanogenesis from acetate. Deletion results in up-regulation of CoB-SH and CoM-SH synthesis and transport, and methylsulfide methyltransferases. Belongs to the HdrA family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase gamma chain family. +(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate Belongs to the 4-hydroxy-2-oxovalerate aldolase family. +Protein that inhibits host translation while promoting late viral translation by ribosome shunting. Blocks host cap-dependent translation by binding to eIF4G, displacing MKNK1 from cap initiation complexes and preventing EIF4E phosphorylation. Binds to the tripartite leader sequence of viral late mRNAs and recruits host eIF4G, PABPC1/poly-A binding protein and 40S ribosomes subunits on viral mRNAs, allowing ribosome shunting and efficient translation of late viral mRNAs even though conventional translation via ribosome scanning from the cap has been shut off in the host cell. During assembly, acts as a chaperone protein that helps hexon proteins assembly into trimers. Monomer. Interacts with hexon protein; this interaction allows chaperoning and trimerization of hexon proteins. Interacts (via N-terminus) with host initiation factor EIF4G (via C-terminus). Interacts (via RRM domain) with viral mRNAs that contain the tripartite leader; this interaction allows ribosome shunting and expression of viral late mRNAs. Expressed in the late phase of the viral replicative cycle. Might be cleaved by the viral protease. Phosphorylated. Tyrosine phosphorylation enhances preferential binding to tripartite leader mRNAs and allows ribosome shunting. Methylated. Asymmetric dimethylation by host PRMT1 of the Arg/Gly-rich region may regulate shutoff protein binding to hexon and promote the capsid assembly in the nucleus. All late proteins expressed from the major late promoter are produced by alternative splicing and alternative polyadenylation of the same gene giving rise to non-overlapping ORFs. A leader sequence is present in the N-terminus of all these mRNAs and is recognized by the viral shutoff protein to provide expression although conventional translation via ribosome scanning from the cap has been shut off in the host cell. Belongs to the adenoviridae shutoff protein family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +Metallophosphoesterase required for transport of GPI-anchor proteins from the endoplasmic reticulum to the Golgi. Acts in lipid remodeling steps of GPI-anchor maturation by mediating the removal of a side-chain ethanolamine-phosphate (EtNP) from the second Man (Man2) of the GPI intermediate, an essential step for efficient transport of GPI-anchor proteins (By similarity). Binds 2 manganese ions per subunit. Also localizes to endoplasmic reticulum exit site. Belongs to the metallophosphoesterase superfamily. MPPE1 family. +Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue. Belongs to the radical SAM superfamily. RlmN family. +Belongs to the universal ribosomal protein uL13 family. +Catalyzes the attachment of tryptophan to tRNA(Trp). ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + H(+) + L-tryptophanyl-tRNA(Trp) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. +A GTPase-activating protein (GAP) that modifies Der/EngA GTPase function. May play a role in ribosome biogenesis. Interacts with Der. Belongs to the YihI family. +May play a role in the developmental transition from cell proliferation to cell differentiation during neurogenesis. Expressed in developing retina and brain, but not in heart, liver or kidney. In brain, located in a narrow strip in the boundary between the ventricular zone (consisting of proliferating cells) and the intermediate zone (consisting of postmitotic, differentiating cells). Expressed in all major regions of the developing brain, including the myelencephalon, the mesencephalon, the telencephalon and the diencephalon. In the developing retina, expression is scattered across the retinal neural epithelium (PubMed:9514522). Expressed in egg white (at protein level). Expressed in the magnum of the oviduct (at protein level) (PubMed:25436390). In brain, not abundant during the early stages of neurogenesis. Expression increases during cytogenesis followed by a rapid decrease towards the end of cytogenesis. Undetectable at E16. In retina, expression is detected at E4 and E6, and becomes scarce by E8. Not detected in the mature retina. Down-regulated by dietary stress. Significantly decreased expression between days 0 to 5 in egg whites of eggs laid by corticosterone-fed hens (at protein level). Decreased expression at day 14 in the magnum of the oviduct in the corticosterone-fed laying hens. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy-D-galactonate. D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O Binds 1 Mg(2+) ion per subunit. Carbohydrate acid metabolism; D-galactonate degradation; D-glyceraldehyde 3-phosphate and pyruvate from D-galactonate: step 1/3. Reaction proceeds via an anti dehydration. Belongs to the mandelate racemase/muconate lactonizing enzyme family. GalD subfamily. +Catalyzes the specific phosphorylation of arginine residues in proteins. ATP + L-arginyl-[protein] = ADP + H(+) + N(omega)-phospho-L-arginyl-[protein] Belongs to the ATP:guanido phosphotransferase family. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. Belongs to the FlgI family. +Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. Binds 3 Zn(2+) ions. Belongs to the AP endonuclease 2 family. +Belongs to the UPF0346 family. +Modulates transcription in response to changes in cellular NADH/NAD(+) redox state. Homodimer. Belongs to the transcriptional regulatory Rex family. +Cytokinin-activating enzyme working in the direct activation pathway. Phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms (By similarity). H2O + N(6)-(dimethylallyl)adenosine 5'-phosphate = D-ribose 5-phosphate + N(6)-dimethylallyladenine 9-ribosyl-trans-zeatin 5'-phosphate + H2O = D-ribose 5-phosphate + trans-zeatin Belongs to the LOG family. +Sequence-specific RNA-binding protein that binds to the cytoplasmic polyadenylation element (CPE), an uridine-rich sequence element (consensus sequence 5'-UUUUUAU-3') within the mRNA 3'-UTR (PubMed:24990967). RNA binding results in a clear conformational change analogous to the Venus fly trap mechanism (PubMed:24990967). Regulates activation of unfolded protein response (UPR) in the process of adaptation to ER stress in liver, by maintaining translation of CPE-regulated mRNAs in conditions in which global protein synthesis is inhibited (By similarity). Required for cell cycle progression, specifically for cytokinesis and chromosomal segregation (PubMed:26398195). Plays a role as an oncogene promoting tumor growth and progression by positively regulating translation of t-plasminogen activator/PLAT (PubMed:22138752). Stimulates proliferation of melanocytes (PubMed:27857118). In contrast to CPEB1 and CPEB3, does not play role in synaptic plasticity, learning and memory (By similarity). Interacts with TOB1. Expressed in pancreas in islets and ductal cells (at protein level) (PubMed:22138752). Expressed in melanocytes (PubMed:27857118). The 2 RRM domains and the C-terminal region mediate interaction with CPE-containing RNA (PubMed:24990967). The interdomain linker (564-579) acts as a hinge to fix the relative orientation of the 2 RRMs (PubMed:24990967). The ZZ domain (509-566) coordinates 2 Zn ions and is probably implicated in mediating interactions with other proteins in addition to increasing the affinity of the RRMs for the CPEs (By similarity). Unlike in CPEB1, a continuous polar interface is formed between the 2 RRMs (PubMed:24990967). Belongs to the RRM CPEB family. +Heterotetramer of two type I and two type II keratins. There are two types of hair/microfibrillar keratin, I (acidic) and II (neutral to basic). Belongs to the intermediate filament family. +Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate + tRNA(n) Homohexameric ring arranged as a trimer of dimers. Belongs to the RNase PH family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin. di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available. Belongs to the UppP family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +a monocarboxylic acid amide + H2O = a monocarboxylate + NH4(+) Belongs to the amidase family. +Na(+)/H(+) antiporter that extrudes sodium in exchange for external protons. 3 H(+)(out) + 2 Na(+)(in) = 3 H(+)(in) + 2 Na(+)(out) Belongs to the NhaB Na(+)/H(+) (TC 2.A.34) antiporter family. +Produced by activated monocytes and neutrophils and expressed at sites of inflammation. Hematoregulatory chemokine, which, in vitro, suppresses hematopoietic progenitor cell proliferation. GRO-beta(5-73) shows a highly enhanced hematopoietic activity. The N-terminal processed form GRO-beta(5-73) is produced by proteolytic cleavage after secretion from bone marrow stromal cells. GRO-beta(5-73) is available under the name Garnocestim as immunomodulator. It is used prior to hematopoietic transplantation for peripheral blood stem cell mobilization and reduction of incidence, duration, and/or severity of chemotherapy induced cytopenias. Belongs to the intercrine alpha (chemokine CxC) family. CXCL2 entry +Belongs to the UPF0434 family. +The 2-keto-3-deoxygluconate permease transports the degraded pectin products into the bacterial cell, where they serve as carbon and energy sources. This is a hydrogen coupled transport system. Belongs to the KdgT transporter family. +Lipase which is essential for lysis of subvacuolar cytoplasm to vacuole targeted bodies and intravacuolar autophagic bodies. Involved in the lysis of intravacuolar multivesicular body (MVB) vesicles. The intravacuolar membrane disintegration by ATG15 is critical to life span extension (By similarity). a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) Binds to both phosphatidylinositol (PI) and phosphatidylinositol 3,5-bisphosphate (PIP2). From ER, targeted to vacuolar lumen at the MVB vesicles via the Golgi and the prevacuolar compartment (PVC). Belongs to the AB hydrolase superfamily. Lipase family. +Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate. ATP + formate + N(1)-(5-phospho-beta-D-ribosyl)glycinamide = ADP + H(+) + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (formate route): step 1/1. Homodimer. Belongs to the PurK/PurT family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single-stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing (By similarity). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. The C-terminal domain (CTD) serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapeptide repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatase, and a 'CTD code' that specifies the position of Pol II within the transcription cycle has been proposed (By similarity). The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucleotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion. Belongs to the RNA polymerase beta' chain family. +Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo-MPT) cofactor (Moco or molybdenum cofactor) to form Mo-molybdopterin guanine dinucleotide (Mo-MGD) cofactor. GTP + H(+) + Mo-molybdopterin = diphosphate + Mo-molybdopterin guanine dinucleotide Monomer. The N-terminal domain determines nucleotide recognition and specific binding, while the C-terminal domain determines the specific binding to the target protein. Belongs to the MobA family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Self-assembles to form an icosahedral capsid with a T=16 symmetry, about 200 nm in diameter, and consisting of 150 hexons and 12 pentons (total of 162 capsomers). Hexons form the edges and faces of the capsid and are each composed of six MCP molecules. In contrast, one penton is found at each of the 12 vertices. Eleven of the pentons are MCP pentamers, while the last vertex is occupied by the portal complex. The capsid is surrounded by a layer of proteinaceous material designated the tegument which, in turn, is enclosed in an envelope of host cell-derived lipids containing virus-encoded glycoproteins. Homomultimer. Makes the hexons and eleven out of twelve pentons. Interacts with triplex proteins 1/TRX1 and 2/TRX2; adjacent capsomers are linked together in groups of three by triplexes, heterotrimeric complexes composed of one molecule of TRX1 and two molecules of TRX2. Interacts with scaffold protein; this interaction allows efficient MCP transport to the host nucleus. Interacts with capsid vertex component 2/CVC2. Interacts with the small capsomere-interacting protein/SCP. Belongs to the herpesviridae major capsid protein family. +Belongs to the EamA transporter family. +Receptor for MSH (alpha, beta and gamma) and ACTH. The activity of this receptor is mediated by G proteins which activate adenylate cyclase. Mediates melanogenesis, the production of eumelanin (black/brown) and phaeomelanin (red/yellow), via regulation of cAMP signaling in melanocytes. Interacts with MGRN1, but does not undergo MGRN1-mediated ubiquitination; this interaction competes with GNAS-binding and thus inhibits agonist-induced cAMP production. Interacts with OPN3; the interaction results in a decrease in MC1R-mediated cAMP signaling and ultimately a decrease in melanin production in melanocytes. Belongs to the G-protein coupled receptor 1 family. +Nitric oxide-sensitive repressor of genes involved in protecting the cell against nitrosative stress. May require iron for activity. Binds 1 [2Fe-2S] cluster per subunit. +Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-terminal L-methionyl-[peptide] Binds 1 Fe(2+) ion. Belongs to the polypeptide deformylase family. +Has antibacterial activity. Expressed by the venom gland. Belongs to the long chain scorpion toxin family. Class 3 subfamily. +Required for the timely initiation of chromosomal replication via direct interactions with the DnaA initiator protein. Homotetramer; dimer of dimers. Belongs to the SIS family. DiaA subfamily. +Important for reducing fluoride concentration in the cell, thus reducing its toxicity. Belongs to the CrcB (TC 9.B.71) family. +Salivary chemokine-binding protein which binds to host chemokines CXCL1, CXCL2, CXCL3, CXCL5, CXCL6 and CXCL13. +Promotes transcriptional elongation by Su(Tpl)/ELL. Essential for development (By similarity). Belongs to the EAF family. +Probable boron transporter. Boron is essential for maintaining the integrity of plants cell walls (By similarity). Belongs to the anion exchanger (TC 2.A.31.3) family. +Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-terminal L-methionyl-[peptide] Binds 1 Fe(2+) ion. Belongs to the polypeptide deformylase family. +Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins. Binds 1 zinc ion per subunit. Homohexamer. In the central section; belongs to the AAA ATPase family. In the C-terminal section; belongs to the peptidase M41 family. +One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. Binds multiple chlorophylls. PSII binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbB/PsbC family. PsbB subfamily. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +Involved in telomere capping. Interacts with ribosomes. Present with 2160 molecules/cell in log phase SD medium. Belongs to the MTC1 family. +Active on elastin and collagen substrates. Contains 1 lysine tyrosylquinone. Interacts (via propeptide) with EFEMP2. The lysine tyrosylquinone cross-link (LTQ) is generated by condensation of the epsilon-amino group of a lysine with a topaquinone produced by oxidation of tyrosine. Belongs to the lysyl oxidase family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II. PSII consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII forms dimeric complexes. Belongs to the PsbX family. Type 2 subfamily. +Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions (By similarity). 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate H(+) + oxaloacetate = CO2 + pyruvate Divalent metal cation. Homotrimer. Belongs to the class II aldolase/RraA-like family. +May act as a scaffolding protein within caveolar membranes. Interacts directly with G-protein alpha subunits and can functionally regulate their activity. Acts as an accessory protein in conjunction with CAV1 in targeting to lipid rafts and driving caveolae formation. The Ser-36 phosphorylated form has a role in modulating mitosis in endothelial cells. Positive regulator of cellular mitogenesis of the MAPK signaling pathway. Required for the insulin-stimulated nuclear translocation and activation of MAPK1 and STAT3, and the subsequent regulation of cell cycle progression (By similarity). Monomer or homodimer. Interacts with CAV1; the interaction forms a stable heterooligomeric complex that is required for targeting to lipid rafts and for caveolae formation. Tyrosine phosphorylated forms do not form heterooligomers with the Tyr-19-phosphorylated form existing as a monomer or dimer. Interacts (tyrosine phosphorylated form) with the SH2 domain-containing proteins, RASA1, NCK1 and SRC. Interacts (tyrosine phosphorylated form) with INSR. Interacts (Tyr-19 phosphorylated form) with MAPK1 (phosphorylated form); the interaction, promoted by insulin, leads to nuclear location and MAPK1 activation. Interacts with STAT3; the interaction is increased on insulin-induced tyrosine phosphorylation leading to STAT activation (By similarity). Potential hairpin-like structure in the membrane. Membrane protein of caveolae. Tyr-19-phosphorylated form is enriched at sites of cell-cell contact and is translocated to the nucleus in complex with MAPK1 in response to insulin. CAV1-mediated Ser-23-phosphorylated form locates to the plasma membrane. Ser-36-phosphorylated form resides in intracellular compartments (By similarity). Phosphorylated on serine and tyrosine residues. CAV1 promotes phosphorylation on Ser-23 which then targets the complex to the plasma membrane, lipid rafts and caveolae. Phosphorylation on Ser-36 appears to modulate mitosis in endothelial cells. Phosphorylation on Tyr-19 is required for insulin-induced phosphorylation of MAPK1 and DNA binding of STAT3. Tyrosine phosphorylation is induced by both EGF and insulin (By similarity). Most abundant form. Belongs to the caveolin family. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Interacts weakly with protein L15. Belongs to the eukaryotic ribosomal protein eL32 family. +Transcription factor required for the development of the heart and the spleen (PubMed:22560297). During heart development, acts as a transcriptional activator of NPPA/ANF in cooperation with GATA4 (By similarity). May cooperate with TBX2 to negatively modulate expression of NPPA/ANF in the atrioventricular canal (By similarity). Binds to the core DNA motif of NPPA promoter (PubMed:22849347, PubMed:26926761). Together with PBX1, required for spleen development through a mechanism that involves CDKN2B repression (PubMed:22560297). Homodimer (via the homeobox); binds DNA as homodimer (PubMed:22849347). Interacts (via the homeobox) with TBX5 (via the T-box); this complex binds DNA (PubMed:26926761). Interacts with HIPK1 and HIPK2, but not HIPK3. Interacts with the C-terminal zinc finger of GATA4 through its homeobox domain. Also interacts with JARID2 which represses its ability to activate transcription of ANF. Interacts with FBLIM1. Interacts with TBX18 (By similarity). Interacts with histone methyltransferase NSD2 (via HMG box) (By similarity). Expressed only in the heart. Expressed at embryonic stages 10 to 11 in the nondifferentiated mesodermal cells at the venous and arterial poles, as well as cells of the dorsal coelomic wall and ruptured mesocardium (at protein level) (PubMed:21403123). Expressed by all myocardial cells at embryonic stages 10 to 11 (at protein level) (PubMed:21403123). The homeobox domain binds to double-stranded DNA (PubMed:22849347). The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the NK-2 homeobox family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 3 family. +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 2 subfamily. +Envelope glycoprotein that binds to the potential host cell entry receptors TNFRSF14/HVEM, NECTIN1 and 3-O-sulfated heparan sulfate. May trigger fusion with host membrane, by recruiting the fusion machinery composed of gB and gH/gL (By similarity). Homodimer (By similarity). Interacts with host receptor TNFRSF14. Interacts with host receptor NECTIN1. Interacts (via profusion domain) with gB; this interaction occurs in the absence of gH/gL. Interacts (via profusion domain) with gH/gL heterodimer; this interaction occurs in the absence of gB. Associates with the gB-gH/gL-gD complex. Interacts (via C-terminus) with UL11 tegument protein (By similarity). Interacts (via C-terminus) with VP22 tegument protein; this interaction might be very weak. Interacts with host RSAD2 (By similarity). During virion morphogenesis, this protein probably accumulates in the endosomes and trans-Golgi where final envelopment occurs. Belongs to the herpesviridae glycoprotein D family. +Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility. In the PRC1 complex, it is required to stimulate the E3 ubiquitin-protein ligase activity of rnf2 (By similarity). Component of a PRC1-like complex (By similarity). Interacts with cbx4. Maternally derived transcript is detected at high levels in blastula. Detected at intermediate levels in the head region, the rhombencephalon, otic vesicle, mesencephalon, optic vesicle and in the anterior parts of the spinal cord in late neurula stages. +Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline. carbamoyl phosphate + L-ornithine = H(+) + L-citrulline + phosphate Amino-acid degradation; L-arginine degradation via ADI pathway; carbamoyl phosphate from L-arginine: step 2/2. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. OTCase family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Expressed in placenta (at protein level) (PubMed:10803597, PubMed:10537154, PubMed:16876275). Expressed in the tail hair follicle, with highest expression detected in the keratinocytes of the outer root sheath (PubMed:10803597). Expressed in ear skin with lesser amounts in small intestine (PubMed:10803597). Not detected in brain at 18 dpc, postnatal day 25 or postnatal day 55 (PubMed:16876275). In placenta, detected at 8 dpc, peaks at 12 dpc and declines thereafter. N-glycosylated and sialylated. Belongs to the somatotropin/prolactin family. +Involved in plant cell wall degradation in cooperation with cellulosome. Hydrolyzes both p-nitrophenyl-alpha-L-arabinopyranoside (pNPAp) and p-nitrophenyl-beta-D-galactopyranoside (pNPGp), with higher activity for pNPAp. Shows hydrolysis activity against p-nitrophenyl-beta-D-fucopyranoside (pNPFp), but not against p-nitrophenyl-alpha-L-arabinofuranoside (pNPAf), o-nitrophenyl-beta-D-galactopyranoside (oNPGp), p-nitrophenyl-beta-D-xylopyranoside (pNPXp), p-nitrophenyl-beta-D-glucopyranoside (pNPGLp), p-nitrophenyl-beta-D-cellobiopyranoside (pNPCp), p-nitrophenyl-beta-lactopyranoside (pNPLp) or p-nitrophenyl-alpha-galactopyranoside (pNPalphaGp). No detectable activity against arabinan or arabinoxylan, but activity against arabinogalactan can be detected. Increases degradation activity of alpha-L-arabinofuranosidase (ArfA) and endo-1,4-beta-xylanase (XynA) when corn fiber gum and corn stem powder are used as substrates. Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. Inhibited by Cu(2+), Hg(2+) and Zn(2+). No effect with Ca(2+), Mg(2+), Mn(2+) or excess EDTA (10 mM). Optimum pH is 6.0 for activities against both pNPAp and pNPGp. Stable in the range of pH 6.0-8.0. Optimum temperature is 30-40 degrees Celsius for activities against both pNPAp and pNPGp when incubated 10 minutes at pH 6.0. Both activities completely lost after heating at 50 degrees Celsius for 20 minutes. Dimer. Belongs to the glycosyl hydrolase 42 family. +Binds to muscle nicotinic acetylcholine receptor (nAChR) and inhibit acetylcholine from binding to the receptor, thereby impairing neuromuscular transmission. Expressed by the venom gland. LD(50) is 0.04 mg/kg by subcutaneous injection. Belongs to the snake three-finger toxin family. Short-chain subfamily. Type I alpha-neurotoxin sub-subfamily. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. Binds 1 heme group covalently. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, petD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer (By similarity). Belongs to the cytochrome f family. +Copper chaperone for cytochrome c oxidase (COX). Binds two copper ions and deliver them to the Cu(A) site of COX. Belongs to the COX17 family. +This iron-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. Other nitrogenase complexes utilize a molybdenum-iron protein or a vanadium-iron protein. 16 ATP + 16 H2O + N2 + 8 reduced [2Fe-2S]-[ferredoxin] = 16 ADP + 6 H(+) + H2 + 2 NH4(+) + 8 oxidized [2Fe-2S]-[ferredoxin] + 16 phosphate Binds 1 [8Fe-7S] cluster per heterodimer. Binds 1 [8Fe-9S-C-homocitryl] cluster per subunit. Hexamer of two alpha, two beta, and two delta chains. The structure of the 8Fe-9S-C-homocitryl cluster is assumed to be analogous to the 7Fe-Mo-9S-C-homocitryl cluster. Belongs to the NifD/NifK/NifE/NifN family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) Binds 2 [4Fe-4S] clusters per subunit. NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I 23 kDa subunit family. +Belongs to the eukaryotic ribosomal protein eL14 family. +Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-methyl-D-erythritol + diphosphate Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. Belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily. +Plays an essential role in virion nuclear egress, the first step of virion release from infected cell. Within the host nucleus, NEC1 interacts with the newly formed capsid through the vertexes and directs it to the inner nuclear membrane by associating with NEC2. Induces the budding of the capsid at the inner nuclear membrane as well as its envelopment into the perinuclear space. There, the NEC1/NEC2 complex promotes the fusion of the enveloped capsid with the outer nuclear membrane and the subsequent release of the viral capsid into the cytoplasm where it will reach the secondary budding sites in the host Golgi or trans-Golgi network. Forms a heterohexameric complex with NEC2. Interacts with capsid vertex specific component 2/CVC2; this interaction directs the capsid to the host inner nuclear membrane to initiate budding. Remains attached to the nucleus inner membrane through interaction with NEC2. Phosphorylated at serine residues in the N-terminus. This phosphorylation regulates the localization within the inner nuclear membrane. Belongs to the herpesviridae NEC1 protein family. +Master enzyme that delivers sulfur to a number of partners involved in Fe-S cluster assembly, tRNA modification or cofactor biosynthesis. Catalyzes the removal of elemental sulfur and selenium atoms from cysteine and selenocysteine to produce alanine. Functions as a sulfur delivery protein for Fe-S cluster synthesis onto IscU, an Fe-S scaffold assembly protein, as well as other S acceptor proteins. Also functions as a selenium delivery protein in the pathway for the biosynthesis of selenophosphate. [sulfur carrier]-H + L-cysteine = [sulfur carrier]-SH + L-alanine Cofactor biosynthesis; iron-sulfur cluster biosynthesis. Homodimer. Forms a heterotetramer with IscU, interacts with other sulfur acceptors. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. NifS/IscS subfamily. +Part of the Tol-Pal system, which plays a role in outer membrane invagination during cell division and is important for maintaining outer membrane integrity. TolB occupies a key intermediary position in the Tol-Pal system because it communicates directly with both membrane-embedded components, Pal in the outer membrane and TolA in the inner membrane. The Tol-Pal system is composed of five core proteins: the inner membrane proteins TolA, TolQ and TolR, the periplasmic protein TolB and the outer membrane protein Pal. They form a network linking the inner and outer membranes and the peptidoglycan layer. Belongs to the TolB family. +May mediate the cellular interaction between myeloid cells and B-cells. Forms a heterodimer, consisting of a large extracellular region (alpha subunit) non-covalently linked to a seven-transmembrane moiety (beta subunit). Predominantly expressed in myeloid cells. Predominantly expressed on resident macrophages. Up-regulated following macrophage activation. The second EGF domain mediates the interaction with the putative ligand. Proteolytically cleaved into 2 subunits, an extracellular alpha subunit and a seven-transmembrane subunit. Glycosylated. Belongs to the G-protein coupled receptor 2 family. Adhesion G-protein coupled receptor (ADGR) subfamily. +Topoisomerase IV is essential for chromosome segregation; it is the principal protein responsible for decatenating newly replicated chromosomes (PubMed:9334322). It relaxes supercoiled DNA (PubMed:15105144, PubMed:21300644, PubMed:23294697, PubMed:23352267). MukB stimulates the relaxation activity of topoisomerase IV and also has a modest effect on decatenation (PubMed:20921377). ATP-dependent breakage, passage and rejoining of double-stranded DNA. Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+). Pyrrolopyrimidines inhibit both GyrB and its paralog in topoisomerase IV (parE) (PubMed:23294697). Heterotetramer composed of ParC and ParE. Belongs to the type II topoisomerase family. ParE type 1 subfamily. +Single-stranded DNA-binding protein that associates with mitochondrial DNA and may play a role in the regulation of the gene expression machinery. Seems also to be required to prevent break-induced DNA rearrangements in the mitochondrial genome. Can bind to melt double-stranded DNA in vivo. Homotetramer. No visible phenotype under normal growth conditions. Plants over-expressing WHY2 are small with dark-green distorted leaves, exhibit early senescence and produces shorter siliques with half the amount of seeds found in wild-type plants. Belongs to the Whirly family. Truncated N-terminus. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Catalyzes the synthesis of beta-nicotinate D-ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP. 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H2O + nicotinate = ADP + diphosphate + nicotinate beta-D-ribonucleotide + phosphate Cofactor biosynthesis; NAD(+) biosynthesis; nicotinate D-ribonucleotide from nicotinate: step 1/1. Transiently phosphorylated on a His residue during the reaction cycle. Phosphorylation strongly increases the affinity for substrates and increases the rate of nicotinate D-ribonucleotide production. Dephosphorylation regenerates the low-affinity form of the enzyme, leading to product release. Belongs to the NAPRTase family. +Acts by delaying the inactivation of presynaptic voltage-sensitive sodium channels (Nav). Acts against insects and cause a progressive spastic paralysis. Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. PD(50) is 0.71 nmol/g in lepidopteran larvae. Belongs to the neurotoxin 26 (DTX) family. The measured molecular weight is 27 daltons higher than the expected one suggesting a sequence error. +Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion. Homodimer. Contains one covalently linked phytochromobilin chromophore. Belongs to the phytochrome family. +Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones. Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines. 2 a quinone + H(+) + NADH = 2 a 1,4-benzosemiquinone + NAD(+) anthranilate + N,N-dimethyl-1,4-phenylenediamine + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 H(+) + 2 NADH Binds 1 FMN per subunit. Homodimer. Belongs to the azoreductase type 1 family. +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Belongs to the urease gamma subunit family. +N-methyltransferase; part of the gene cluster that mediates the biosynthesis of imizoquins A to D, tripeptide-derived alkaloids that serve a protective role against oxidative stress that are essential for normal germination (PubMed:29182847). ImqB is a canonical three-module NRPS that assembles the tripeptide backbone of the imizoquins via condensation of Trp, Tyr, and Leu-derived precursors (PubMed:29182847). N-methylation by imqF and phenol oxidation by imqC, followed by cyclization via the FAD-dependent oxidase imqH carry out the three-step transformation of L-tyrosine into tetrahydroisoquinoline (PubMed:29182847). Importantly, this sequence requires the presence of a free amine in the tyrosine moiety, indicating that isoquinoline formation occurs prior to peptide bond formation (PubMed:29182847). The imidazolidin-4-one ring of imizoquins could form following additional oxidation of the methyl-derived bridgehead carbon by imqH (PubMed:29182847). Lastly, O-methylation by imqG and leucine hydroxylation by imqE complete biosynthesis of the imizoquins (PubMed:29182847). Secondary metabolite biosynthesis. Expression is down-regulated by ralstonins, lipopeptides produced by the plant pathogenic bacteria Ralstonia solanacearum (PubMed:29182847). Expression is positively regulated by the imizoquins cluster-specific transcription regulator imqK (PubMed:29182847). Belongs to the methyltransferase superfamily. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Converts the preformed base xanthine, a product of nucleic acid breakdown, to xanthosine 5'-monophosphate (XMP), so it can be reused for RNA or DNA synthesis. diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine Purine metabolism; XMP biosynthesis via salvage pathway; XMP from xanthine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. Xpt subfamily. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Transcriptional activator of the thermally regulated virulent yopE gene. LcrF activity could be modulated by the interaction with an inducer molecule serving as a temperature messenger. The availability of the messenger would in turn be controlled by a temperature-responsive process serving as a cellular thermometer. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1). 7-aminomethyl-7-carbaguanine + 2 NADP(+) = 7-cyano-7-deazaguanine + 3 H(+) + 2 NADPH tRNA modification; tRNA-queuosine biosynthesis. Belongs to the GTP cyclohydrolase I family. QueF type 1 subfamily. +Glycosyltransferase required for the biosynthesis of heparan-sulfate. The EXT1/EXT2 complex possesses substantially higher glycosyltransferase activity than EXT1 or EXT2 alone. Appears to be a tumor suppressor. Required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). 3-O-{[(1->4)-beta-D-GlcA-(1->4)-alpha-D-GlcNAc](n)-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-{alpha-D-GlcNAc-[(1->4)-beta-D-GlcA-(1->4)-alpha-D-GlcNAc](n)-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + H(+) + UDP 3-O-{alpha-D-GlcNAc-[(1->4)-beta-D-GlcA-(1->4)-alpha-D-GlcNAc](n)-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + UDP-alpha-D-glucuronate = 3-O-{[(1->4)-beta-D-GlcA-(1->4)-alpha-D-GlcNAc](n+1)-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + H(+) + UDP Protein modification; protein glycosylation. Forms a homo/heterooligomeric complex with EXT1. Interacts with GALNT5. Interacts with NDST1. The EXT1/EXT2 complex is localized in the Golgi apparatus. Ubiquitous. The disease is caused by variants affecting the gene represented in this entry. The gene represented in this entry is involved in disease pathogenesis. The disease is caused by variants affecting the gene represented in this entry. Belongs to the glycosyltransferase 47 family. +Probable transcription factor which exert its primary action widely during early neural development and in a very limited set of neurons in the mature brain. Interacts with HNRNPU. Brain specific. Belongs to the POU transcription factor family. Class-3 subfamily. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein. Belongs to the DsbB family. +Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + UDP-N-acetyl-alpha-D-glucosamine = a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + holo-[ACP] Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 1/6. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxA subfamily. +Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons. Belongs to the HrcA family. +Insulin decreases blood glucose concentration. It increases cell permeability to monosaccharides, amino acids and fatty acids. It accelerates glycolysis, the pentose phosphate cycle, and glycogen synthesis in liver. Heterodimer of a B chain and an A chain linked by two disulfide bonds. Belongs to the insulin family. +Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids. Homotetramer. Belongs to the glycosyl hydrolase 27 family. +Positively coregulated with aaeA and aaeB by AaeR. Belongs to the AaeX family. +Catalyzes the conversion of 7,8-dihydroneopterin triphosphate (H2NTP) to 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) and acetaldehyde. 7,8-dihydroneopterin 3'-triphosphate + H2O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + 2 H(+) + triphosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. The active site is at the interface between 2 subunits. The proton acceptor Cys is on one subunit, and the charge relay system is on the other subunit (By similarity). Belongs to the PTPS family. QueD subfamily. +O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway. a 3-demethylubiquinol + S-adenosyl-L-methionine = a ubiquinol + H(+) + S-adenosyl-L-homocysteine a 3-(all-trans-polyprenyl)benzene-1,2-diol + S-adenosyl-L-methionine = a 2-methoxy-6-(all-trans-polyprenyl)phenol + H(+) + S-adenosyl-L-homocysteine Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the methyltransferase superfamily. UbiG/COQ3 family. +H2O + 2 NAD(+) + UDP-alpha-D-glucose = 3 H(+) + 2 NADH + UDP-alpha-D-glucuronate Nucleotide-sugar biosynthesis; UDP-alpha-D-glucuronate biosynthesis; UDP-alpha-D-glucuronate from UDP-alpha-D-glucose: step 1/1. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the UDP-glucose/GDP-mannose dehydrogenase family. +Component of the cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery required for the maturation of extramitochondrial Fe-S proteins. Part of an electron transfer chain functioning in an early step of cytosolic Fe-S biogenesis, facilitating the de novo assembly of a [4Fe-4S] cluster on the scaffold complex CFD1-NBP35. Electrons are transferred to DRE2 from NADPH via the FAD- and FMN-containing protein TAH18. TAH18-DRE2 are also required for the assembly of the diferric tyrosyl radical cofactor of ribonucleotide reductase (RNR), probably by providing electrons for reduction during radical cofactor maturation in the catalytic small subunit RNR2. Monomer. Interacts with TAH18. Interacts with MIA40. The C-terminal domain binds 2 Fe-S clusters but is otherwise mostly in an intrinsically disordered conformation. The N-terminal domain has structural similarity with S-adenosyl-L-methionine-dependent methyltransferases, but does not bind S-adenosyl-L-methionine. It is required for correct assembly of the 2 Fe-S clusters. The twin Cx2C motifs are involved in the recognition by the mitochondrial MIA40-ERV1 disulfide relay system. The formation of 2 disulfide bonds in the Cx2C motifs through dithiol/disulfide exchange reactions effectively traps the protein in the mitochondrial intermembrane space. Belongs to the anamorsin family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +Could be involved in insertion of integral membrane proteins into the membrane. Belongs to the UPF0161 family. +Involved in the modification of secondary bile acids into iso-bile acids (3beta-bile acids) via epimerization of the 3-OH group through a 3-oxo-intermediate. Catalyzes the oxidation of deoxycholate (DCA) and lithocholate (LCA) to yield 12-alpha-hydroxy-3-oxo-5-beta-cholan-24-oate (3-oxo-DCA) and 3-oxo-5-beta-cholan-24-oate (3-oxo-LCA), respectively. Is also able to catalyze the oxidation of cholate (CA) and chenodeoxycholate (CDCA) into 3-dehydrocholate (3-oxo-CA) and 7-alpha-hydroxy-3-oxo-5-beta-cholan-24-oate (3-oxo-CDCA), respectively. Can also catalyze the reverse reactions in vitro. Accepts both NADPH and NADH as cosubstrates. The conversion of the abundant bile acid DCA into isoDCA by the gut bacterium R.gnavus favors the growth of the keystone commensal genus Bacteroides, since isoDCA is less cytotoxic than its parent compound, DCA; iso-bile acids have thus a potential role in modulating gut community composition. lithocholate + NADP(+) = 3-oxo-5beta-cholan-24-oate + H(+) + NADPH deoxycholate + NADP(+) = 12alpha-hydroxy-3-oxo-5beta-cholan-24-oate + H(+) + NADPH deoxycholate + NAD(+) = 12alpha-hydroxy-3-oxo-5beta-cholan-24-oate + H(+) + NADH cholate + NADP(+) = 7alpha,12alpha-dihydroxy-3-oxo-5beta-cholan-24-oate + H(+) + NADPH chenodeoxycholate + NADP(+) = 7alpha-hydroxy-3-oxo-5beta-cholan-24-oate + H(+) + NADPH kcat is 99.3 min(-1) with deoxycholate as substrate. Transformation of DCA is more efficient at pH 10 than pH 7. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Belongs to the UPF0304 family. +Myoinhibiting neuropeptide. Belongs to the myosuppressin family. +Transports viral genome to neighboring plant cells directly through plasmodesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier. Engages in homologous interactions leading to the formation of a ribonucleoprotein complex containing viral genomic and messenger RNAs (vRNPs). TGBp2 and TGBp3 are necessary for intracellular delivery of TGBp1-containing vRNPs to plasmodesmata (By similarity). Homooligomer. Interacts with movement protein TGB3 (By similarity). Belongs to the virgaviridae/benyvirus TGB1 movement protein family. +Might be involved in cobalt reduction leading to cobalt(I) corrinoids. Cofactor biosynthesis; adenosylcobalamin biosynthesis. Belongs to the SIMIBI class G3E GTPase family. CobW subfamily. +Part of an ABC transporter complex involved in D-apiose import (Probable). Binds D-apiose, D-ribose and D-ribulose (PubMed:29867142). Belongs to the bacterial solute-binding protein 2 family. +Belongs to the UPF0145 family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +Plays a key role in glycolysis and gluconeogenesis. beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 4/4. Homotetramer. A number of isoforms are produced. According to EST sequences. Highly expressed in rosettes leaves and cauline leaves. By sucrose (PubMed:22561114). Induced by drought stress (PubMed:22561114). Can be trimethylated at Lys-395 by LSMT-L, but the trimethylation has no effect in vitro on the kinetic properties of the enzyme. S-glutathionylated. Belongs to the class I fructose-bisphosphate aldolase family. +NAD(+) + S-(hydroxymethyl)mycothiol = H(+) + NADH + S-formylmycothiol Binds 2 Zn(2+) ions per subunit. Homotrimer. Belongs to the zinc-containing alcohol dehydrogenase family. +Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position. Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain. Glycan biosynthesis; glycogen biosynthesis. Monomer. Belongs to the glycosyl hydrolase 13 family. GlgB subfamily. +Transcriptional repressor with bimodal DNA-binding specificity. Represses transcription in a methyl-CpG-dependent manner. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' but can also bind to the non-methylated consensus sequence 5'-CTGCNA-3' also known as the consensus kaiso binding site (KBS). Can also bind specifically to a single methyl-CpG pair and can bind hemimethylated DNA but with a lower affinity compared to methylated DNA. Plays a role in postnatal myogenesis, may be involved in the regulation of satellite cells self-renewal (By similarity). Interacts with HIPK2. Interacts with CBFA2T3. Interacts with ZBTB38. Localizes to chromocenters. Phosphorylated by HIPK2. This phosphorylation reduces stability and triggers ZBTB4 protein degradation in response to DNA damage. +Has antibacterial activity against the Gram-positive bacterium B.flexus and the Gram-negative bacteria E.coli and V.harveyi along with two other Vibrio species. +acetyl-CoA + L-glutamate = CoA + H(+) + N-acetyl-L-glutamate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 1/4. Belongs to the acetyltransferase family. ArgA subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Highly expressed in heart and kidney. Specifically interacts with PI3P, PI4P, PI5P, and PI(3,5)P2. Specifically expressed in brain. Contaminating sequence. Potential poly-A sequence. +Translation regulator that binds to the 3'-UTR of specific mRNAs such as nanos (nos) and prevent their translation. Prevents translation of unlocalized nos in the bulk cytoplasm via the recruitment of cup (By similarity). Interacts with oskar (osk). Binds to the 3'-UTR of nos. Interacts with cup, which in turn recruits eIF4-E, leading to an indirect interaction between smg and eIF4-E that prevents mRNA translation (By similarity). The SAM domain mediates the association with the 3'-UTR of specific mRNAs. Belongs to the SMAUG family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Catalyzes the covalent attachment of ubiquitin to other proteins. Acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. Acts by specifically elongating polyubiquitin chains initiated by the E2 enzyme vih/UbcH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine. Protein modification; protein ubiquitination. Belongs to the ubiquitin-conjugating enzyme family. +Belongs to the UPF0270 family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase B chain family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity and assembly of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 1 family. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL9 family. +This protein mediates the voltage-dependent potassium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient (By similarity). Homotetramer (Probable). Heterotetramer of potassium channel proteins (By similarity). The segment S4 is probably the voltage-sensor and is characterized by a series of positively charged amino acids at every third position. The tail may be important in modulation of channel activity and/or targeting of the channel to specific subcellular compartments. Phosphorylation of serine residues in the inactivation gate inhibits rapid channel closure. Belongs to the potassium channel family. C (Shaw) (TC 1.A.1.2) subfamily. Kv3.4/KCNC4 sub-subfamily. +Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide. D-alanyl-D-alanine + H2O = 2 D-alanine Binds 1 zinc ion per subunit. Can also be activated by other divalent cations such as iron, cobalt, or nickel. Inhibited by aminoalkyl phosphinate analogs. kcat is 4.7 sec(-1) with D-Ala-D-Ala. kcat is 1.8 sec(-1) with D-Ala-D-Ser. kcat is 0.35 sec(-1) with D-Ser-D-Ala. kcat is 0.005 sec(-1) with D-Ala-D-lactate. Optimum pH is 7-9. Homodimer. By vancomycin, mediated by VanS/VanR. Does not hydrolyze D-Ala-D-lactate, which remains intact for subsequent incorporation into peptidoglycan precursors. Production of precursors ending in D-Ala-D-lactate instead of D-Ala-D-Ala decreases affinity of vancomycin for the peptidoglycan chain and leads to vancomycin resistance (PubMed:7873524). Belongs to the peptidase M15D family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 13 different subunits. Subunits NuoB, CD, E, F, and G constitute the peripheral sector of the complex. In the N-terminal section; belongs to the complex I 30 kDa subunit family. In the C-terminal section; belongs to the complex I 49 kDa subunit family. +E1-like activating enzyme involved in the 2 ubiquitin-like systems required for cytoplasm to vacuole transport (Cvt) and autophagy. Activates ATG12 for its conjugation with ATG5 and ATG8 for its conjugation with phosphatidylethanolamine. Both systems are needed for the ATG8 association to Cvt vesicles and autophagosomes membranes. Autophagy is essential for maintenance of amino acid levels and protein synthesis under nitrogen starvation. Required for selective autophagic degradation of the nucleus (nucleophagy) as well as for mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. Plays a role in the regulation of filamentous growth and chronological longevity (By similarity). Homodimer. The GxGxxG motif is important for the function, possibly through binding with ATP. Belongs to the ATG7 family. +Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Is not required for association of CNOT7 to the CCR4-NOT complex (By similarity). Component of the CCR4-NOT complex; distinct complexes seem to exist that differ in the participation of probably mutually exclusive catalytic subunits. CNOT10 and CNOT11 form a subcomplex docked to the CNOT1 scaffold (By similarity). Belongs to the CNOT10 family. +Binds RpoD and negatively regulates RpoD-mediated transcription activation by preventing the interaction between the primary sigma factor RpoD with the catalytic core of the RNA polymerase and with promoter DNA. May be involved in replacement of the RNA polymerase sigma subunit from RpoD to RpoS during the transition from exponential growth to the stationary phase. Interacts with RpoD. Belongs to the Rsd/AlgQ family. +Required for the timely initiation of chromosomal replication via direct interactions with the DnaA initiator protein. Homotetramer; dimer of dimers. Belongs to the SIS family. DiaA subfamily. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Acts in the modification of cell walls via demethylesterification of cell wall pectin. [(1->4)-alpha-D-galacturonosyl methyl ester](n) + n H2O = [(1->4)-alpha-D-galacturonosyl](n) + n H(+) + n methanol Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-gluconate from pectin: step 1/5. Expressed in siliques but not in flower buds. Expression restricted to early to mid-stage of silique development. The PMEI region may act as an autoinhibitory domain and prevent untimely PME activity during transport. In the N-terminal section; belongs to the PMEI family. In the C-terminal section; belongs to the pectinesterase family. +Beta toxins bind voltage-independently at site-4 of sodium channels (Nav) and shift the voltage of activation toward more negative potentials thereby affecting sodium channel activation and promoting spontaneous and repetitive firing. Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). Belongs to the long (4 C-C) scorpion toxin superfamily. Sodium channel inhibitor family. Beta subfamily. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +Regulates G protein-coupled receptor signaling cascades. Inhibits signal transduction by increasing the GTPase activity of G protein alpha subunits, thereby driving them into their inactive GDP-bound form. The RGS7/GNB5 dimer enhances GNAO1 GTPase activity. May play a role in synaptic vesicle exocytosis. Modulates the activity of potassium channels that are activated by GNAO1 in response to muscarinic acetylcholine receptor M2/CHRM2 signaling. Interacts with PKD1; this prevents rapid proteasomal degradation. Interacts with GNB5 (By similarity). Interacts with RGS7BP, leading to regulate the subcellular location of the heterodimer formed with GNB5 (PubMed:15632198, PubMed:15897264). Interacts (phosphorylated form) with 14-3-3 protein YWHAQ (PubMed:10862767). Interacts with SNAPIN. Interacts with GNAI1 (By similarity). Interacts with GNAO1, GNAI3 and GNAZ (By similarity). Interaction with PKD1 promotes location at the cell membrane. Interaction with RGS7BP promotes location at the cell membrane. Detected in brain (at protein level). Palmitoylated. Ubiquitinated, leading to rapid proteasomal degradation. Phosphorylation and subsequent interaction with 14-3-3 proteins inhibits GAP activity. +Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. (2S,6S)-2,6-diaminoheptanedioate = meso-2,6-diaminoheptanedioate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. Homodimer. Belongs to the diaminopimelate epimerase family. +Negative regulator of FtsZ ring formation; modulates the frequency and position of FtsZ ring formation. Inhibits FtsZ ring formation at polar sites. Interacts either with FtsZ or with one of its binding partners to promote depolymerization. Colocalized with FtsZ to the nascent septal site. Belongs to the EzrA family. +Catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. 4-deoxy-4-formamido-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + H2O = 4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + formate Glycolipid biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate from UDP-4-deoxy-4-formamido-beta-L-arabinose and undecaprenyl phosphate: step 2/2. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the polysaccharide deacetylase family. ArnD deformylase subfamily. +Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccA family. +Specifically methylates the cytosine at position 1407 (m5C1407) of 16S rRNA. cytidine(1407) in 16S rRNA + S-adenosyl-L-methionine = 5-methylcytidine(1407) in 16S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family. +Involved in vitamin K metabolism. Catalytic subunit of the vitamin K epoxide reductase (VKOR) complex which reduces inactive vitamin K 2,3-epoxide to active vitamin K. Vitamin K is required for the gamma-carboxylation of various proteins, including clotting factors, and is required for normal blood coagulation, but also for normal bone development. [protein]-disulfide + H2O + phylloquinone = 2,3-epoxyphylloquinone + [protein]-dithiol [protein]-disulfide + phylloquinol = [protein]-dithiol + phylloquinone Inhibited by warfarin (coumadin). Detected in liver. The number of transmembrane domains and the membrane topology are controversial; supporting evidence is available both for models with three transmembrane domains and four transmembrane domains. Mice are born at the expected Mendelian rate and appear normal, but die between one and twenty days after birth, due to severe bleeding. In about 75% of the cases, subdural bleeding is observed, in addition to intracerebral and intramuscular bleeding. Daily oral administration of vitamin K to the mutant mice leads to normal survival, but the mice die within seven days after the cessation of vitamin K administration. Besides, both homozygous and heterozygous mutant mice display defects in bone development with reduced length of the calcified part of the long bones in front and hind limbs. The location of two cysteine active-site residues within a proposed transmembrane is consistent both with the known hydrophobic environment of the thiol redox site of the enzyme and with the lipophilicity of vitamin K and warfarin (coumadin). Belongs to the VKOR family. +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily. +Part of the ABC transporter complex MglABC involved in galactose/methyl galactoside import. Responsible for energy coupling to the transport system. ATP + D-galactose(out) + H2O = ADP + D-galactose(in) + H(+) + phosphate The complex is composed of two ATP-binding proteins (MglA), two transmembrane proteins (MglC) and a solute-binding protein (MglB). Belongs to the ABC transporter superfamily. Galactose/methyl galactoside importer (TC 3.A.1.2.3) family. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +Belongs to the HflD family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +Transcription factor which may be involved in developmental processes. A number of isoforms are produced. According to EST sequences. Belongs to the WUS homeobox family. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Male-specific peptide with moderate activity against Gram-positive bacteria. Ejaculatory duct of adult males. In response to mating. Belongs to the andropin family. +Catalyzes the phosphorolysis of diverse nucleosides, yielding D-ribose 1-phosphate and the respective free bases. Can use uridine, adenosine, guanosine, cytidine, thymidine, inosine and xanthosine as substrates. Also catalyzes the reverse reactions. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha-D-ribose 1-phosphate adenosine + phosphate = adenine + alpha-D-ribose 1-phosphate cytidine + phosphate = alpha-D-ribose 1-phosphate + cytosine guanosine + phosphate = alpha-D-ribose 1-phosphate + guanine inosine + phosphate = alpha-D-ribose 1-phosphate + hypoxanthine phosphate + thymidine = 2-deoxy-alpha-D-ribose 1-phosphate + thymine phosphate + uridine = alpha-D-ribose 1-phosphate + uracil phosphate + xanthosine = alpha-D-ribose 1-phosphate + xanthine Belongs to the nucleoside phosphorylase PpnP family. +Has a role in pre-mRNA splicing. Phosphorylates SF2/ASF (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Identified in the spliceosome C complex. Interacts with Clk1 C-terminus. Phosphorylated by Clk1. Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. +Involved in the efflux of sugars. The physiological role may be the reduction of the intracellular concentration of toxic sugars or sugar metabolites. Belongs to the major facilitator superfamily. SotB (TC 2.A.1.2) family. +Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 magnesium ions per subunit. Monomer. Belongs to the DNA polymerase type-Y family. +Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP). isopentenyl diphosphate = dimethylallyl diphosphate Binds 1 Mg(2+) ion per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1. Monomer. Belongs to the IPP isomerase type 1 family. +The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. Belongs to the RecF family. +Catalyzes the NADPH-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5-carboxylate. L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 2/2. Belongs to the gamma-glutamyl phosphate reductase family. +Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity. Interacts with OCLN. Belongs to the claudin family. +Converts seryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis. H(+) + L-seryl-tRNA(Sec) + selenophosphate = L-selenocysteinyl-tRNA(Sec) + phosphate Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; selenocysteinyl-tRNA(Sec) from L-seryl-tRNA(Sec) (bacterial route): step 1/1. Homodecamer; pentamer of dimers. Binds only one seryl-tRNA(Sec) per dimer. Belongs to the SelA family. +Methylamine dehydrogenase carries out the oxidation of methylamine. Electrons are passed from methylamine dehydrogenase to amicyanin. H2O + methylamine + 2 oxidized [amicyanin] = formaldehyde + 2 H(+) + NH4(+) + 2 reduced [amicyanin] Uses a protein-derived tryptophan tryptophylquinone (TTQ) cofactor. One-carbon metabolism; methylamine degradation; formaldehyde from methylamine: step 1/1. Heterotetramer of two light and two heavy chains. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Tryptophan tryptophylquinone (TTQ) is formed by oxidation of the indole ring of a tryptophan to form tryptophylquinone followed by covalent cross-linking with another tryptophan residue. Belongs to the aromatic amine dehydrogenase light chain family. +E3 ubiquitin-protein ligase that mediates ubiquitination of cd86 and MHC class II proteins, such as hla-dr alpha and beta, and promotes their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. The RING-CH-type zinc finger domain is required for E3 ligase activity. Truncated N-terminus. +Catalyzes the hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA), a reaction involved in phylloquinone (vitamin K1) biosynthesis. 1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA + H(+) Cofactor biosynthesis; phylloquinone biosynthesis. Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 7/7. Belongs to the 4-hydroxybenzoyl-CoA thioesterase family. DHNA-CoA hydrolase subfamily. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Required for proper proteasome assembly. Belongs to the proteasome subunit p55 family. +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Belongs to the urease gamma subunit family. +Acts as an inhibitory receptor for myeloid cells and mast cells. Positively regulates the phagocytosis of apoptotic cells (efferocytosis) via phosphatidylserine (PS) recognition; recognizes and binds PS as a ligand which is expressed on the surface of apoptotic cells. Plays an important role in the maintenance of immune homeostasis, by promoting macrophage-mediated efferocytosis and by inhibiting dendritic cell-mediated efferocytosis. Negatively regulates Fc epsilon receptor-dependent mast cell activation and allergic responses via binding to ceramide and sphingomyelin which act as ligands. May act as a coreceptor for interleukin 4 (IL-4). Associates with and regulates IL-4 receptor alpha-mediated responses by augmenting IL-4- and IL-13-induced signaling. Negatively regulates the Toll-like receptor (TLR) signaling mediated by MYD88 and TRIF through activation of PTPN6/SHP-1 and PTPN11/SHP-2. Inhibits osteoclast formation. Induces macrophage cell death upon engagement. Interacts with PTPN6/SHP-1 in a tyrosine phosphorylation dependent manner. Interacts with IL4R. Phosphorylated on tyrosine. Belongs to the CD300 family. +Belongs to the bacterial ribosomal protein bS16 family. +Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate. (R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA + diphosphate Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 4/5. Homohexamer. Belongs to the bacterial CoaD family. +Inhibits TNF-alpha signaling and seems to block apoptosis in host infected cells. Belongs to the rubulavirus small hydrophobic protein family. +Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP. Allosterically activated by GTP. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uracil: step 1/1. Belongs to the UPRTase family. +Catalyzes the conversion of cobalt-precorrin-8 to cobyrinate. Co-precorrin-8X = cob(II)yrinate Cofactor biosynthesis; adenosylcobalamin biosynthesis; cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route): step 9/10. Homodimer. Belongs to the CobH/CbiC family. +Belongs to the bacterial ribosomal protein bL36 family. +Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II. Binds 1 heme c group covalently per subunit. The cyanobacterial oxygen-evolving complex is composed of PsbO, PsbP, PsbQ, PsbV and PsbU. Associated with photosystem II at the lumenal side of the thylakoid membrane. Belongs to the cytochrome c family. PsbV subfamily. +Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. [sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Monomer. Belongs to the methylthiotransferase family. MiaB subfamily. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +Mutations in ORF 239 affects the incN plasmid pUC1 E.coli polA-independence but not its autonomous replication ability. Belongs to the initiator RepB protein family. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Binds cyclosporin A (CsA). CsA mediates some of its effects via an inhibitory action on PPIase (By similarity). Belongs to the cyclophilin-type PPIase family. PPIase A subfamily. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG. Belongs to the RnfG family. +Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser) ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec) Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. Homodimer. The tRNA molecule binds across the dimer. Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Involved in the synthesis of both phthiocerol dimycocerosates (PDIMs) and phenolic glycolipids (PGLs), which are structurally related lipids non-covalently bound to the outer cell wall layer of M.tuberculosis and are important virulence factors. a fatty acyl-CoA + H2O = a fatty acid + CoA + H(+) Deletion of the gene leads to a drastic reduction in PDIM and PGL production (PubMed:21592957, PubMed:21375593). Mutant shows increased susceptibility to several antibiotics (PubMed:21592957, PubMed:21375593). Mutant is highly attenuated when injected into the zebrafish embryo bloodstream, but virulence is retained when bacteria are injected into the notochord (PubMed:21375593). Deletion leads to an increase in growth yield in vitro (PubMed:21592957). Belongs to the thioesterase family. +Required for the formation of axial filaments and for anchoring the origin regions at the cell poles in sporulating cells, thus ensuring proper chromosome segregation in the prespore. Binds in a dispersed manner throughout the chromosome but preferentially to sites clustered in the origin portion of the chromosome, causing condensation of the chromosome and its remodeling into an elongated, anchored structure. Localizes to cell poles and nucleoid. Belongs to the RacA family. +Heterogeneous nuclear ribonucleoprotein (hnRNP) that associates with nascent pre-mRNAs, packaging them into hnRNP particles. The hnRNP particle arrangement on nascent hnRNA is non-random and sequence-dependent and serves to condense and stabilize the transcripts and minimize tangling and knotting. Packaging plays a role in various processes such as transcription, pre-mRNA processing, RNA nuclear export, subcellular location, mRNA translation and stability of mature mRNAs. Forms hnRNP particles with at least 20 other different hnRNP and heterogeneous nuclear RNA in the nucleus. Involved in transport of specific mRNAs to the cytoplasm in oligodendrocytes and neurons: acts by specifically recognizing and binding the A2RE (21 nucleotide hnRNP A2 response element) or the A2RE11 (derivative 11 nucleotide oligonucleotide) sequence motifs present on some mRNAs, and promotes their transport to the cytoplasm (By similarity). Specifically binds single-stranded telomeric DNA sequences, protecting telomeric DNA repeat against endonuclease digestion (By similarity). Also binds other RNA molecules, such as primary miRNA (pri-miRNAs): acts as a nuclear 'reader' of the N6-methyladenosine (m6A) mark by specifically recognizing and binding a subset of nuclear m6A-containing pri-miRNAs. Binding to m6A-containing pri-miRNAs promotes pri-miRNA processing by enhancing binding of DGCR8 to pri-miRNA transcripts. Involved in miRNA sorting into exosomes following sumoylation, possibly by binding (m6A)-containing pre-miRNAs. Acts as a regulator of efficiency of mRNA splicing, possibly by binding to m6A-containing pre-mRNAs (By similarity). Plays a role in the splicing of pyruvate kinase PKM by binding repressively to sequences flanking PKM exon 9, inhibiting exon 9 inclusion and resulting in exon 10 inclusion and production of the PKM M2 isoform (By similarity). Also plays a role in the activation of the innate immune response. Mechanistically, senses the presence of viral DNA in the nucleus, homodimerizes and is demethylated by JMJD6. In turn, translocates to the cytoplasm where it activates the TBK1-IRF3 pathway, leading to interferon alpha/beta production (PubMed:31320558). Homodimer; dimerization is required for nucleocytoplasmic translocation (PubMed:31320558). Identified in the spliceosome C complex. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with IGF2BP1. Interacts with C9orf72. Interacts with DGCR8. Interacts with TARDBP. Interacts with CKAP5. Interacts with TBK1 (PubMed:31320558). Interacts with STING1 (PubMed:31320558). Interacts with SRC (PubMed:31320558). Interacts with PPIA/CYPA (By similarity). Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Component of ribonucleosomes. Not found in the nucleolus. Found in exosomes following sumoylation. The disordered region, when incubated at high concentration, is able to polymerize into labile, amyloid-like fibers and form cross-beta polymerization structures, probably driving the formation of hydrogels. In contrast to irreversible, pathogenic amyloids, the fibers polymerized from LC regions disassemble upon dilution. A number of evidence suggests that formation of cross-beta structures by LC regions mediate the formation of RNA granules, liquid-like droplets, and hydrogels. Sumoylated in exosomes, promoting miRNAs-binding. Asymmetric dimethylation at Arg-266 constitutes the major methylation site (By similarity). According to a report, methylation affects subcellular location and promotes nuclear localization (By similarity). According to another report, methylation at Arg-266 does not influence nucleocytoplasmic shuttling (By similarity). +Nucleoside triphosphate pyrophosphatase that hydrolyzes dTTP and UTP. May have a dual role in cell division arrest and in preventing the incorporation of modified nucleotides into cellular nucleic acids. dTTP + H2O = diphosphate + dTMP + H(+) H2O + UTP = diphosphate + H(+) + UMP Belongs to the Maf family. YhdE subfamily. +Autocatalytically cleaves itself from the polyprotein at the L/VP0 junction. Cleaves also the host translation initiation factors EIF4G1 and EIF4G3, in order to shutoff the capped cellular mRNA transcription. Plays a role in counteracting host innate antiviral response using diverse mechanisms. Possesses a deubiquitinase activity acting on both 'Lys'-48 and 'Lys'-63-linked polyubiquitin chains. In turn, inhibits the ubiquitination and subsequent activation of key signaling molecules of type I IFN response such as host DDX58, TBK1, TRAF3 and TRAF6. Inhibits host NF-kappa-B activity by inducing a decrease in RELA mRNA levels. Cleaves a peptide bond in the C-terminus of host ISG15, resulting in the damaging of this mofidier that can no longer be attached to target proteins. Cleaves also host G3BP1 and G3BP2 in order to inhibit cytoplasmic stress granules assembly. Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. Capsid protein VP4 is released, capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm. After genome has been released, the channel shrinks. Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP1 and VP3. The capsid is composed of 60 copies of each capsid protein organized in the form of twelve pentamers and encloses the viral positive strand RNA genome. Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is composed of 60 copies of each capsid protein organized in the form of twelve pentamers and encloses the viral positive strand RNA genome. Mediates cell entry by attachment to an integrin receptor, usually host ITGAV/ITGB6. In addition, targets host MAVS to suppress type I IFN pathway. Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP0 and VP3. The capsid is composed of 60 copies of each capsid protein organized in the form of twelve pentamers and encloses the viral positive strand RNA genome. Mediates self-processing of the polyprotein by a translational effect termed 'ribosome skipping'. Mechanistically, 2A-mediated cleavage occurs between the C-terminal glycine and the proline of the downstream protein 2B. In the case of foot-and-mouth disease virus, the 2A oligopeptide is post-translationally 'trimmed' from the C-terminus of the upstream protein 1D by 3C proteinase. Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host reticulum endoplasmic and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cytoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication. Associates with and induces structural rearrangements of intracellular membranes. Triggers host autophagy by interacting with host BECN1 and thereby promotes viral replication. Participates in viral replication and interacts with host DHX9. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3. Plays important roles in virus replication, virulence and host range. Covalently linked to the 5'-end of both the positive-strand and negative-strand genomic RNAs. Acts as a genome-linked replication primer. Covalently linked to the 5'-end of both the positive-strand and negative-strand genomic RNAs. Acts as a genome-linked replication primer. Covalently linked to the 5'-end of both the positive-strand and negative-strand genomic RNAs. Acts as a genome-linked replication primer. Cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, binds to viral RNA and thus influences viral genome replication. RNA and substrate bind cooperatively to the protease. RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals. Covalently attaches UMP to a tyrosine of VPg, which is used to prime RNA synthesis. The positive stranded RNA genome is first replicated at virus induced membranous vesicles, creating a dsRNA genomic replication form. This dsRNA is then used as template to synthesize positive stranded RNA genomes. ss(+)RNA genomes are either translated, replicated or encapsidated. Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-. a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. Interacts with host ISG15. Capsid protein VP1: Interacts (via R-G-D motif) with host ITGAV/ITGB6. Forms homooligomers. Interacts with host VIM. Interacts with host BECN1. Interacts with host DCTN3. Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum (By similarity). Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum (By similarity). Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum (By similarity). Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum (By similarity). Both isoforms are able to cleave the L/VP0 junction and the host translation initiation factor EIF4G1. Specific enzymatic cleavages in vivo by the viral proteases yield a variety of precursors and mature proteins. Polyprotein processing intermediates such as VP0 which is a VP4-VP2 precursor are produced. During virion maturation, non-infectious particles are rendered infectious following cleavage of VP0. This maturation cleavage is followed by a conformational change of the particle. The polyprotein seems to be cotranslationally cleaved at the 2A/2B junction by a ribosomal skip from one codon to the next without formation of a peptide bond. This process would release the L-P1-2A peptide from the translational complex (By similarity). Myristoylation of VP4 is required during RNA encapsidation and formation of the mature virus particle. Protein 3B-1, 3B-2 and 3B-3 are uridylylated by the polymerase and are covalently linked to the 5'-end of genomic RNA. These uridylylated forms act as a nucleotide-peptide primer for the polymerase (By similarity). The capsid protein VP1 contains the main antigenic determinants of the virion; therefore, changes in its sequence must be responsible for the high antigenic variability of the virus. Belongs to the picornaviruses polyprotein family. +Transfers an acetyl group from acetyl-CoA to L-homoserine, forming acetyl-L-homoserine. acetyl-CoA + L-homoserine = CoA + O-acetyl-L-homoserine Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; O-acetyl-L-homoserine from L-homoserine: step 1/1. Belongs to the MetA family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 49 kDa subunit family. +With CysN forms the ATP sulfurylase (ATPS) that catalyzes the adenylation of sulfate producing adenosine 5'-phosphosulfate (APS) and diphosphate, the first enzymatic step in sulfur assimilation pathway. APS synthesis involves the formation of a high-energy phosphoric-sulfuric acid anhydride bond driven by GTP hydrolysis by CysN coupled to ATP hydrolysis by CysD. ATP + H(+) + sulfate = adenosine 5'-phosphosulfate + diphosphate Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 1/3. Heterodimer composed of CysD, the smaller subunit, and CysN. Belongs to the PAPS reductase family. CysD subfamily. +May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine. H2O + S-adenosyl-L-homocysteine = adenosine + L-homocysteine Binds 1 NAD(+) per subunit. Amino-acid biosynthesis; L-homocysteine biosynthesis; L-homocysteine from S-adenosyl-L-homocysteine: step 1/1. Belongs to the adenosylhomocysteinase family. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase C chain family. +Part of the ABC transporter complex RbsABC involved in ribose import. Responsible for energy coupling to the transport system. ATP + D-ribose(out) + H2O = ADP + D-ribose(in) + H(+) + phosphate The complex is composed of an ATP-binding protein (RbsA), two transmembrane proteins (RbsC) and a solute-binding protein (RbsB). Belongs to the ABC transporter superfamily. Ribose importer (TC 3.A.1.2.1) family. +Thiol protease involved in osteoclastic bone resorption and may participate partially in the disorder of bone remodeling. Displays potent endoprotease activity against fibrinogen at acid pH. May play an important role in extracellular matrix degradation. Involved in the release of thyroid hormone thyroxine (T4) by limited proteolysis of TG/thyroglobulin in the thyroid follicle lumen. Broad proteolytic activity. With small-molecule substrates and inhibitors, the major determinant of specificity is P2, which is preferably Leu, Met > Phe, and not Arg. Localizes to the lumen of thyroid follicles and to the apical membrane of thyroid epithelial cells. Predominantly expressed in osteclasts (bones). Belongs to the peptidase C1 family. +Magnesium transporter that may mediate the influx of magnesium. Expressed in the whole plant. Has the ability to complement a mutant in yeast lacking magnesium transport capability. Belongs to the CorA metal ion transporter (MIT) (TC 1.A.35.5) family. +Belongs to the SRP1/TIP1 family. Seripauperin subfamily. +Increases frequency of mitochondrial genome loss. Belongs to the AIM32 family. +Belongs to the bacterial ribosomal protein bL34 family. +Methyltransferase required for the conversion of demethylmenaquinol (DMKH2) to menaquinol (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2). a 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + H(+) + S-adenosyl-L-homocysteine a 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-methionine = a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + H(+) + S-adenosyl-L-homocysteine Quinol/quinone metabolism; menaquinone biosynthesis; menaquinol from 1,4-dihydroxy-2-naphthoate: step 2/2. Cofactor biosynthesis; ubiquinone biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. MenG/UbiE family. +Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm. This transfer involves a cascade of disulfide bond formation and reduction steps. [protein]-dithiol + NAD(+) = [protein]-disulfide + H(+) + NADH [protein]-dithiol + NADP(+) = [protein]-disulfide + H(+) + NADPH Belongs to the thioredoxin family. DsbD subfamily. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA. Forms a complex with SecF. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Belongs to the SecD/SecF family. SecD subfamily. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Part of an energy-coupled inorganic carbon pump. Forms a complex with DabB. Belongs to the inorganic carbon transporter (TC 9.A.2) DabA family. +May function as a transcriptional regulator that controls feoABC expression. Belongs to the FeoC family. +Catalyzes the transfer of 4-deoxy-4-formamido-L-arabinose from UDP to undecaprenyl phosphate. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. di-trans,octa-cis-undecaprenyl phosphate + UDP-4-deoxy-4-formamido-beta-L-arabinose = 4-deoxy-4-formamido-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + UDP Glycolipid biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate from UDP-4-deoxy-4-formamido-beta-L-arabinose and undecaprenyl phosphate: step 1/2. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the glycosyltransferase 2 family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Precursors of the cornified envelope of the stratum corneum. Skin-specific. Expression was readily detected in adult trunk skin, adult arm skin, fetal skin, penal skin, vulva, esophagus and tongue. Not expressed in the cervix, rectum, lung, colon, or placenta. Expression is observed in the heart. Belongs to the LCE cluster present on 1q21. Belongs to the LCE family. +Serine protease inhibitor. Expressed by the venom gland. Belongs to the venom Kunitz-type family. +Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + UDP-N-acetyl-alpha-D-glucosamine = a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + holo-[ACP] Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 1/6. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxA subfamily. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Belongs to the SecA family. +Part of the ABC transporter complex CcmAB involved in the biogenesis of c-type cytochromes; once thought to export heme, this seems not to be the case, but its exact role is uncertain. Responsible for energy coupling to the transport system. ATP + H2O + heme b(in) = ADP + H(+) + heme b(out) + phosphate The complex is composed of two ATP-binding proteins (CcmA) and two transmembrane proteins (CcmB). Belongs to the ABC transporter superfamily. CcmA exporter (TC 3.A.1.107) family. +Belongs to the PsiE family. +Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. 2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2 The D1/D2 heterodimer binds P680, chlorophylls that are the primary electron donor of PSII, and subsequent electron acceptors. It shares a non-heme iron and each subunit binds pheophytin, quinone, additional chlorophylls, carotenoids and lipids. D1 provides most of the ligands for the Mn4-Ca-O5 cluster of the oxygen-evolving complex (OEC). There is also a Cl(-1) ion associated with D1 and D2, which is required for oxygen evolution. The PSII complex binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Tyr-161 forms a radical intermediate that is referred to as redox-active TyrZ, YZ or Y-Z. C-terminally processed by CTPA; processing is essential to allow assembly of the oxygen-evolving complex and thus photosynthetic growth. 2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water. Herbicides such as atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer. Belongs to the reaction center PufL/M/PsbA/D family. +Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA. ATP + oxaloacetate = ADP + CO2 + phosphoenolpyruvate Binds 1 Mn(2+) ion per subunit. Carbohydrate biosynthesis; gluconeogenesis. Belongs to the phosphoenolpyruvate carboxykinase (ATP) family. +Sphingolipid transporter. Expressed in yolk cells. Expressed both maternally and zygotically throughout embryogenesis, and also in adults. Presence in early embryos of an opaque substance in the posterior yolk cell extension at approximately 1 day after fertilization. This material progressively accumulates and by 48 hours after fertilization fills the entire yolk. By day 3 of embryogenesis, embryos are severely reduced in size compared with their wild-type siblings and they die a few hours later. Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family. +Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY. Part of the signal recognition particle protein translocation system, which is composed of SRP and FtsY. Archaeal SRP consists of a 7S RNA molecule of 300 nucleotides and two protein subunits: SRP54 and SRP19. The SRP-RNC complex is targeted to the cytoplasmic membrane. Composed of three domains: the N-terminal N domain, which is responsible for interactions with the ribosome, the central G domain, which binds GTP, and the C-terminal M domain, which binds the RNA and the signal sequence of the RNC. Belongs to the GTP-binding SRP family. SRP54 subfamily. +Involved in the biosynthesis of osmoregulated periplasmic glucans (OPGs). Glycan metabolism; osmoregulated periplasmic glucan (OPG) biosynthesis. Belongs to the OpgD/OpgG family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Has a low intrinsic ATPase activity which is markedly stimulated by HscB. Belongs to the heat shock protein 70 family. +Required for pre-mRNA splicing as component of the activated spliceosome. May have a scaffolding role in the spliceosome assembly as it contacts all other components of the core complex. Component of the pre-catalytic and catalytic spliceosome complexes. Component of the postcatalytic spliceosome P complex. Belongs to the SPF27 family. +Essential for the production of a quorum sensing system signal molecule, the autoinducing peptide (AIP). This quorum sensing system is responsible for the regulation of the expression of virulence factor genes. Involved in the proteolytic processing of AgrD, the precursor of AIP. Belongs to the AgrB family. +D-arabinose 5-phosphate + H2O + phosphoenolpyruvate = 3-deoxy-alpha-D-manno-2-octulosonate-8-phosphate + phosphate Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate: step 2/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsA family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +GTPase-activating protein for the ADP ribosylation factor family (Potential). GTPase which may be involved in the degradation of expanded polyglutamine proteins through the ubiquitin-proteasome pathway. GTPase activity is stimulated by oxidative stress. Interacts with PML. Interacts with expanded polyglutamine proteins (By similarity). Upon oxidative stress, translocates to PML nuclear bodies. Widely expressed, with highest levels in brain. Highly expressed in the developing brain. Belongs to the centaurin gamma-like family. +Component of the spindle pole body (SPB) required for the proper execution of spindle pole body (SPB) duplication. Potential role in cross-linking filaments or anchoring other molecules. It is essential for growth (By similarity). Homodimer. Component of the SPC110 complex containing at least CMD1, SPC29 and SCP110. Interacts with SPC97 and SPC98. Tightly associated with the nucleus. It is present in a granular pattern that excludes the nucleolus. Belongs to the SPC110 family. +Monoterpene synthase (mono-TPS) involved in the biosynthesis of monoterpenes natural products, constituent of coffee beverage aroma (PubMed:23398891). Catalyzes the conversion of (2E)-geranyl diphosphate (GPP) into linalool and beta-myrcene, and, as minor products, cis-ocimene and trans-ocimene (PubMed:23398891). Not able to use geranylgeranyl pyrophosphate (GGPP) and farnesyl pyrophosphate (FPP) as substrates (PubMed:23398891). (2E)-geranyl diphosphate = beta-myrcene + diphosphate (2E)-geranyl diphosphate + H2O = diphosphate + linalool (2E)-geranyl diphosphate = (Z)-beta-ocimene + diphosphate (2E)-geranyl diphosphate = (E)-beta-ocimene + diphosphate Binds 3 Mg(2+) or Mn(2+) ions per subunit. Secondary metabolite biosynthesis; terpenoid biosynthesis. Monomer. Expressed in flowers and fruits. Observed at early stages of flowers and fruits development (PubMed:23398891). Expressed in flowers and drupes at 10 weeks after pollination, and, at low levels, in fruits at 15 weeks of ripening (PubMed:23398891). The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg(2+). Belongs to the terpene synthase family. Tpsb subfamily. Truncated N-terminus. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Essential cell division protein. May link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic. Part of a complex composed of FtsB, FtsL and FtsQ. Localizes to the division septum. Belongs to the FtsB family. +May function as a virulence determinant. +The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Depending on the isoform, progesterone receptor functions as transcriptional activator or repressor. Ligand-dependent transdominant repressor of steroid hormone receptor transcriptional activity including repression of its isoform B, MR and ER. Transrepressional activity may involve recruitment of corepressor NCOR2. Transcriptional activator of several progesteron-dependent promoters in a variety of cell types. Involved in activation of SRC-dependent MAPK signaling on hormone stimulation. Increases mitochondrial membrane potential and cellular respiration upon stimulation by progesterone. Interacts with SMARD1 and UNC45A. Interacts with CUEDC2; the interaction promotes ubiquitination, decreases sumoylation, and represses transcriptional activity. Interacts with PIAS3; the interaction promotes sumoylation of PR in a hormone-dependent manner, inhibits DNA-binding, and alters nuclear export. Interacts with SP1; the interaction requires ligand-induced phosphorylation on Ser-345 by ERK1/2 MAPK. Interacts with PRMT2. Isoform A interacts with NCOR2. Isoform B (but not isoform A) interacts with NCOA2 and NCOA1. Isoform B (but not isoform A) interacts with KLF9. Interacts with GTF2B (PubMed:1517211). Nucleoplasmic shuttling is both hormone- and cell cycle-dependent. On hormone stimulation, retained in the cytoplasm in the G(1) and G(2)/M phases. Mainly nuclear. In reproductive tissues the expression of isoform A and isoform B varies as a consequence of developmental and hormonal status. Isoform A and isoform B are expressed in comparable levels in uterine glandular epithelium during the proliferative phase of the menstrual cycle. Expression of isoform B but not of isoform A persists in the glands during mid-secretory phase. In the stroma, isoform A is the predominant form throughout the cycle. Heterogeneous isoform expression between the glands of the endometrium basalis and functionalis is implying region-specific responses to hormonal stimuli. Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain. Phosphorylated on multiple serine sites. Several of these sites are hormone-dependent. Phosphorylation on Ser-294 occurs preferentially on isoform B, is highly hormone-dependent and modulates ubiquitination and sumoylation on Lys-388. Phosphorylation on Ser-102 and Ser-345 also requires induction by hormone. Basal phosphorylation on Ser-81, Ser-162, Ser-190 and Ser-400 is increased in response to progesterone and can be phosphorylated in vitro by the CDK2-A1 complex. Increased levels of phosphorylation on Ser-400 also in the presence of EGF, heregulin, IGF, PMA and FBS. Phosphorylation at this site by CDK2 is ligand-independent, and increases nuclear translocation and transcriptional activity. Phosphorylation at Ser-162 and Ser-294, but not at Ser-190, is impaired during the G(2)/M phase of the cell cycle. Phosphorylation on Ser-345 by ERK1/2 MAPK is required for interaction with SP1. Sumoylation is hormone-dependent and represses transcriptional activity. Sumoylation on all three sites is enhanced by PIAS3. Desumoylated by SENP1. Sumoylation on Lys-388, the main site of sumoylation, is repressed by ubiquitination on the same site, and modulated by phosphorylation at Ser-294. Ubiquitination is hormone-dependent and represses sumoylation on the same site. Promoted by MAPK-mediated phosphorylation on Ser-294. Palmitoylated by ZDHHC7 and ZDHHC21. Palmitoylation is required for plasma membrane targeting and for rapid intracellular signaling via ERK and AKT kinases and cAMP generation. Produced by alternative promoter usage. Produced by alternative promoter usage. Produced by alternative splicing of isoform B. Produced by alternative promoter usage. Produced by alternative splicing of isoform B. Belongs to the nuclear hormone receptor family. NR3 subfamily. Progesterone receptor entry +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +Serine/threonine-protein kinase involved in the regulation of the mitotic cell cycle, cell proliferation, apoptosis, organization of the cytoskeleton and neurite outgrowth. Functions in part via its role in ubiquitin-dependent proteasomal protein degradation. Functions downstream of ATM and phosphorylates p53/TP53 at 'Ser-46', and thereby contributes to the induction of apoptosis in response to DNA damage. Phosphorylates NFATC1, and thereby inhibits its accumulation in the nucleus and its transcription factor activity. Phosphorylates EIF2B5 at 'Ser-544', enabling its subsequent phosphorylation and inhibition by GSK3B. Likewise, phosphorylation of NFATC1, CRMP2/DPYSL2 and CRMP4/DPYSL3 promotes their subsequent phosphorylation by GSK3B. May play a general role in the priming of GSK3 substrates. Inactivates GYS1 by phosphorylation at 'Ser-641', and potentially also a second phosphorylation site, thus regulating glycogen synthesis. Mediates EDVP E3 ligase complex formation and is required for the phosphorylation and subsequent degradation of KATNA1. Phosphorylates TERT at 'Ser-457', promoting TERT ubiquitination by the EDVP complex. Phosphorylates SIAH2, and thereby increases its ubiquitin ligase activity. Promotes the proteasomal degradation of MYC and JUN, and thereby regulates progress through the mitotic cell cycle and cell proliferation. Promotes proteasomal degradation of GLI2 and GLI3, and thereby plays a role in smoothened and sonic hedgehog signaling. Phosphorylates CRMP2/DPYSL2, CRMP4/DPYSL3, DCX, EIF2B5, EIF4EBP1, GLI2, GLI3, GYS1, JUN, MDM2, MYC, NFATC1, p53/TP53, TAU/MAPT and KATNA1. Can phosphorylate histone H1, histone H3 and histone H2B (in vitro). Can phosphorylate CARHSP1 (in vitro) (By similarity). Plays a role in cytoskeleton organization and neurite outgrowth via its phosphorylation of DCX. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein] Activated by autophosphorylation on the second tyrosine residue in the Tyr-X-Tyr motif in the activation loop. Component of an E3 ligase complex containing DYRK2, EDD/UBR5, DDB1 and DCAF1 (EDVP complex). Interacts directly with EDD/UBR5, DDB1 and DCAF1. Interacts with SIAH2 and MDM2. Interacts with MAP3K10 and NFATC1. May also interact with CCNL2 (By similarity). Translocates into the nucleus following DNA damage. Autophosphorylates cotranslationally on the second tyrosine residue in the Tyr-X-Tyr motif in the activation loop, but once mature, does not have any protein tyrosine kinase activity. Phosphorylated at Thr-104 and Ser-440 by ATM in response to genotoxic stress. Under normal conditions, polyubiquitinated in the nucleus by MDM2, leading to its proteasomal degradation. Phosphorylation on Thr-104 and Ser-440 by ATM in response to genotoxic stress disrupts MDM2 binding and prevents MDM2-mediated ubiquitination and subsequent proteasomal degradation. Polyubiquitinated by SIAH2, leading to its proteasomal degradation. Polyubiquitinated by SIAH2 occurs under normal conditions, and is enhanced in response to hypoxia. Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. MNB/DYRK subfamily. +Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA. Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding. Three molecules of FEN1 bind to one PCNA trimer with each molecule binding to one PCNA monomer (PubMed:15616578). PCNA stimulates the nuclease activity without altering cleavage specificity (PubMed:15616578). The C-terminal domain binds EP300; can bind simultaneously to both PCNA and EP300 (PubMed:11430825). Interacts with PCNA; can bind simultaneously to both PCNA and EP300 (PubMed:9305916, PubMed:11430825). Interacts with DDX11; this interaction is direct and increases flap endonuclease activity of FEN1 (PubMed:18499658). Interacts with WDR4; regulating its endonuclease activity (PubMed:26751069). Resides mostly in the nucleoli and relocalizes to the nucleoplasm upon DNA damage. Acetylated by EP300. Acetylation inhibits both endonuclease and exonuclease activity. Acetylation also reduces DNA-binding activity but does not affect interaction with PCNA or EP300. Phosphorylation upon DNA damage induces relocalization to the nuclear plasma. Phosphorylation at Ser-187 by CDK2 occurs during late S-phase and results in dissociation from PCNA. Methylation at Arg-192 by PRMT5 impedes Ser-187 phosphorylation and increases interaction with PCNA. No nuclease activity. Binds preferentially to RNA flap structures and R-loops. Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily. +Has nucleotide phosphatase activity towards ATP, GTP, CTP, TTP and UTP. May hydrolyze nucleoside diphosphates with lower efficiency. a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate Belongs to the THEP1 NTPase family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy-D-galactonate. D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O Binds 1 Mg(2+) ion per subunit. Carbohydrate acid metabolism; D-galactonate degradation; D-glyceraldehyde 3-phosphate and pyruvate from D-galactonate: step 1/3. Reaction proceeds via an anti dehydration. Belongs to the mandelate racemase/muconate lactonizing enzyme family. GalD subfamily. +Belongs to the universal ribosomal protein uL16 family. +Plays a critical role in the sodium-dependent reabsorption of bile acids from the lumen of the small intestine. Plays a key role in cholesterol metabolism. Monomer and homodimer. The disease is caused by variants affecting the gene represented in this entry. Belongs to the bile acid:sodium symporter (BASS) (TC 2.A.28) family. +Catalyzes the deamination of dCTP to dUTP. dCTP + H(+) + H2O = dUTP + NH4(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 1/2. Homotrimer. Belongs to the dCTP deaminase family. +Binds 1 zinc ion. Belongs to the SprT family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. Truncated N-terminus. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +May play a role in the regulation of mRNA stability. Binds to the 3'-most 134 nt of the SERPINE1/PAI1 mRNA, a region which confers cyclic nucleotide regulation of message decay. Seems to play a role in PML-nuclear bodies formation (PubMed:28695742). Interacts with SPIN1 (By similarity). Interacts with CHD3 and TDRD3 (PubMed:12505151, PubMed:18632687). Interacts with ZDHHC17 (via ANK repeats) (PubMed:28882895). Expressed at high level in the heart, skeletal muscle and kidney, and at low levels in placenta, liver and brain. May be due to a competing acceptor splice site. May be due to a competing acceptor splice site. +Belongs to the YejK family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Component of the ubiquinol-cytochrome c oxidoreductase, a multisubunit transmembrane complex that is part of the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. The cytochrome b-c1 complex catalyzes electron transfer from ubiquinol to cytochrome c, linking this redox reaction to translocation of protons across the mitochondrial inner membrane, with protons being carried across the membrane as hydrogens on the quinol. In the process called Q cycle, 2 protons are consumed from the matrix, 4 protons are released into the intermembrane space and 2 electrons are passed to cytochrome c. Cytochrome c1 is a catalytic core subunit containing a c-type heme. It transfers electrons from the [2Fe-2S] iron-sulfur cluster of the Rieske protein to cytochrome c. a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)-[cytochrome c](out) + 2 H(+)(out) Binds 1 heme c group covalently per subunit. Component of the ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), a multisubunit enzyme composed of 3 respiratory subunits cytochrome b, cytochrome c1 and Rieske protein, 2 core protein subunits, and additional low-molecular weight protein subunits. The complex exists as an obligatory dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with cytochrome c oxidase (complex IV, CIV). Belongs to the cytochrome c family. +Involved in a peptide intake transport system that plays a role in the resistance to antimicrobial peptides. Part of the sapA-sapB-sapC-sapD-sapF operon, RNA detected in mid-log phase cells. Belongs to the binding-protein-dependent transport system permease family. OppBC subfamily. +Strong platelet aggregation inhibitor. Binds specifically to platelet glycoprotein Ibalpha (GP1BA) with high affinity and inhibits vWF-dependent platelet aggregation (PubMed:7599152). Has also been observed to induce small agglutinates in washed platelets by binding to GPIb (PubMed:10688335). Tetramer of heterodimers of alpha and beta subunits (alphabeta)(4); disulfide-linked. Expressed by the venom gland. Has no effect on ADP- and collagen-induced platelet aggregation in platelet rich plasma. Belongs to the snaclec family. +Radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3-[(1-carboxyvinyl)oxy]benzoate, leading to aminodeoxyfutalosine (AFL), a key intermediate in the formation of menaquinone (MK, vitamin K2) from chorismate. 3-[(1-carboxyvinyl)-oxy]benzoate + H2O + S-adenosyl-L-methionine = 6-amino-6-deoxyfutalosine + H(+) + hydrogencarbonate + L-methionine Binds 1 [4Fe-4S] cluster. The cluster is likely coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Quinol/quinone metabolism; menaquinone biosynthesis. Belongs to the radical SAM superfamily. MqnE family. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +Transcriptional corepressor that binds to a number of transcription factors. At gastrulation, expression is absent within the axial mesoderm. After gastrulation is complete, expressed in the presomitic mesoderm, but expression in the tailbud doesn't begin until the six to seven somite stage, after which it becomes abundant. Expression is abundant throughout somitogenesis within the posterior half of the somites, but is absent from older somites. Also expressed in a dynamic manner within the neural plate. Expressed both maternally and zygotically. Expression decreases from the mid-blastula stages onwards before increasing again at the start of gastrulation. Belongs to the WD repeat Groucho/TLE family. +Probable transcription factor. +Regulatory protein of the TOL plasmid xyl operons. In the presence of m-xylene or m-methylbenzyl alcohol XylR activates both the xylCMABN operon and the regulatory gene xylS; xylS itself activates the xylXYZLTEGFJQKIH operon. XylR interacts with sigma-54. +Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position. Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain. Glycan biosynthesis; glycogen biosynthesis. Monomer. Belongs to the glycosyl hydrolase 13 family. GlgB subfamily. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Interacts with PHB2; the interaction decreases in absence of SPHK2 (By similarity). Interacts with AFG1L (By similarity). Interacts with ABCB7; this interaction allows the regulation of cellular iron homeostasis and cellular reactive oxygen species (ROS) levels in cardiomyocytes (By similarity). Belongs to the cytochrome c oxidase IV family. +Interacts with the SecY protein in vivo. May bind preferentially to an uncomplexed state of SecY, thus functioning either as a chelating agent for excess SecY in the cell or as a regulatory factor that negatively controls the translocase function. Loosely associated with the cytoplasmic side of the inner membrane, probably via SecY. Belongs to the Syd family. +Interacts with the 40S ribosomal subunit. The SUI1 domain may be involved in RNA binding. Belongs to the DENR family. +The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. Belongs to the RecF family. +Functions as a weak apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. Also displays double-stranded DNA 3'-5' exonuclease, 3'-phosphodiesterase activities. Shows robust 3'-5' exonuclease activity on 3'-recessed heteroduplex DNA and is able to remove mismatched nucleotides preferentially. Shows fairly strong 3'-phosphodiesterase activity involved in the removal of 3'-damaged termini formed in DNA by oxidative agents. In the nucleus functions in the PCNA-dependent BER pathway. Required for somatic hypermutation (SHM) and DNA cleavage step of class switch recombination (CSR) of immunoglobulin genes. Required for proper cell cycle progression during proliferation of peripheral lymphocytes. Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. Probably binds two magnesium or manganese ions per subunit. 3'-5' exonuclease activity is activated by sodium and manganese. 3'-5' exonuclease and 3'-phosphodiesterase activities are stimulated in presence of PCNA (By similarity). Interacts with PCNA. This interaction is increased by misincorporation of uracil in nuclear DNA (By similarity). Together with PCNA, is redistributed in discrete nuclear foci in presence of oxidative DNA damaging agents. Expressed in lymphocytes, thymocytes and splenocytes (at protein level). Highly expressed in the thymus and weakly expressed in the bone marrow, spleen, eye, kidney, lung, brain and uterus. Up-regulated in both the nucleus and the cytosol of B cells stimulated to switch. Mice show abnormalities in proliferating haemopoietic organs, such as dyshematopoiesis, defect in lymphopoiesis, and delayed S-phase and G2/M-phase arrest. Belongs to the DNA repair enzymes AP/ExoA family. +Protein kinase with a significantly reduced Ca(2+)/CAM affinity and dependence compared to other members of the CaMK family. May play a role in the down-regulation of CRE-dependent gene activation probably by phosphorylation of the CREB coactivator CRTC2/TORC2 and the resulting retention of TORC2 in the cytoplasm (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Binds to and stabilizes microtubules. Interacts with MAPK8IP1/JIP-1, MAPK8IP2/JIP-2, MAPK9/JNK2, PPP1R9B/NEURABIN-2 and actin. Colocalizes with microtubules. The doublecortin domains are involved in the colocalization with microtubules. Autophosphorylated. Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. CaMK subfamily. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Belongs to the V-ATPase D subunit family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery. ATP-dependent cleavage of peptide bonds with broad specificity. Allosterically activated by HslU binding. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the peptidase T1B family. HslV subfamily. +Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-terminal L-methionyl-[peptide] Binds 1 Fe(2+) ion. Belongs to the polypeptide deformylase family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Activates transcription of virulence factors alpha- and beta hemolysin genes (hla and hlb). Also, activates RNAIII expression, a central regulator transcribed from the agr locus (By similarity). Transcriptionally activated by CvfA. Belongs to the SarZ family. +Belongs to the UPF0235 family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvP family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +Probably part of the inner envelope. Expressed in the late phase of the viral replicative cycle. Belongs to the asfivirus H108R family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. In this organism, the P 'protein' is a heterodimer of two subunits. Belongs to the GcvP family. N-terminal subunit subfamily. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Usually encoded in the trnK tRNA gene intron. Probably assists in splicing its own and other chloroplast group II introns. Belongs to the intron maturase 2 family. MatK subfamily. +Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA. ATP + oxaloacetate = ADP + CO2 + phosphoenolpyruvate Binds 1 Mn(2+) ion per subunit. Carbohydrate biosynthesis; gluconeogenesis. Monomer. Belongs to the phosphoenolpyruvate carboxykinase (ATP) family. +The N-terminus is blocked. Belongs to the universal ribosomal protein uS2 family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +May be involved in transcriptional regulation as a transcriptional corepressor. The DEPDC1A-ZNF224 complex may play a critical role in bladder carcinogenesis by repressing the transcription of the A20 gene, leading to transport of NF-KB protein into the nucleus, resulting in suppression of apoptosis of bladder cancer cells. Isoform 2 and isoform 5 can form homodimers and heterodimers. Interacts with ZNF224. Colocalizes with ZNF224 at the nucleus. Expressed in testis. Up-regulated in bladder cancer cells (at protein level). Contaminating sequence. Potential poly-A sequence. Truncated N-terminus. Truncated N-terminus. Probable cloning artifact. +Belongs to the UPF0301 (AlgH) family. +Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. It is subsequently lost, together with VP7, following virus entry into the host cell. Following entry into the host cell, low intracellular or intravesicular Ca(2+) concentration probably causes the calcium-stabilized VP7 trimers to dissociate from the virion. This step is probably necessary for the membrane-disrupting entry step and the release of VP4, which is locked onto the virion by VP7. During the virus exit from the host cell, VP4 seems to be required to target the newly formed virions to the host cell lipid rafts. Forms the spike 'foot' and 'body' and acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. During entry, the part of VP5* that protrudes from the virus folds back on itself and reorganizes from a local dimer to a trimer. This reorganization may be linked to membrane penetration by exposing VP5* hydrophobic region. In integrin-dependent strains, VP5* targets the integrin heterodimer ITGA2/ITGB1 for cell attachment. Forms the head of the spikes and mediates the recognition of specific host cell surface glycans. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact. In some other strains, VP8* mediates the attachment to histo-blood group antigens (HBGAs) for viral entry. Homotrimer. VP4 adopts a dimeric appearance above the capsid surface, while forming a trimeric base anchored inside the capsid layer. Only hints of the third molecule are observed above the capsid surface. It probably performs a series of molecular rearrangements during viral entry. Prior to trypsin cleavage, it is flexible. The priming trypsin cleavage triggers its rearrangement into rigid spikes with approximate two-fold symmetry of their protruding parts. After an unknown second triggering event, cleaved VP4 may undergo another rearrangement, in which two VP5* subunits fold back on themselves and join a third subunit to form a tightly associated trimer, shaped like a folded umbrella. Interacts with VP6. Interacts with VP7. Homotrimer. The trimer is coiled-coil stabilized by its C-terminus, however, its N-terminus, known as antigen domain or 'body', seems to be flexible allowing it to self-associate either as a dimer or a trimer. The outer layer contains 180 copies of VP4, grouped as 60 dimers. Immature double-layered particles assembled in the cytoplasm bud across the membrane of the endoplasmic reticulum, acquiring during this process a transient lipid membrane that is modified with the ER resident viral glycoproteins NSP4 and VP7; these enveloped particles also contain VP4. As the particles move towards the interior of the ER cisternae, the transient lipid membrane and the non-structural protein NSP4 are lost, while the virus surface proteins VP4 and VP7 rearrange to form the outermost virus protein layer, yielding mature infectious triple-layered particles. VP4 also seems to associate with lipid rafts of the host cell membrane probably for the exit of the virus from the infected cell by an alternate pathway. Outer capsid protein. Outer capsid protein. The VP4 spike is divided into a foot, a stalk and body, and a head. Proteolytic cleavage by trypsin results in activation of VP4 functions and greatly increases infectivity. The penetration into the host cell is dependent on trypsin treatment of VP4. It produces two peptides, VP5* and VP8* that remain associated with the virion. Cleavage of VP4 by trypsin probably occurs in vivo in the lumen of the intestine prior to infection of enterocytes. Trypsin seems to be incorporated into the three-layered viral particles but remains inactive as long as the viral outer capsid is intact and would only be activated upon the solubilization of the latter. In group A rotaviruses, VP4 defines the P serotype. Some rotavirus strains are neuraminidase-sensitive and require sialic acid to attach to the cell surface. Some rotavirus strains are integrin-dependent. Some rotavirus strains depend on ganglioside for their entry into the host cell. Hsp70 also seems to be involved in the entry of some strains. This strain probably uses sialic acid to attach to the host cell. Belongs to the rotavirus VP4 family. +May act as a negative regulator of salt tolerance. Belongs to the NST1 family. +Actin cytoskeleton-organizing protein that plays a role in the formation of cell projections (By similarity). Required for actin polymerization at immunological synapses (IS) and for the recruitment of the chemokine receptor CXCR4 to IS (By similarity). Plays a role in dendritic spine morphogenesis and organization, including the localization of the dopamine receptor DRD1 to the dendritic spines (By similarity). Involved in memory-related synaptic plasticity in the hippocampus (By similarity). Interacts with RUFY (By similarity). Interacts with CXCR4; this interaction is enhanced by antigenic stimulation (By similarity). Interacts (via ADF-H domain) with ZMYND8 (via PHD-type Zinc finger, Bromo and PWWP domains); the interaction leads to sequestering of ZMYND8 in the cytoplasm (By similarity). In the absence of antigen, evenly distributed throughout subcortical regions of the T-cell membrane and cytoplasm. In the presence of antigen, distributes to the immunological synapse forming at the T-cell-APC contact area, where it localizes at the peripheral and distal supramolecular activation clusters (SMAC). Colocalized with RUFY3 and F-actin at the transitional domain of the axonal growth cone. Brain neurons. ISGylated. Drebrins are classified into two forms of the embryonic type (E1 and E2) and one form of the adult type (A). The time course of their appearance are different from each other. Their structures are closely related. Adult rat brain expresses only drebrin A while drebrin E1 or E2 is observed in immature animals. +Molecular chaperone capable of stabilizing a range of proteins. Seems to fulfill an ATP-independent, HSP70-like function in archaeal de novo protein folding. Heterohexamer of two alpha and four beta subunits. Belongs to the prefoldin alpha subunit family. +Required for normal vault structure. Vaults are multi-subunit structures that may act as scaffolds for proteins involved in signal transduction. Vaults may also play a role in nucleo-cytoplasmic transport (By similarity). The vault ribonucleoprotein particle is a huge (400 A x 670 A) cage structure of 12.9 MDa. It consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains, PARP4 and one or more vault RNAs (vRNAs) (By similarity). +Catalyzes the NADPH-dependent reduction of N-acetyl-5-glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde. N-acetyl-L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + N-acetyl-L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 3/4. Belongs to the NAGSA dehydrogenase family. Type 1 subfamily. +Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-methyl-D-erythritol + diphosphate Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. Belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Deiminated on Arg-4 in granulocytes upon calcium entry. Monoubiquitination of Lys-120 (H2AK119Ub) by RING1, TRIM37 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. It is involved in the initiation of both imprinted and random X inactivation. Ubiquitinated H2A is enriched in inactive X chromosome chromatin. Ubiquitination of H2A functions downstream of methylation of 'Lys-27' of histone H3 (H3K27me). H2AK119Ub by RNF2/RING2 can also be induced by ultraviolet and may be involved in DNA repair. Following DNA double-strand breaks (DSBs), it is ubiquitinated through 'Lys-63' linkage of ubiquitin moieties by the E2 ligase UBE2N and the E3 ligases RNF8 and RNF168, leading to the recruitment of repair proteins to sites of DNA damage. Ubiquitination at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) in response to DNA damage is initiated by RNF168 that mediates monoubiquitination at these 2 sites, and 'Lys-63'-linked ubiquitin are then conjugated to monoubiquitin; RNF8 is able to extend 'Lys-63'-linked ubiquitin chains in vitro. H2AK119Ub and ionizing radiation-induced 'Lys-63'-linked ubiquitination (H2AK13Ub and H2AK15Ub) are distinct events. Phosphorylation on Ser-2 (H2AS1ph) is enhanced during mitosis. Phosphorylation on Ser-2 by RPS6KA5/MSK1 directly represses transcription. Acetylation of H3 inhibits Ser-2 phosphorylation by RPS6KA5/MSK1. Phosphorylation at Thr-121 (H2AT120ph) by DCAF1 is present in the regulatory region of many tumor suppresor genes and down-regulates their transcription. Symmetric dimethylation on Arg-4 by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage. Glutamine methylation at Gln-105 (H2AQ104me) by FBL is specifically dedicated to polymerase I. It is present at 35S ribosomal DNA locus and impairs binding of the FACT complex. Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes. Lactylated in macrophages by EP300/P300 by using lactoyl-CoA directly derived from endogenous or exogenous lactate, leading to stimulates gene transcription. Belongs to the histone H2A family. +Component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. The TIM22 complex forms a twin-pore translocase that uses the membrane potential as the external driving force. Required for the stability of the TIM22 complex and functions in the assembly of the TIMM22 protein into the TIM22 complex. May facilitate cooperation between TIM22 and TOM complexes by interacting with TOMM40. Component of the TIM22 complex, which core is composed of TIMM22, associated with TIMM10 (TIMM10A and/or TIMM10B), TIMM9, AGK and TIMM29 (PubMed:27554484, PubMed:27718247, PubMed:28712724, PubMed:28712726). Interacts with TIMM10B; the interaction is direct (PubMed:27554484). Interacts with TOMM40; linking the TIM22 complex to the TOM complex (PubMed:27554484). Interacts with TIMM22 (when oxidized); the interaction is direct (PubMed:27718247). +Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle. oxaloacetate + phosphate = hydrogencarbonate + phosphoenolpyruvate Belongs to the PEPCase type 1 family. +Reductase component of a two-component system that supplies reduced FMN (FMNH2) to the oxygenase component to catalyze the hydroxylation of 4-hydroxyphenylacetic acid, leading to the production of 3,4-dihydroxyphenylacetate (3,4-DHPA). Catalyzes the reduction of free flavins (FMN, FAD and riboflavin) by NADH. Subsequently, the reduced flavins diffuse to the oxygenase component C2. a reduced flavin + NAD(+) = an oxidized flavin + 2 H(+) + NADH Flavin concentrations greater than 15 uM do not inhibit the NADH oxidation activity of the reductase component C1 but do affect the hydroxylation activity of the C1-C2 complex. Maximal reductase activity is achieved only upon HPA binding to the reductase component C1 before interaction with NADH. HPA stimulates the rates of both the reduction of FMN and release of reduced FMN from the reductase component. Values measured using the C1-C2 complex. kcat is 343 min(-1) for the reduction of FMN with NADH. E(0) is -236 mV for C1, and -245 mV for C1-HPA complex. Aromatic compound metabolism; 4-hydroxyphenylacetate degradation; pyruvate and succinate semialdehyde from 4-hydroxyphenylacetate: step 1/7. Homodimer. The p-hydroxyphenylacetate 3-hydroxylase (HpaH) is composed of an oxygenase component C2 and a reductase component C1. Belongs to the non-flavoprotein flavin reductase family. +Inhibitor of serine proteases chymotrypsin, pepsin and trypsin. Has strong antifungal activity against the human pathogenic fungi C.albicans TIMM 1768, S.cerevisiae KCTC 7296 and T.beigelli KCTC 7707, but lacks antifungal activity against the plant pathogenic fungi C.gloeosporioides KACC 40003, C.coccodes KACC 40803 and D.bryoniae KACC 40669. Lacks hemolytic activity against human erythrocytes. Belongs to the protease inhibitor I3 (leguminous Kunitz-type inhibitor) family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +Regulates myosin phosphatase activity. PP1 comprises a catalytic subunit, PPP1CA, PPP1CB or PPP1CC, and one or several targeting or regulatory subunits. PPP1R12C mediates binding to myosin. Interacts via its N-terminus with PPP1CB. Interacts with IL16. Interacts with the coiled-coil domain of MPRIP. Interacts with NOD2 (By similarity). Phosphorylation at Thr-560 is essential for its interaction with PPP1CB. +Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. This function is generally fulfilled by the C-terminal part of HisG, which is missing in some bacteria such as this one. Belongs to the class-II aminoacyl-tRNA synthetase family. HisZ subfamily. +Has endoglucanase activity on substrates containing beta-1,4 glycosidic bonds, like in carboxymethylcellulose (CMC), hydroxyethylcellulose (HEC) and beta-glucan. Involved in the degradation of complex natural cellulosic substrates. Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. Optimum pH is 6.0. Optimum temperature is 70 degrees Celsius. Expression is under the control of the xylanolytic transcriptional activator xlnR. Belongs to the glycosyl hydrolase 5 (cellulase A) family. +Initiates the repair of damaged proteins by catalyzing methyl esterification of L-isoaspartyl and D-aspartyl residues produced by spontaneous isomerization and racemization of L-aspartyl and L-asparaginyl residues in aging peptides and proteins. [protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine Monomer. Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Belongs to the mitochondrial carrier (TC 2.A.29) family. +Catalyzes the reversible epimerization at C-2 of UDP-N-acetylglucosamine (UDP-GlcNAc) and thereby provides bacteria with UDP-N-acetylmannosamine (UDP-ManNAc), the activated donor of ManNAc residues. UDP-N-acetyl-alpha-D-glucosamine = UDP-N-acetyl-alpha-D-mannosamine Bacterial outer membrane biogenesis; enterobacterial common antigen biosynthesis. Homodimer. Belongs to the UDP-N-acetylglucosamine 2-epimerase family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Dual specificity enzyme that catalyzes the synthesis of pseudouridine from uracil-746 in 23S ribosomal RNA and from uracil-32 in the anticodon stem and loop of transfer RNAs. uridine(32) in tRNA = pseudouridine(32) in tRNA uridine(746) in 23S rRNA = pseudouridine(746) in 23S rRNA Belongs to the pseudouridine synthase RluA family. +Has antibacterial activity against E.coli HP101BA (MIC=12.3 uM), K.pneumoniae PTCC1388 (MIC=9.8 uM), M.luteus PTCC1625 (MIC=8.3 uM) and S.aureus PTCC1431 (MIC=10.6 uM). Has no or very limited (<3%) hemolytic activity at concentrations of 15 ug/ml and 60 ug/ml, respectively. Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Temporin subfamily. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Endoribonuclease that initiates mRNA decay. Belongs to the RNase Y family. +Belongs to the UPF0246 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 49 kDa subunit family. +This protein is found in nasal epithelium and it binds a wide variety of chemical odorants. Monomer. Belongs to the calycin superfamily. Lipocalin family. +Binds to 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29. Belongs to the universal ribosomal protein uL23 family. +Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair. Component of the 19S proteasome regulatory particle complex. The 26S proteasome consists of a 20S core particle (CP) and two 19S regulatory subunits (RP). The regulatory particle is made of a lid composed of 9 subunits including PSMD7, a base containing 6 ATPases and few additional components. Within the complex, PSMD7 interacts with subunit PSMD4 through their respective MPN domain. Interacts with TRIM5. Disruption of the Mov-34 locus is a recessive embryonic lethal mutation. Does not bind a metal ion. Belongs to the peptidase M67A family. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system. ATP + H2O + phosphate(out) = ADP + H(+) + 2 phosphate(in) The complex is composed of two ATP-binding proteins (PstB), two transmembrane proteins (PstC and PstA) and a solute-binding protein (PstS). Belongs to the ABC transporter superfamily. Phosphate importer (TC 3.A.1.7) family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome. Phosphorylation by EF-2 kinase completely inactivates EF-2. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily. +Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. ATP + NAD(+) = ADP + H(+) + NADP(+) Belongs to the NAD kinase family. +Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH. 6-phospho-D-gluconate + NADP(+) = CO2 + D-ribulose 5-phosphate + NADPH Carbohydrate degradation; pentose phosphate pathway; D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 3/3. Homodimer. Belongs to the 6-phosphogluconate dehydrogenase family. +Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. Laminin is a complex glycoprotein, consisting of three different polypeptide chains (alpha, beta, gamma), which are bound to each other by disulfide bonds into a cross-shaped molecule comprising one long and three short arms with globules at each end. Gamma-3 is a subunit of laminin-12 (laminin-213), laminin-14 (laminin-423) and laminin-15 (laminin-523). Broadly expressed in: skin, heart, lung, and the reproductive tracts. The alpha-helical domains I and II are thought to interact with other laminin chains to form a coiled coil structure. Domain IV is globular. The disease is caused by variants affecting the gene represented in this entry. +Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA. Heteromultimer composed of small subunits (RfcS) and large subunits (RfcL). Belongs to the activator 1 small subunits family. RfcS subfamily. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides. Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low. Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids. Binds 2 manganese ions per subunit. Belongs to the peptidase M17 family. +Belongs to the bacterial ribosomal protein bL27 family. +Nuclear hormone receptor. The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Ligand-dependent nuclear transactivation involves either direct homodimer binding to a palindromic estrogen response element (ERE) sequence or association with other DNA-binding transcription factors, such as AP-1/c-Jun, c-Fos, ATF-2, Sp1 and Sp3, to mediate ERE-independent signaling. Ligand binding induces a conformational change allowing subsequent or combinatorial association with multiprotein coactivator complexes through LXXLL motifs of their respective components. Mutual transrepression occurs between the estrogen receptor (ER) and NF-kappa-B in a cell-type specific manner. Decreases NF-kappa-B DNA-binding activity and inhibits NF-kappa-B-mediated transcription from the IL6 promoter and displace RELA/p65 and associated coregulators from the promoter. Recruited to the NF-kappa-B response element of the CCL2 and IL8 promoters and can displace CREBBP. Present with NF-kappa-B components RELA/p65 and NFKB1/p50 on ERE sequences. Can also act synergistically with NF-kappa-B to activate transcription involving respective recruitment adjacent response elements; the function involves CREBBP. Can activate the transcriptional activity of TFF1. Also mediates membrane-initiated estrogen signaling involving various kinase cascades. Essential for MTA1-mediated transcriptional regulation of BRCA1 and BCAS3 (By similarity). Binds DNA as a homodimer. Can form a heterodimer with ESR2. Interacts with coactivator NCOA5. Interacts with NCOA7; the interaction is ligand-inducible. Interacts with AKAP13, CUEDC2, HEXIM1, KDM5A, MAP1S, PELP1, SMARD1, and UBE1C. Interacts with MUC1; the interaction is stimulated by 7 beta-estradiol (E2) and enhances ERS1-mediated transcription. Interacts with DNTTIP2, and UIMC1. Interacts with KMT2D/MLL2. Interacts with ATAD2; the interaction is enhanced by estradiol. Interacts with KIF18A and LDB1. Interacts with RLIM (via its C-terminus). Interacts with MACROD1. Interacts with SH2D4A and PLCG. Interacts with SH2D4A; the interaction blocks binding to PLCG and inhibits estrogen-induced cell proliferation. Interacts with DYNLL1. Interacts with CCDC62; the interaction requires estradiol and appears to enhance the transcription of target genes. Interacts with NR2C1; the interaction prevents homodimerization of ESR1 and suppresses its transcriptional activity and cell growth. Interacts with DNAAF4. Interacts with PRMT2. Interacts with PI3KR1 or PIK3R2, SRC and PTK2/FAK1. Interacts with RBFOX2. Interacts with EP300; the interaction is estrogen-dependent and enhanced by CITED1. Interacts with CITED1; the interaction is estrogen-dependent. Interacts with FAM120B, FOXL2, PHB2 and SLC30A9. Interacts with coactivators NCOA3 and NCOA6. Interacts with STK3/MST2 only in the presence of SAV1 and vice-versa. Binds to CSNK1D. Interacts with NCOA2; NCOA2 can interact with ESR1 AF-1 and AF-2 domains simultaneously and mediate their transcriptional synergy. Interacts with DDX5. Interacts with NCOA1; the interaction seems to require a self-association of N-terminal and C-terminal regions. Interacts with ZNF366, DDX17, NFKB1, RELA, SP1 and SP3. Interacts with NRIP1. Interacts with GPER1; the interaction occurs in an estrogen-dependent manner. Interacts with CLOCK and the interaction is stimulated by estrogen. Interacts with TRIP4 (ufmylated); estrogen dependent. Interacts with LMTK3; the interaction phosphorylates ESR1 (in vitro) and protects it against proteasomal degradation. Interacts with CCAR2 (via N-terminus) in a ligand-independent manner. Interacts with ZFHX3. Interacts with SFR1 in a ligand-dependent and -independent manner. Interacts with DCAF13, LATS1 and DCAF1; regulates ESR1 ubiquitination and ubiquitin-mediated proteasomal degradation. Interacts (via DNA-binding domain) with POU4F2 (C-terminus); this interaction increases the estrogen receptor ESR1 transcriptional activity in a DNA- and ligand 17-beta-estradiol-independent manner. Interacts with ESRRB isoform 1. Interacts with UBE3A and WBP2. Interacts with GTF2B. Interacts with RBM39. In the absence of hormonal ligand, interacts with TACC1 (By similarity). Colocalizes with ZDHHC7 and ZDHHC21 in the Golgi apparatus where most probably palmitoylation occurs. Associated with the plasma membrane when palmitoylated. Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain. The modulating domain, also known as A/B or AF-1 domain has a ligand-independent transactivation function. The C-terminus contains a ligand-dependent transactivation domain, also known as E/F or AF-2 domain which overlaps with the ligand binding domain. AF-1 and AF-2 activate transcription independently and synergistically and act in a promoter- and cell-specific manner (By similarity). Ubiquitinated; regulated by LATS1 via DCAF1 it leads to ESR1 proteasomal degradation. Deubiquitinated by OTUB1. Palmitoylated at Cys-45 by ZDHHC7 and ZDHHC21. Palmitoylation is required for plasma membrane targeting and for rapid intracellular signaling via ERK and AKT kinases and cAMP generation, but not for signaling mediated by the nuclear hormone receptor (By similarity). Phosphorylated by cyclin A/CDK2 and CK1. Phosphorylation probably enhances transcriptional activity. Dephosphorylation by PPP5C inhibits its transactivation activity (By similarity). Phosphorylated by LMTK3 (in vitro) (By similarity). Dimethylated by PRMT1. Demethylated by JMJD6. Belongs to the nuclear hormone receptor family. NR3 subfamily. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. Was originally thought to originate from Chlamydia trachomatis. +Pyrophosphatase that hydrolyzes non-canonical purine nucleotides such as inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) or xanthosine 5'-triphosphate (XTP) to their respective monophosphate derivatives. The enzyme does not distinguish between the deoxy- and ribose forms. Probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions. a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-phosphate + diphosphate + H(+) a 2'-deoxyribonucleoside 5'-triphosphate + H2O = a 2'-deoxyribonucleoside 5'-phosphate + diphosphate + H(+) H2O + ITP = diphosphate + H(+) + IMP dITP + H2O = dIMP + diphosphate + H(+) H2O + XTP = diphosphate + H(+) + XMP Binds 1 divalent metal cation per subunit; can use either Mg(2+) or Mn(2+). Homodimer. Belongs to the HAM1 NTPase family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Belongs to the imidazoleglycerol-phosphate dehydratase family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I 49 kDa subunit family. +Putative transcription factor. Belongs to the bZIP family. +Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP). isopentenyl diphosphate = dimethylallyl diphosphate Binds 1 Mg(2+) ion per subunit. The magnesium ion binds only when substrate is bound. Binds 1 Mn(2+) ion per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1. Belongs to the IPP isomerase type 1 family. +Specifically hydrolyzes 7-methylguanosine monophosphate (m(7)GMP) to 7-methylguanosine and inorganic phosphate (PubMed:23223233, PubMed:24603684). The specific activity for m(7)GMP may protect cells against undesired salvage of m(7)GMP and its incorporation into nucleic acids (PubMed:23223233). Also has weak activity for CMP (PubMed:23223233, PubMed:24603684). UMP and purine nucleotides are poor substrates (PubMed:23223233). H2O + N(7)-methyl-GMP = N(7)-methylguanosine + phosphate CMP + H2O = cytidine + phosphate a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate kcat is 0.24 sec(-1) with m(7)GMP. kcat is 7 sec(-1) with CMP. kcat is 0.07 sec(-1) with GMP. kcat is 0.04 sec(-1) with AMP. kcat is 6.2 sec(-1) with UMP. Monomer. Belongs to the pyrimidine 5'-nucleotidase family. +Belongs to the universal ribosomal protein uS9 family. +Non-catalytic subunit of the queuine tRNA-ribosyltransferase (TGT) that catalyzes the base-exchange of a guanine (G) residue with queuine (Q) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine). Binds 1 zinc ion per subunit. Heterodimer of a catalytic subunit and an accessory subunit. Belongs to the queuine tRNA-ribosyltransferase family. QTRT2 subfamily. +Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development and controls hematopoietic differentiation. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. Interacts with REST. Interacts with the SMARCE1/BAF57, suggesting that the BHC complex may recruit the ATP-dependent chromatin-remodeling SWI-SNF complex (By similarity). Interacts directly with GFI1 AND GFI1B in a RCOR/GFI/KDM1A/HDAC complex. Interacts with INMS1. Expressed in the external germinal layer (EGL) and internal granular layer (IGL) of the cerebellum and in Purkinje cells (at protein level). At embryonic day 8.5, it is highly expressed in the head mesenchyme, but neither in the somites nor in the presomitic mesoderm. By day 11.5 it is expressed fairly ubiquitously throughout the embryo. Down-regulated by the transcriptional repressor ZEB1 during NEUROD2-induced neurogenesis. The SANT domains may bridge the nucleosomal substrates and the demethylase KDM1A. Belongs to the CoREST family. Truncated N-terminus. +beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Binds 2 magnesium ions per subunit. Carbohydrate biosynthesis; gluconeogenesis. Homotetramer. Belongs to the FBPase class 1 family. +Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. 2-oxoglutarate + O-phospho-L-serine = 3-phosphooxypyruvate + L-glutamate 2-oxoglutarate + 4-(phosphooxy)-L-threonine = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate Binds 1 pyridoxal phosphate per subunit. Optimum pH is 9.0. At pH 9.5, retains more 60% of its maximum activity. Inactive below pH 6. Thermal denaturation midpoint (Tm) is 71 degrees Celsius at pH 6 and is lowered around 58 degrees Celsius at pH 8.5 and 10. Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 2/3. Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 3/5. Homodimer. Significant conformational rearrangements are involved in response to pH changes. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. SerC subfamily. +Part of the Tol-Pal system, which plays a role in outer membrane invagination during cell division and is important for maintaining outer membrane integrity. The Tol-Pal system is composed of five core proteins: the inner membrane proteins TolA, TolQ and TolR, the periplasmic protein TolB and the outer membrane protein Pal. They form a network linking the inner and outer membranes and the peptidoglycan layer. Belongs to the TolB family. +Mitochondrial methyltransferase which suppresses respiratory defects caused by OXA1 mutations when overexpressed. Present with 504 molecules/cell in log phase SD medium. Belongs to the methyltransferase superfamily. METL family. +Has a role in mRNA export from the nucleus. Belongs to the SMY2/mpd2 family. +Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP). diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 1/2. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrE subfamily. +Transports viral genome to neighboring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier. Forms a ribonucleoprotein complex with viral RNA. Binds microtubules and modulates microtubule stability. Can bind double-stranded DNA. Belongs to the tobamovirus movement protein family. +NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. a ubiquinone + H(+) + n Na(+)(in) + NADH = a ubiquinol + n Na(+)(out) + NAD(+) Composed of six subunits; NqrA, NqrB, NqrC, NqrD, NqrE and NqrF. Belongs to the NqrDE/RnfAE family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Cell wall formation. NADP(+) + UDP-N-acetyl-alpha-D-muramate = H(+) + NADPH + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurB family. +Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III. 4 H(+) + uroporphyrinogen III = 4 CO2 + coproporphyrinogen III Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 4/4. Homodimer. Belongs to the uroporphyrinogen decarboxylase family. +Expressed by the venom duct. The cysteine framework is III (CC-C-C-CC). Classified in the M-2 branch, since 2 residues stand between the fourth and the fifth cysteine residues. Belongs to the conotoxin M superfamily. +May catalyze the ATP-dependent phosphorylation of lipids other than diacylglycerol (DAG). In fact, is not able to exhibit diacylglycerol kinase activity in vitro. Binds 1 Mg(2+) ion per subunit. This ion appears to have a structural role and is required for catalytic activity. Belongs to the diacylglycerol/lipid kinase family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis. Cofactor biosynthesis; ubiquinone biosynthesis [regulation]. Belongs to the ABC1 family. UbiB subfamily. +Efflux pump involved in export of fusaric acid, a mycotoxin with low to moderate toxicity to animals and humans, but with high phytotoxic properties (PubMed:25372119). Constitutes a self-protecting mechanism of the fungus against critical levels of FSA within the cell (By similarity). Fusaric acid is phytotoxic to plants such as cotton and banana (PubMed:20955724, PubMed:23922960). It has been shown to induce programmed cell death in plants (PubMed:16868776, PubMed:23838885). In addition to a mild toxicity to animals, fusaric acid exhibits acanthamoebicidal, antioomycete, and antimycobacterial activities (PubMed:17927749, PubMed:22864988, PubMed:21811925). Belongs to the major facilitator superfamily. DHA1 family. Polyamines/proton antiporter (TC 2.A.1.2.16) subfamily. +Almost exclusively expressed in testis. Expressed in spermatocytes in the pachytene stage of the first meiotic prophase. Belongs to the TALE/PBX homeobox family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Bifunctional serine/threonine kinase and phosphorylase involved in the regulation of the pyruvate, phosphate dikinase (PPDK) by catalyzing its phosphorylation/dephosphorylation. ADP + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] = AMP + H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] H(+) + N(tele)-phospho-L-histidyl/O-phospho-L-threonyl-[pyruvate, phosphate dikinase] + phosphate = diphosphate + N(tele)-phospho-L-histidyl/L-threonyl-[pyruvate, phosphate dikinase] Belongs to the pyruvate, phosphate/water dikinase regulatory protein family. PDRP subfamily. +Belongs to the UPF0754 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Present with 704 molecules/cell in log phase SD medium. +Belongs to the UPF0260 family. +Regulates microtubule dynamics in uterine muscle cells. RNAi-mediated knockdown at the L1 larval stage causes a reduction in egg-laying, likely due to a defect in the egg-laying apparatus muscles and in hermaphrodite specific neurons. Belongs to the tubulin--tyrosine ligase family. Although it belongs to the tubulin--tyrosine ligase family, the TTL domain lacks some of the ATP binding sites predicted to be essential for TTL activity (By similarity). Lacks tyrosine ligase activity in vitro (By similarity). Lacks glutamylation activity in vitro (By similarity). +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +Important for reducing fluoride concentration in the cell, thus reducing its toxicity. Belongs to the CrcB (TC 9.B.71) family. +Catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose via an epimerization at carbon 6 of the heptose. ADP-D-glycero-beta-D-manno-heptose = ADP-L-glycero-beta-D-manno-heptose Binds 1 NADP(+) per subunit. Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate: step 4/4. Homopentamer. Contains a large N-terminal NADP-binding domain, and a smaller C-terminal substrate-binding domain. Belongs to the NAD(P)-dependent epimerase/dehydratase family. HldD subfamily. +Omega-conotoxins act at presynaptic membranes, they bind and block voltage-gated calcium channels (Cav). Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). Belongs to the conotoxin O1 superfamily. +Necessary for the succinyl substitution of periplasmic glucans. Could catalyze the transfer of succinyl residues from the cytoplasmic side of the membrane to the nascent glucan backbones on the periplasmic side of the membrane. Glycan metabolism; osmoregulated periplasmic glucan (OPG) biosynthesis. Belongs to the acyltransferase 3 family. OpgC subfamily. +The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins (By similarity). Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits. The coatomer is cytoplasmic or polymerized on the cytoplasmic side of the Golgi, as well as on the vesicles/buds originating from it. Belongs to the COPG family. +One of the proteins required for the normal export of some preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. For 2 proteins (MBP, MalE and PhoA) the substrate is wrapped around the homotetramer, which prevents it from folding (PubMed:27501151). It also specifically binds to its receptor SecA. Its substrates include DegP, FhuA, FkpA, GBP, LamB, MalE (MBP), OmpA, OmpF, OmpT, OmpX, OppA, PhoE, TolB, TolC, YbgF, YcgK, YgiW and YncE (PubMed:16352602). Homotetramer, a dimer of dimers (PubMed:14643199, PubMed:27501151). One homotetramer interacts with 1 SecA dimer. Growth continues, but export of its substrates is blocked (PubMed:16352602, PubMed:16522795). Expression of chaperones DnaK, GroEL/ES, ClpB, and HslU increases (PubMed:16352602). Belongs to the SecB family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Involved in the control of reactive oxygen species levels and the regulation of mitochondrial redox homeostasis (By similarity). Maintains thioredoxin in a reduced state. May play a role in redox-regulated cell signaling. [thioredoxin]-dithiol + NADP(+) = [thioredoxin]-disulfide + H(+) + NADPH Inhibited by 1-chloro-2,4-dinitrobenzene and by zinc, calcium, magnesium and Fe(2+) ions. kcat is 1200 sec(-1) with thioredoxin as substrate. Optimum pH is 7.5. Homodimer. The active site is a redox-active disulfide bond. The selenocysteine residue is also essential for catalytic activity (By similarity). Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Belongs to the bacterial ribosomal protein bS16 family. +Plasma. The reactive center loop (RCL) extends out from the body of the protein and directs binding to the target protease. The protease cleaves the serpin at the reactive site within the RCL, establishing a covalent linkage between the carboxyl group of the serpin reactive site and the serine hydroxyl of the protease. The resulting inactive serpin-protease complex is highly stable (By similarity). N-glycosylated; contains biantennary glycans. Belongs to the serpin family. +6-O-sulfation enzyme which catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to position 6 of the N-sulfoglucosamine residue (GlcNS) of heparan sulfate. Also transfers sulfate to CDSNS-heparin and performs the crucial step modification in the biosynthesis of anticoagulant heparan sulfate (HSact). Critical for normal neuronal development where it may play a role in neuron branching. May also play a role in limb development. May prefer iduronic acid. 3'-phosphoadenylyl sulfate + alpha-D-glucosaminyl-[heparan sulfate](n) = 6-sulfo-alpha-D-glucosaminyl-[heparan sulfate](n) + adenosine 3',5'-bisphosphate + H(+) Inhibited by dithiothreitol and stimulated by protamine. Optimum pH is 6.3. N-glycosylated. Belongs to the sulfotransferase 6 family. +Catalyzes the hydrolysis of N(4)-acetylcytidine (ac4C). H2O + N(4)-acetylcytidine = acetate + cytidine + H(+) H2O + N(4)-acetyl-2'-deoxycytidine = 2'-deoxycytidine + acetate + H(+) H2O + N(4)-acetylcytosine = acetate + cytosine + H(+) Belongs to the N(4)-acetylcytidine amidohydrolase family. +Orphan receptor. Belongs to the G-protein coupled receptor 1 family. +Toxin which activates the particulate form of guanylate cyclase and increases cyclic GMP levels within the host intestinal epithelial cells. Highly toxic. Belongs to the heat-stable enterotoxin family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein, biotin carboxylase and 2 subunits each of ACCase subunit alpha and ACCase plastid-coded subunit beta (accD). Belongs to the AccD/PCCB family. +Probable substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Recognizes type II iodothyronine deiodinase/DIO2. Confers constitutive instability to HIPK2 through proteasomal degradation (By similarity). Protein modification; protein ubiquitination. Interacts with DIO2. Component of the probable ECS(WSB1) E3 ubiquitin-protein ligase complex which contains CUL5, RNF7/RBX2, Elongin BC complex and WSB1. Component of a probable ECS-like E3 ubiquitin-protein ligase complex which contains CUL5, RBX1, Elongin BC complex and WSB1. Interacts with CUL5, RNF7, ELOB and ELOC. Binds to HIPK2 through WD40 repeats (By similarity). The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module in different E3 ubiquitin ligase complexes. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system. ATP + H2O + phosphate(out) = ADP + H(+) + 2 phosphate(in) The complex is composed of two ATP-binding proteins (PstB), two transmembrane proteins (PstC and PstA) and a solute-binding protein (PstS). Belongs to the ABC transporter superfamily. Phosphate importer (TC 3.A.1.7) family. +Catalyzes one of the two ATP producing reactions in the glycolytic pathway via the reversible conversion of 1,3-diphosphoglycerate to 3-phosphoglycerate. In addition to its role as a glycolytic enzyme, it seems that PGK-1 acts as a polymerase alpha cofactor protein (primer recognition protein). May play a role in sperm motility. (2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +Nuclear transcriptional activator of viral gene expression, that is essential for viral transcription from the LTR promoter and replication. Acts as a sequence-specific molecular adapter, directing components of the cellular transcription machinery to the viral RNA to promote processive transcription elongation by the RNA polymerase II (RNA pol II) complex, thereby increasing the level of full-length transcripts. In the absence of Tat, the RNA Pol II generates short or non-processive transcripts that terminate at approximately 60 bp from the initiation site. Tat associates with the CCNT1/cyclin-T1 component of the P-TEFb complex (CDK9 and CCNT1), which promotes RNA chain elongation. This binding increases Tat's affinity for a hairpin structure at the 5'-end of all nascent viral mRNAs referred to as the transactivation responsive RNA element (TAR RNA) and allows Tat/P-TEFb complex to bind cooperatively to TAR RNA. The CDK9 component of P-TEFb and other Tat-activated kinases hyperphosphorylate the C-terminus of RNA Pol II that becomes stabilized and much more processive. Other factors such as HTATSF1/Tat-SF1, SUPT5H/SPT5, and HTATIP2 are also important for Tat's function. Besides its effect on RNA Pol II processivity, Tat induces chromatin remodeling of proviral genes by recruiting the histone acetyltransferases (HATs) CREBBP, EP300 and PCAF to the chromatin. This also contributes to the increase in proviral transcription rate, especially when the provirus integrates in transcriptionally silent region of the host genome. To ensure maximal activation of the LTR, Tat mediates nuclear translocation of NF-kappa-B by interacting with host RELA. Through its interaction with host TBP, Tat may also modulate transcription initiation. Tat can reactivate a latently infected cell by penetrating in it and transactivating its LTR promoter. In the cytoplasm, Tat is thought to act as a translational activator of HIV-1 mRNAs. Extracellular circulating Tat can be endocytosed by surrounding uninfected cells via the binding to several surface receptors such as CD26, CXCR4, heparan sulfate proteoglycans (HSPG) or LDLR. Neurons are rarely infected, but they internalize Tat via their LDLR. Through its interaction with nuclear HATs, Tat is potentially able to control the acetylation-dependent cellular gene expression. Modulates the expression of many cellular genes involved in cell survival, proliferation or in coding for cytokines or cytokine receptors. Tat plays a role in T-cell and neurons apoptosis. Tat induced neurotoxicity and apoptosis probably contribute to neuroAIDS. Circulating Tat also acts as a chemokine-like and/or growth factor-like molecule that binds to specific receptors on the surface of the cells, affecting many cellular pathways. In the vascular system, Tat binds to ITGAV/ITGB3 and ITGA5/ITGB1 integrins dimers at the surface of endothelial cells and competes with bFGF for heparin-binding sites, leading to an excess of soluble bFGF. Interacts with host CCNT1. Associates with the P-TEFb complex composed at least of Tat, P-TEFb (CDK9 and CCNT1), TAR RNA, RNA Pol II. Recruits the HATs CREBBP, TAF1/TFIID, EP300, PCAF and GCN5L2. Interacts with host KAT5/Tip60; this interaction targets the latter to degradation. Interacts with the host deacetylase SIRT1. Interacts with host capping enzyme RNGTT; this interaction stimulates RNGTT. Binds to host KDR, and to the host integrins ITGAV/ITGB3 and ITGA5/ITGB1. Interacts with host KPNB1/importin beta-1 without previous binding to KPNA1/importin alpha-1. Interacts with EIF2AK2. Interacts with host nucleosome assembly protein NAP1L1; this interaction may be required for the transport of Tat within the nucleus, since the two proteins interact at the nuclear rim. Interacts with host C1QBP/SF2P32; this interaction involves lysine-acetylated Tat. Interacts with the host chemokine receptors CCR2, CCR3 and CXCR4. Interacts with host DPP4/CD26; this interaction may trigger an anti-proliferative effect. Interacts with host LDLR. Interacts with the host extracellular matrix metalloproteinase MMP1. Interacts with host PRMT6; this interaction mediates Tat's methylation. Interacts with, and is ubiquitinated by MDM2/Hdm2. Interacts with host PSMC3 and HTATIP2. Interacts with STAB1; this interaction may overcome SATB1-mediated repression of IL2 and IL2RA (interleukin) in T cells by binding to the same domain than HDAC1. Interacts (when acetylated) with human CDK13, thereby increasing HIV-1 mRNA splicing and promoting the production of the doubly spliced HIV-1 protein Nef.Interacts with host TBP; this interaction modulates the activity of transcriptional pre-initiation complex. Interacts with host RELA. Probably localizes to both nuclear and nucleolar compartments. Nuclear localization is mediated through the interaction of the nuclear localization signal with importin KPNB1. Secretion occurs through a Golgi-independent pathway. Tat is released from infected cells to the extracellular space where it remains associated to the cell membrane, or is secreted into the cerebrospinal fluid and sera. Extracellular Tat can be endocytosed by surrounding uninfected cells via binding to several receptors depending on the cell type. The cell attachment site mediates the interaction with ITGAV/ITGB3 and ITGA5/ITGB1 integrins, leading to vascular cell migration and invasion. This interaction also provides endothelial cells with the adhesion signal they require to grow in response to mitogens. The Cys-rich region may bind 2 zinc ions. This region is involved in binding to KAT5. The transactivation domain mediates the interaction with CCNT1, GCN5L2, and MDM2. The Arg-rich RNA-binding region binds the TAR RNA. This region also mediates the nuclear localization through direct binding to KPNB1 and is involved in Tat's transfer across cell membranes (protein transduction). The same region is required for the interaction with EP300, PCAF, EIF2AK2 and KDR. Asymmetrical arginine methylation by host PRMT6 seems to diminish the transactivation capacity of Tat and affects the interaction with host CCNT1. Acetylation by EP300, CREBBP, GCN5L2/GCN5 and PCAF regulates the transactivation activity of Tat. EP300-mediated acetylation of Lys-50 promotes dissociation of Tat from the TAR RNA through the competitive binding to PCAF's bromodomain. In addition, the non-acetylated Tat's N-terminus can also interact with PCAF. PCAF-mediated acetylation of Lys-28 enhances Tat's binding to CCNT1. Lys-50 is deacetylated by SIRT1. Polyubiquitination by host MDM2 does not target Tat to degradation, but activates its transactivation function and fosters interaction with CCNT1 and TAR RNA. Phosphorylated by EIF2AK2 on serine and threonine residues adjacent to the basic region important for TAR RNA binding and function. Phosphorylation of Tat by EIF2AK2 is dependent on the prior activation of EIF2AK2 by dsRNA. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Expressed in the late stage of the infection cycle, when unspliced viral RNAs are exported to the cytoplasm by the viral Rev protein. Belongs to the lentiviruses Tat family. +Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing (By similarity). a 3'-end 3'-phospho-ribonucleotide-RNA + ATP = a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + AMP + diphosphate Belongs to the RNA 3'-terminal cyclase family. Type 1 subfamily. +Does not inhibit strain RB-1 of the fish pathogen, infectious hematopoietic necrosis virus (IHNV). Displays diffuse uniform expression throughout the cytoplasm. By polyinosinic-polycytidylic acid (poly I:C) and viral haemorrhagic septicaemia virus (VHSV) strain 07.71 in muscle, head kidney, spleen and liver. Belongs to the TRAFAC class dynamin-like GTPase superfamily. Dynamin/Fzo/YdjA family. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Catalyzes the NADPH-dependent reduction of beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, the first reductive step in the elongation cycle of fatty acid biosynthesis. a (3R)-hydroxyacyl-[ACP] + NADP(+) = a 3-oxoacyl-[ACP] + H(+) + NADPH Lipid metabolism; fatty acid biosynthesis. Homotetramer. Calcium ions stabilize the structure, and may inhibit FabG activity by obstructing access to the active site. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +ATP + H2O = ADP + H(+) + phosphate Expressed in testis. Wide expression in various cancer tissues and cancer cell lines. Belongs to the DEAD box helicase family. +DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. Belongs to the NAD-dependent DNA ligase family. LigA subfamily. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Central component in the thioredoxin system. Reduces thioredoxins 1 and 2. [thioredoxin]-dithiol + NADP(+) = [thioredoxin]-disulfide + H(+) + NADPH Binds 1 FAD per subunit. Homodimer. The active site is a redox-active disulfide bond. Present with 292000 molecules/cell in log phase SD medium. Belongs to the class-II pyridine nucleotide-disulfide oxidoreductase family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +ATP + D-tagatofuranose 6-phosphate = ADP + D-tagatofuranose 1,6-bisphosphate + H(+) Carbohydrate metabolism; D-tagatose 6-phosphate degradation; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-tagatose 6-phosphate: step 1/2. Belongs to the carbohydrate kinase PfkB family. LacC subfamily. +Acts on phosphatidylinositol (PtdIns) in the first committed step in the production of the second messenger inositol-1,4,5,-trisphosphate. a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + ATP = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate) + ADP + H(+) Activated by Triton X-100, insensitive to inhibition by adenosine and inhibited by wortmannin (By similarity). Isoform 2 is activated by detergents such as Triton X-100 and inhibited by adenosine (PubMed:7961848). The PI4K complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis (PubMed:23229899, PubMed:26571211). Interaction with TMEM150A regulates PtdIns(4)P synthesis (PubMed:25608530). Component of a phosphatidylinositol 4-kinase (PI4K) complex, composed of PI4KA, EFR3 (EFR3A or EFR3B), TTC7 (TTC7A or TTC7B) and FAM126 (FAM126A or FAM126B) (PubMed:23229899, PubMed:24417819, PubMed:26571211, PubMed:34415310). Interacts with TMEM150A; regulating recruitment to the plasma membrane (PubMed:25608530). Interacts with TTC7A (PubMed:34415310). (Microbial infection) Interacts with CHKA/Choline Kinase-alpha; CHKA bridges PI4KA and hepatitis C virus (HCV) non-structural protein 5A (NS5A) and potentiates NS5A-stimulated PI4KA activity, which then facilitates the targeting of the ternary complex to the ER for viral replication. Localization to the plasma membrane is mediated by the PI4K complex and association with EFR3 (EFR3A or EFR3B), TTC7 (TTC7A or TTC7B) and FAM126 (FAM126A or FAM126B) (PubMed:23229899). Localization to the plasma membrane is regulated by TMEM150A (PubMed:25608530). Expressed ubiquitously. Highest levels in placenta and brain. Little or no expression in lung, liver, pancreas, testis or leukocytes. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the PI3/PI4-kinase family. Type III PI4K subfamily. +Gating modifier of Kv2.1/KCNB1 channels. Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 10 (Hwtx-1) family. 28 (Jztx-11) subfamily. +Plays an essential role in viral RNA transcription and replication by forming the heterotrimeric polymerase complex together with PB1 and PB2 subunits. The complex transcribes viral mRNAs by using a unique mechanism called cap-snatching. It consists in the hijacking and cleavage of host capped pre-mRNAs. These short capped RNAs are then used as primers for viral mRNAs. The PB2 subunit is responsible for the binding of the 5' cap of cellular pre-mRNAs which are subsequently cleaved after 10-13 nucleotides by the PA subunit that carries the endonuclease activity. Binds 2 manganese ions per subunit. Influenza RNA polymerase is composed of three subunits: PB1, PB2 and PA. Interacts (via C-terminus) with PB1 (via N-terminus). PB1 and PA are transported in the host nucleus as a complex. Phosphorylated on serines and threonines by host kinases, including human casein kinase II. Belongs to the influenza viruses PA family. +Scaffold protein for the de novo synthesis of iron-sulfur (Fe-S) clusters within mitochondria, which is required for maturation of both mitochondrial and cytoplasmic [2Fe-2S] and [4Fe-4S] proteins. First, a [2Fe-2S] cluster is transiently assembled on the scaffold protein ISU1. In a second step, the cluster is released from ISU1, transferred to a glutaredoxin, followed by the formation of mitochondrial [2Fe-2S] proteins, the synthesis of [4Fe-4S] clusters and their target-specific insertion into the recipient apoproteins. Cluster assembly on ISU1 depends on the function of the cysteine desulfurase complex NFS1-ISD11, which serves as the sulfur donor for cluster synthesis, the iron-binding protein frataxin as the putative iron donor, and the electron transfer chain comprised of ferredoxin reductase and ferredoxin, which receive their electrons from NADH. Binds 1 [2Fe-2S] cluster per subunit. Cofactor biosynthesis; iron-sulfur cluster biosynthesis. Component of the core Fe-S cluster (ISC) assembly machinery. Belongs to the NifU family. +Proposed to be involved in regulation of apoptosis; the exact mechanism may differ between cell types/tissues (PubMed:15082785). May be involved in hypoxia-induced cell death of transformed cells implicating cytochrome C release and caspase activation (such as CASP9) and inducing mitochondrial permeability transition (PubMed:15082785). May be involved in hypoxia-induced cell death of neuronal cells probably by promoting release of AIFM1 from mitochondria to cytoplasm and its translocation to the nucleus; however, the involvement of caspases has been reported conflictingly (By similarity). Interacts with HSP90AB1; HSP90AB1 is essential for FAM162A mitochondrial localization and pro-apoptotic activity (PubMed:16698020). Interacts with VDAC2; the interaction is probably involved in inducing mitochondrial permeability transition (PubMed:15082785). By 17-beta-estradiol. By hypoxia. Belongs to the UPF0389 family. +Potential transporter for phosphate. Belongs to the inorganic phosphate transporter (PiT) (TC 2.A.20) family. +Electrogenic Na(+)-coupled sugar simporter that actively transports D-glucose or D-galactose at the plasma membrane, with a Na(+) to sugar coupling ratio of 2:1. Transporter activity is driven by a transmembrane Na(+) electrochemical gradient set by the Na(+)/K(+) pump (PubMed:22124465, PubMed:28974690). Has a primary role in the transport of dietary monosaccharides from enterocytes to blood. Responsible for the absorption of D-glucose or D-galactose across the apical brush-border membrane of enterocytes, whereas basolateral exit is provided by GLUT2. Additionally, functions as a D-glucose sensor in enteroendocrine cells, triggering the secretion of the incretins GCG and GIP that control food intake and energy homeostasis (PubMed:22124465). Together with SGLT2, functions in reabsorption of D-glucose from glomerular filtrate, playing a nonredundant role in the S3 segment of the proximal tubules (PubMed:22124465). Transports D-glucose into endometrial epithelial cells, controlling glycogen synthesis and nutritional support for the embryo as well as the decidual transformation of endometrium prior to conception (PubMed:28974690). Acts as a water channel enabling passive water transport in response to the osmotic gradient created upon sugar and Na(+) uptake. Has high water conductivity comparable to aquaporins and therefore is expected to play an important role in transepithelial water permeability, especially in the small intestine. D-glucose(out) + 2 Na(+)(out) = D-glucose(in) + 2 Na(+)(in) D-galactose(out) + 2 Na(+)(out) = D-galactose(in) + 2 Na(+)(in) Expressed in enterocytes and enteroendocrine cells of small intestine (at protein level) (PubMed:22124465). Expressed in S3 segments of renal proximal tubules (at protein level) (PubMed:22124465). Expressed in endometrial glandular and epithelial cells (at protein level) (PubMed:28974690). The cholesterol-binding site is formed by transmembrane helices TM1, TM7 and TM13. N-glycosylation is not necessary for the cotransporter function. Mutant mice had significantly lower embryo implantation rate associated with lower litter size (PubMed:28974690). On a standard diet, they developed symptoms of the glucose and galactose malabsorption and died within 2 days after weaning, a phenotype reminiscent of GGM syndrome in humans (PubMed:22124465). Weaned mice survived and were fertile when maintained on a glucose and galactose free diet (PubMed:22124465). Belongs to the sodium:solute symporter (SSF) (TC 2.A.21) family. +Mediates the electroneutral exchange of acylcarnitines (O-acyl-(R)-carnitine or L-acylcarnitine) of different acyl chain lengths (ranging from O-acetyl-(R)-carnitine to long-chain O-acyl-(R)-carnitines) with free carnitine ((R)-carnitine or L-carnitine) across the mitochondrial inner membrane, via a ping-pong mechanism (PubMed:12892634, PubMed:18307102) (Probable). Key player in the mitochondrial oxidation pathway, it translocates the fatty acids in the form of acylcarnitines into the mitochondrial matrix, where the carnitine palmitoyltransferase 2 (CPT-2) activates them to undergo fatty acid beta-oxidation (Probable). Catalyzes the unidirectional transport (uniport) of carnitine at lower rates than the antiport (exchange) (PubMed:18307102). (R)-carnitine(out) + O-acetyl-(R)-carnitine(in) = (R)-carnitine(in) + O-acetyl-(R)-carnitine(out) (R)-carnitine(out) + O-acyl-(R)-carnitine(in) = (R)-carnitine(in) + O-acyl-(R)-carnitine(out) (R)-carnitine(out) + O-propanoyl-(R)-carnitine(in) = (R)-carnitine(in) + O-propanoyl-(R)-carnitine(out) (R)-carnitine(out) + O-hexadecanoyl-(R)-carnitine(in) = (R)-carnitine(in) + O-hexadecanoyl-(R)-carnitine(out) (R)-carnitine(out) + O-octanoyl-(R)-carnitine(in) = (R)-carnitine(in) + O-octanoyl-(R)-carnitine(out) (R)-carnitine(in) = (R)-carnitine(out) The disease is caused by variants affecting the gene represented in this entry. Belongs to the mitochondrial carrier (TC 2.A.29) family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Allosterically activated by GTP. Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Belongs to the UPF0758 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Interacts with nop5. Component of box C/D small ribonucleoprotein (sRNP) particles that contain rpl7ae, FlpA and nop5, plus a guide RNA. Belongs to the methyltransferase superfamily. Fibrillarin family. +Involved in the resistance (detoxification) of the fungal toxin fusaric acid. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. Binds 3 Zn(2+) ions. Belongs to the AP endonuclease 2 family. +With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS5 family. +Belongs to the nematode receptor-like protein srd family. +Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism. adenine + H(+) + H2O = hypoxanthine + NH4(+) Binds 1 zinc ion per subunit. Belongs to the metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. Adenine deaminase type 2 subfamily. +Acyl-CoA dehydrogenase, that exhibits maximal activity towards saturated C22-CoA. Probably participates in beta-oxydation and energy production but could also play a role in the metabolism of specific fatty acids to control fatty acids composition of cellular lipids in brain. a 2,3-saturated acyl-CoA + H(+) + oxidized [electron-transfer flavoprotein] = a (2E)-enoyl-CoA + reduced [electron-transfer flavoprotein] docosanoyl-CoA + H(+) + oxidized [electron-transfer flavoprotein] = (2E)-docosenoyl-CoA + reduced [electron-transfer flavoprotein] H(+) + oxidized [electron-transfer flavoprotein] + tetracosanoyl-CoA = (2E)-tetracosenoyl-CoA + reduced [electron-transfer flavoprotein] eicosanoyl-CoA + H(+) + oxidized [electron-transfer flavoprotein] = (2E)-eicosenoyl-CoA + reduced [electron-transfer flavoprotein] H(+) + hexacosanoyl-CoA + oxidized [electron-transfer flavoprotein] = (2E)-hexacosenoyl-CoA + reduced [electron-transfer flavoprotein] H(+) + oxidized [electron-transfer flavoprotein] + tricosanoyl-CoA = (2E)-tricosenoyl-CoA + reduced [electron-transfer flavoprotein] Lipid metabolism; fatty acid beta-oxidation. Homodimer. Belongs to the acyl-CoA dehydrogenase family. +Non-catalytic subunit of the queuine tRNA-ribosyltransferase (TGT) that catalyzes the base-exchange of a guanine (G) residue with queuine (Q) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine). Binds 1 zinc ion per subunit. Heterodimer of a catalytic subunit and an accessory subunit. Belongs to the queuine tRNA-ribosyltransferase family. QTRT2 subfamily. +Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and/or repair of Fe-S clusters in biosynthetic enzymes. Belongs to the Fe(2+)-trafficking protein family. +Bifunctional enzyme which can phosphorylate or dephosphorylate isocitrate dehydrogenase (IDH) on a specific serine residue. This is a regulatory mechanism which enables bacteria to bypass the Krebs cycle via the glyoxylate shunt in response to the source of carbon. When bacteria are grown on glucose, IDH is fully active and unphosphorylated, but when grown on acetate or ethanol, the activity of IDH declines drastically concomitant with its phosphorylation. ATP + L-seryl-[isocitrate dehydrogenase] = ADP + H(+) + O-phospho-L-seryl-[isocitrate dehydrogenase] Belongs to the AceK family. +Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls. H2O + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-2,6-diaminoheptanedioate + succinate Binds 2 Zn(2+) or Co(2+) ions per subunit. Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route): step 3/3. Homodimer. Belongs to the peptidase M20A family. DapE subfamily. +IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. Monomer. Belongs to the IF-3 family. +Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+) Binds 1 dipyrromethane group covalently. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. Monomer. The porphobilinogen subunits are added to the dipyrromethane group. Belongs to the HMBS family. +May bind zinc and other divalent cations and recruit them to vesicular organelles. Glutamatergic synaptic vesicles. Specifically expressed in brain. Mainly expressed in the glutaminergic neuron subpopulations. Belongs to the TMEM163 family. +ATP + thymidine = ADP + dTMP + H(+) Homotetramer. Belongs to the thymidine kinase family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 1 subfamily. +A cytochrome P450 monooxygenase that selectively catalyzes the epoxidation of the last double bond of the arachidonoyl moiety of anandamide, potentially modulating endocannabinoid signaling. Has no hydroxylase activity toward various fatty acids, steroids and prostaglandins. Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (CPR; NADPH-ferrihemoprotein reductase). N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H(+) + H2O + N-(14,15-epoxy-5Z,8Z,11Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase] Expressed in brain and aorta. In the brain, expressed in the Purkinje cells of the cerebellum, pyramidal neurons in the dentate gyrus of the hippocampus, cortical forebrain neurons and those of brain stem nuclei (at protein level). In addition to neurons, also expressed in cerebral vascular endothelial cells (at protein level). Also expressed in epithelial cells of the choroid plexus (at protein level). Hardly detectable in heart, lung, kidney and spleen. Belongs to the cytochrome P450 family. +The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpA family. +Involved in chromosome condensation, segregation and cell cycle progression. May participate in facilitating chromosome segregation by condensation DNA from both sides of a centrally located replisome during cell division. Probably acts via its interaction with MukB and MukF. Interacts, and probably forms a ternary complex, with MukF and MukB. The complex formation is stimulated by calcium or magnesium. Restricted to the nucleoid region. Belongs to the MukE family. +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Part of the gene cluster that mediates the biosynthesis of squalestatin S1 (SQS1, also known as zaragozic acid A), a heavily oxidized fungal polyketide that offers potent cholesterol lowering activity by targeting squalene synthase (SS) (PubMed:28605916). SQS1 is composed of a 2,8-dioxobicyclic[3.2.1]octane-3,4,5-tricarboxyclic acid core that is connected to two lipophilic polyketide arms (PubMed:28605916). These initial steps feature the priming of an unusual benzoic acid starter unit onto the highly reducing polyketide synthase clz14, followed by oxaloacetate extension and product release to generate a tricarboxylic acid containing product (PubMed:28605916). The phenylalanine ammonia lyase (PAL) clz10 and the acyl-CoA ligase clz12 are involved in transforming phenylalanine into benzoyl-CoA (PubMed:28605916). The citrate synthase-like protein clz17 is involved in connecting the C-alpha-carbons of the hexaketide chain and oxaloacetate to afford the tricarboxylic acid unit (PubMed:28605916). The potential hydrolytic enzymes, clz11 and clz13, are in close proximity to pks2 and may participate in product release (PubMed:28605916). On the other side, the tetraketide arm is synthesized by a the squalestatin tetraketide synthase clz2 and enzymatically esterified to the core in the last biosynthetic step, by the acetyltransferase clz6 (By similarity). The biosynthesis of the tetraketide must involve 3 rounds of chain extension (By similarity). After the first and second rounds methyl-transfer occurs, and in all rounds of extension the ketoreductase and dehydratase are active (By similarity). The enoyl reductase and C-MeT of clz2 are not active in the final round of extension (By similarity). The acetyltransferase clz6 appears to have a broad substrate selectivity for its acyl CoA substrate, allowing the in vitro synthesis of novel squalestatins (By similarity). The biosynthesis of SQS1 requires several oxidative steps likely performed by oxidoreductases clz3, clz15 and clz16 (Probable). Finally, in support of the identification of the cluster as being responsible for SQS1 production, the cluster contains a gene encoding a putative squalene synthase (SS) clz20, suggesting a likely mechanism for self-resistance (Probable). Secondary metabolite biosynthesis. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl-tRNA(Gln) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Voltage-gated potassium channel that mediates transmembrane potassium transport in excitable membranes, primarily in the brain. Contributes to the regulation of the fast action potential repolarization and in sustained high-frequency firing in neurons of the central nervous system. Homotetramer channels mediate delayed-rectifier voltage-dependent potassium currents that activate rapidly at high-threshold voltages and inactivate slowly. Forms tetrameric channels through which potassium ions pass in accordance with their electrochemical gradient. The channel alternates between opened and closed conformations in response to the voltage difference across the membrane (PubMed:15709110). Can form functional homotetrameric and heterotetrameric channels that contain variable proportions of KCNC1, and possibly other family members as well; channel properties depend on the type of alpha subunits that are part of the channel. Channel properties may be modulated either by the association with ancillary subunits, such as KCNE1, KCNE2 or KCNE3 or indirectly by nitric oxide (NO) through a cGMP- and PKG-mediated signaling cascade, slowing channel activation and deactivation of delayed rectifier potassium channels (By similarity). Contributes to fire sustained trains of very brief action potentials at high frequency in retinal ganglion cells, thalamocortical and suprachiasmatic nucleus (SCN) neurons and in hippocampal and neocortical interneurons (PubMed:15709110). Sustained maximal action potential firing frequency in inhibitory hippocampal interneurons is negatively modulated by histamine H2 receptor activation in a cAMP- and protein kinase (PKA) phosphorylation-dependent manner. Plays a role in maintaining the fidelity of synaptic transmission in neocortical GABAergic interneurons by generating action potential (AP) repolarization at nerve terminals, thus reducing spike-evoked calcium influx and GABA neurotransmitter release. Required for long-range synchronization of gamma oscillations over distance in the neocortex. Contributes to the modulation of the circadian rhythm of spontaneous action potential firing in suprachiasmatic nucleus (SCN) neurons in a light-dependent manner (By similarity). Inhibited by Stichodactyla helianthus peptide ShK (PubMed:15709110). Inhibited by millimolar levels of tetraethylammonium (TEA). Contrary to other channels, inhibited only by millimolar levels of 4-aminopyridine (4-AP) (By similarity). Homotetrameric channels expressed in xenopus oocytes or in mammalian non-neuronal cells display delayed-rectifier voltage-dependent potassium currents, that are rapidly activated during membrane depolarization, i.e within a risetime of a few msec. After that, inactivates very slowly, i.e within about >800 msec. Their activation requires a threshold potential at about -10 mV, with a midpoint activation at about 12.1 mV and a steepness parameter of about 8.4 mV. The voltage-dependence of activation and inactivation and other channel characteristics vary depending on the experimental conditions, the expression system, the presence or absence of ancillary subunits and post-translational modifications. Homotetramer and heterotetramer with other channel-forming alpha subunits, such as KCNC1. Interacts with KCNC1. Homotetramer or heterotetramer channel activity is regulated by association with modulating ancillary subunits such as KCNE1, KCNE2 and KCNE3, creating a functionally diverse range of channel complexes. Interacts with KCNE1, KCNE2 and KCNE3. Colocalizes with parvalbumin in globus pallidus neurons. Localizes in thalamocortical axons and synapses. Localizes on the surface of cell somata, proximal dendrites and axonal membranes. Also detected throughout the neuropil. Localized in starburst cell somata and proximal dendrite processes. Colocalized with GABA in presynaptic terminals. Clustered in patches in somatic and proximal dendritic membrane as well as in axons and presnypatic terminals of GABAergic interneurons; some of these patches are found near postsynaptic sites. The transmembrane segment S4 functions as voltage-sensor and is characterized by a series of positively charged amino acids at every third position. Channel opening and closing is effected by a conformation change that affects the position and orientation of the voltage-sensor paddle formed by S3 and S4 within the membrane. A transmembrane electric field that is positive inside would push the positively charged S4 segment outwards, thereby opening the pore, while a field that is negative inside would pull the S4 segment inwards and close the pore. Changes in the position and orientation of S4 are then transmitted to the activation gate formed by the inner helix bundle via the S4-S5 linker region. Phosphorylated by PKA in cortical synaptosomes. cAMP-dependent phosphorylation inhibits channel activity (By similarity). Histamine H2 receptor- and PKA-induced phosphorylation extends action potential spike duration, reduces action potential spike amplitude, sustains maximum firing frequency in hippocampal interneurons; also reduces the incidence of high-frequency oscillations in hippocampal CA3 pyramidal cell layers. A chromosomal aberration involving KCNC2 has been found in a mother and her two children with varying degrees of neurodevelopmental delay and cerebellar ataxia. One child also exhibits episodes of unresponsiveness suggestive of absence seizures and facial dysmorphism. Deletion at 12q21.1 deletes exons 3-5 of KCNC2. Belongs to the potassium channel family. C (Shaw) (TC 1.A.1.2) subfamily. Kv3.2/KCNC2 sub-subfamily. +Belongs to the bacterial ribosomal protein bL34 family. +Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Binds 2 divalent ions per subunit. Binds 1 potassium ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Homotetramer; dimer of dimers. Belongs to the AdoMet synthase family. +Pore-forming subunit of a potassium efflux system that confers protection against electrophiles. Catalyzes K(+)/H(+) antiport. Interacts with the regulatory subunit KefG. Belongs to the monovalent cation:proton antiporter 2 (CPA2) transporter (TC 2.A.37) family. KefB subfamily. +Part of the ABC transporter complex CcmAB involved in the biogenesis of c-type cytochromes; once thought to export heme, this seems not to be the case, but its exact role is uncertain. Responsible for energy coupling to the transport system. ATP + H2O + heme b(in) = ADP + H(+) + heme b(out) + phosphate The complex is composed of two ATP-binding proteins (CcmA) and two transmembrane proteins (CcmB). Belongs to the ABC transporter superfamily. CcmA exporter (TC 3.A.1.107) family. +Major acute phase reactant. Apolipoprotein of the HDL complex. Expressed by the liver; secreted in plasma. Belongs to the SAA family. +Endoplasmic reticulum (ER) protein that functions as a co-chaperone for BIP1 during ER stress (PubMed:26487566). Might be specifically involved in the refolding of N-glycosylated proteins (PubMed:26487566). Interacts with the ER chaperone BIP1. Expression is induced by the unfolded protein response (UPR) and controled by the UPR-specific transcription factor CIP1. The TPR repeats mediate interaction with unfolded polypeptides and the J-domain is essential to stimulate the ATPase activity of the chaperone and to increase its substrate affinity during the folding cycle. Leads to hypersensitivity to endoplasmic reticulum (ER) stress caused by the N-glycosylation inhibitor tunicamycin, but only to slight reduction of virulence (PubMed:26487566). Severely affects growth and displays an altered morphology, when the calnexin CNE1 is also deleted (PubMed:26487566). +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Beta-amylase activity. Major cytosolic beta-amylase isoform in rosette leaves and inflorescences stems. Hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains. Present in the continuous phloem cytoplasm. Detected in phloem sieve elements. Circadian-regulated, with a peak in expression just before the light period in short day conditions. Almost complete loss of beta-amylase activity in rosette leaves and inflorescences (stems). Belongs to the glycosyl hydrolase 14 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. Participates in UV-tolerance of Synechocystis PCC 6803. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. 2-3 fold induced by UV light. No visible phenotype; cells are more sensitive to UV-C light, H(2)O(2), CdSO(4), SeO(3) and SeO(4). This bacterium is considerably more resistant to UV and gamma irradiation than E.coli; the E.coli-like SOS regulon model is not an appropriate model for DNA repair in this cyanobacterium. Belongs to the RuvB family. +Peroxisomal 2-OH acyl-CoA lyase involved in the cleavage (C1 removal) reaction in the fatty acid alpha-oxydation in a thiamine pyrophosphate (TPP)-dependent manner (PubMed:28289220, PubMed:21708296, PubMed:10468558). Involved in the degradation of 3-methyl-branched fatty acids like phytanic acid and the shortening of 2-hydroxy long-chain fatty acids (PubMed:28289220, PubMed:21708296, PubMed:10468558). Plays a significant role in the biosynthesis of heptadecanal in the liver (By similarity). a 2-hydroxy-3-methyl fatty acyl-CoA = a 2-methyl-branched fatty aldehyde + formyl-CoA an (R)-2-hydroxy-long-chain-fatty acyl-CoA = a long-chain fatty aldehyde + formyl-CoA 2-hydroxy-3-methylhexadecanoyl-CoA = 2-methylpentadecanal + formyl-CoA 2-hydroxyoctadecanoyl-CoA = formyl-CoA + heptadecanal 2-hydroxyphytanoyl-CoA = 2,6,10,14-tetramethylpentadecanal + formyl-CoA Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Lipid metabolism; fatty acid metabolism. Homotetramer. Widely expressed. Belongs to the TPP enzyme family. Extended N-terminus. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +(6S)-5,6,7,8-tetrahydrofolate + ATP + formate = (6S)-10-formyltetrahydrofolate + ADP + phosphate One-carbon metabolism; tetrahydrofolate interconversion. Belongs to the formate--tetrahydrofolate ligase family. +Catalyzes the transfer of the AMP portion of ATP to flavin mononucleotide (FMN) to produce flavin adenine dinucleotide (FAD) coenzyme. ATP + FMN + H(+) = diphosphate + FAD Cofactor biosynthesis; FAD biosynthesis; FAD from FMN: step 1/1. Homodimer. Belongs to the archaeal FAD synthase family. +The light-harvesting complex (LHC) functions as a light receptor, it captures and delivers excitation energy to photosystems with which it is closely associated. May channel protons produced in the catalytic Mn center of water oxidation into the thylakoid lumen. Binds at least 14 chlorophylls (8 Chl-a and 6 Chl-b) and carotenoids such as lutein and neoxanthin. The LHC complex consists of chlorophyll a-b binding proteins. The N-terminus of the protein extends into the stroma where it is involved with adhesion of granal membranes and post-translational modifications; both are believed to mediate the distribution of excitation energy between photosystems I and II. Photoregulated by reversible phosphorylation of its threonine residues. Belongs to the light-harvesting chlorophyll a/b-binding (LHC) protein family. +Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin. di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available. Belongs to the UppP family. +Transcriptional activator. Belongs to the LBH family. +Required for activity of HDA1 histone deacetylase complex. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Heterodimer with HDA3. Component of the HDA1 histone deacetylase complex composed of at least one HDA1 homodimer and one HDA2/HDA3 heterodimer. Interacts with HDA1 and HDA3. Present with 1500 molecules/cell in log phase SD medium. Belongs to the HDA2/3 family. HDA2 subfamily. +Required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis. PQQ is probably formed by cross-linking a specific glutamate to a specific tyrosine residue and excising these residues from the peptide (By similarity). Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. Belongs to the PqqA family. +Catalyzes the ATP-dependent phosphorylation of N-acetyl-L-glutamate. ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamyl 5-phosphate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 2/4. Belongs to the acetylglutamate kinase family. ArgB subfamily. +H(+) + NADP(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADPH + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Homodimer. Belongs to the ferredoxin--NADP reductase type 2 family. +Confers resistance to puromycin, tosufloxacin and norfloxacin. Expression is dependent on the growth phase and decreases in the late log phase. Belongs to the major facilitator superfamily. EmrB family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids. Binds 2 magnesium ions per subunit. Homodimer. Belongs to the UPP synthase family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +Involved in the catabolism of quinolinic acid (QA). CO2 + diphosphate + nicotinate beta-D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate Activity toward QA is slightly repressed by phosphoribosylpyrophosphate (PRPP) in both a competitive and a non-competitive manner (PubMed:17868694). Competitively inhibited by phthalic acid (PHT) (PubMed:24038671). Cofactor biosynthesis; NAD(+) biosynthesis; nicotinate D-ribonucleotide from quinolinate: step 1/1. Hexamer formed by 3 homodimers. Belongs to the NadC/ModD family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) Expressed by the venom gland. Belongs to the phospholipase A2 family. Group II subfamily. D49 sub-subfamily. +Aquaporins facilitate the transport of water and small neutral solutes across cell membranes. Expressed in leaves and at lower levels in roots and anthers. Aquaporins contain two tandem repeats each containing three membrane-spanning domains and a pore-forming loop with the signature motif Asn-Pro-Ala (NPA). Belongs to the MIP/aquaporin (TC 1.A.8) family. NIP (TC 1.A.8.12) subfamily. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Acts as a regulatory subunit for serine/threonine-protein phosphatase 2A (PP2A) modulating its activity or substrate specificity, probably by inducing a conformational change in the catalytic subunit, a proposed direct target of the PPIase. Can reactivate inactive phosphatase PP2A-phosphatase methylesterase complexes (PP2A(i)) in presence of ATP and Mg(2+). Reversibly stimulates the variable phosphotyrosyl phosphatase activity of PP2A core heterodimer PP2A(D) in presence of ATP and Mg(2+) (in vitro). The phosphotyrosyl phosphatase activity is dependent of an ATPase activity of the PP2A(D):PPP2R4 complex. Is involved in apoptosis; the function appears to be independent from PP2A (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Associates with the serine/threonine-protein phosphatase 2A PP2A(D) heterodimeric core enzyme, composed of a 36 kDa catalytic subunit (subunit C) and a 65 kDa constant regulatory subunit (PR65 or subunit A). Interacts with PPP2CB. Widely expressed. Belongs to the PTPA-type PPIase family. +Chemotactic activity for neutrophils and lymphocytes. Binds to heparin. Plasma serum. Belongs to the intercrine beta (chemokine CC) family. +Involved in pinching off the separated nuclei at the cleavage furrow and in cytokinesis. Required for mitotic integrity and maintenance of chromosomal stability. Protects cells against mitotic errors, centrosomal amplification, micronucleus formation and aneuploidy. Plays a key role of midbody function involving abscission of the daughter cells during cytokinesis and appropriate chromosomal and nuclear segregation into the daughter cells. In mitotic cells, concentrates in the midbody of the cytoplasmic bridge linking daughter cells as they are about to separate during cytokinesis. +Catalyzes the rearrangement of 1-deoxy-D-xylulose 5-phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S. 1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + [sulfur-carrier protein ThiS]-C-terminal Gly-Gly + 2 H(+) + 2 H2O Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homotetramer. Forms heterodimers with either ThiH or ThiS. Belongs to the ThiG family. +Agglutinates erythrocytes. Belongs to the peptidase C25 family. +Belongs to the UPF0352 family. +Seems to promote the survival of visceral and proprioceptive sensory neurons. Belongs to the NGF-beta family. +Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. The EJC marks the position of the exon-exon junction in the mature mRNA for the gene expression machinery and the core components remain bound to spliced mRNAs throughout all stages of mRNA metabolism thereby influencing downstream processes including nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD) (By similarity). Part of the EJC core complex that contains casc3, eif4a3, magoh and rbm8a. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRNA. Belongs to the mago nashi family. +Involved in the synthesis of meso-diaminopimelate (m-DAP or DL-DAP), required for both lysine and peptidoglycan biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate. (2S,6S)-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O + L-glutamate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route): step 1/1. Homodimer. Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. LL-diaminopimelate aminotransferase subfamily. +Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a lipid X + a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a lipid A disaccharide + H(+) + UDP Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Belongs to the LpxB family. +Belongs to the UPF0250 family. +Catalyzes the GTP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A (CoA). 3'-dephospho-CoA + GTP = CoA + GDP + H(+) Cofactor biosynthesis; coenzyme A biosynthesis. Belongs to the GTP-dependent DPCK family. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Small GTPase which cycles between active GTP-bound and inactive GDP-bound states. In its active state, binds to a variety of effector proteins to regulate homeostasis of late endocytic pathway, including endosomal positioning, maturation and secretion. Plays a role in cytotoxic granule exocytosis in lymphocytes. Required for both granule maturation and granule docking and priming at the immunologic synapse. GTP + H2O = GDP + H(+) + phosphate Regulated by guanine nucleotide exchange factors (GEFs) which promote the exchange of bound GDP for free GTP, GTPase activating proteins (GAPs) which increase the GTP hydrolysis activity, and GDP dissociation inhibitors which inhibit the dissociation of the nucleotide from the GTPase. Activated by GEFs such as DENND10. Binds SYTL1, SLAC2B, MYRIP, SYTL3, SYTL4 and SYTL5. Interacts with RPH3A and RPH3A (By similarity). Binds MLPH and SYTL2. Interacts with UNC13D. Does not interact with the BLOC-3 complex (heterodimer of HPS1 and HPS4) (By similarity). Interacts (GDP-bound form preferentially) with DENND10 (By similarity). Identified by mass spectrometry in melanosome fractions from stage I to stage IV. Localizes to endosomal exocytic vesicles. Belongs to the small GTPase superfamily. Rab family. +DNA-dependent ATPase and 5'-3' DNA helicase. ATP + H2O = ADP + H(+) + phosphate Binds 1 [4Fe-4S] cluster. Belongs to the helicase family. DinG subfamily. Type 1 sub-subfamily. +acetyl-CoA + L-lysyl-[protein] = CoA + H(+) + N(6)-acetyl-L-lysyl-[protein] Belongs to the HAT1 family. +May subvert the host innate immune response by interacting with host IL1B and interfering with its function. Interacts with host IL1B. Expressed in the early phase of the viral replicative cycle. Belongs to the asfivirus L83L family. +Catalyzes the dehydration of methylthioribulose-1-phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P). S-methyl-5-thio-D-ribulose 1-phosphate = 5-methylsulfanyl-2,3-dioxopentyl phosphate + H2O Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 2/6. Homotetramer. Belongs to the aldolase class II family. MtnB subfamily. +Belongs to the UPF0342 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Essential for tRNA synthesis. The RPC53/RPC4-RPC37/RPC5 subcomplex is required for terminator recognition and reinitiation. Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits. Interacts with RPC37/RPC5. RPC53/RPC4, RPC37/RPC5 and RPC11/RPC10 probably form a Pol III subcomplex. Present with 998 molecules/cell in log phase SD medium. Belongs to the eukaryotic RPC4/POLR3D RNA polymerase subunit family. +Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS11 family. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Component of the type II secretion system required for the energy-dependent secretion of extracellular factors such as proteases and toxins from the periplasm (By similarity). Part of the pseudopilus tip complex that is critical for the recognition and binding of secretion substrates (PubMed:18241884, PubMed:24316251). Type II secretion is composed of four main components: the outer membrane complex, the inner membrane complex, the cytoplasmic secretion ATPase and the periplasm-spanning pseudopilus. Interacts with core component EpsG. Cleaved by prepilin peptidase. Methylated by prepilin peptidase at the amino group of the N-terminal phenylalanine once the leader sequence is cleaved by prepilin peptidase. Belongs to the GSP H family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the cytochrome b family. PetD subfamily. +Involved in nonsense-mediated mRNA decay (NMD) by acting as a bridge between the mRNA decapping complex and the NMD machinery. May act by targeting the NMD machinery to the P-body and recruiting the decapping machinery to aberrant mRNAs. Required for upf1/rent1 localization to the P-body. Also acts as a nuclear receptor coactivator (By similarity). Belongs to the PNRC family. PNRC2 subfamily. +ATP + L-aspartate + L-citrulline = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 2/3. Homotetramer. Belongs to the argininosuccinate synthase family. Type 1 subfamily. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +Kills a number of Gram-positive bacteria. Acts at the level of cell wall biosynthesis by interfering with bacterial peptidoglycan biosynthesis. Specifically inhibits the conversion of the lipid II intermediate into polymeric nascent glycan strands by transglycosylation. May interact with the peptidoglycan precursor rather than with the enzyme. Maturation of lantibiotics involves the enzymatic conversion of Thr, and Ser into dehydrated AA and the formation of thioether bonds with cysteine. The carboxy-terminal beta-methyllanthionine undergoes decarboxylation. This is followed by membrane translocation and cleavage of the modified precursor. Belongs to the type B lantibiotic family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the PetM family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase epsilon chain family. Truncated N-terminus. Truncated N-terminus. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Acts as a negative regulator of transcription. Highly expressed in developing brain and spinal cord. +Belongs to the bacterial ribosomal protein bL32 family. +Structural protein that stabilizes microvessels and muscle cells, both in heart and in skeletal muscle. Restin potently inhibits angiogenesis. Trimer; disulfide-linked. Interacts moderately with EFEMP2. Expressed predominantly in internal organs such as adrenal gland, pancreas and kidney. Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains. O-glycosylated; with core 1 or possibly core 8 glycans. An N-terminal peptide contains chondroitin sulfate. Belongs to the multiplexin collagen family. The name restin has also been used for CAP-Gly domain-containing linker protein 1 the product of the CLIP1 gene. +Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both independently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. Involved in polyadenylation of mRNA precursors. Connects PAF1C to Wnt signaling (By similarity). Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61 (By similarity). The PAF1 complex interacts with PHF5A (By similarity). Interacts with TCEA1, SUPT5H and CTNNB1 (By similarity). Interacts with SETD5 (By similarity). Belongs to the LEO1 family. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Involved in regulation of pyruvate dehydrogenase activity. H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 magnesium or manganese ions per subunit. Belongs to the PP2C family. +A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis. Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes. Belongs to the type II topoisomerase GyrA/ParC subunit family. Truncated N-terminus. +Part of the 30S ribosomal subunit. Belongs to the eukaryotic ribosomal protein eS8 family. +Transcriptional regulator that may regulate the expression of the loline biosynthesis cluster 1, one of the 2 clusters involved in the biosynthesis of loline alkaloids, potent insecticidal agents composed of a pyrrolizidine ring system and an uncommon ether bridge linking carbons 2 and 7 (PubMed:15654104). Expression is induced in loline alkaloid-producing cultures as well as in planta (PubMed:15654104). +Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H(+) + UDP L-threonyl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H(+) + UDP Protein modification; protein glycosylation. There are two conserved domains in the glycosyltransferase region: the N-terminal domain (domain A, also called GT1 motif), which is probably involved in manganese coordination and substrate binding and the C-terminal domain (domain B, also called Gal/GalNAc-T motif), which is probably involved in catalytic reaction and UDP-Gal binding. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. Belongs to the glycosyltransferase 2 family. GalNAc-T subfamily. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity (By similarity). Belongs to the DNA mismatch repair MutS family. +Catalyzes cross-linking of the peptidoglycan cell wall at the division septum (By similarity). Binds penicillin (PubMed:20580675). Preferential cleavage: (Ac)2-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine. Cell wall biogenesis; peptidoglycan biosynthesis. Mainly produced during exponential phase of growth. Belongs to the transpeptidase family. FtsI subfamily. +Methionine-sulfoxide reductase that specifically reduces methionine (R)-sulfoxide back to methionine (PubMed:11929995, PubMed:14699060, PubMed:23911929, PubMed:20605785). While in many cases, methionine oxidation is the result of random oxidation following oxidative stress, methionine oxidation is also a post-translational modification that takes place on specific residue (PubMed:14699060, PubMed:20605785). Acts as a regulator of actin assembly by reducing methionine (R)-sulfoxide mediated by MICALs (MICAL1, MICAL2 or MICAL3) on actin, thereby promoting filament repolymerization (PubMed:23911929). Plays a role in innate immunity by reducing oxidized actin, leading to actin repolymerization in macrophages (PubMed:23911929). [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(R)-S-oxide-[protein] [thioredoxin]-disulfide + H2O + L-methionine = [thioredoxin]-dithiol + L-methionine (R)-S-oxide Binds 1 zinc ion per subunit. Truncated MSRB1/SEPX1 proteins produced by failed UGA/Sec decoding are ubiquitinated by the CRL2(FEM1C) E3 ubiquitin-protein ligase complex. Belongs to the MsrB Met sulfoxide reductase family. +Regulates arginine biosynthesis genes. Amino-acid biosynthesis; L-arginine biosynthesis [regulation]. Belongs to the ArgR family. +Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetE route): step 1/1. Belongs to the vitamin-B12 independent methionine synthase family. +Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons. Belongs to the HrcA family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate. AH2 + GTP + S-adenosyl-L-methionine = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + A + H(+) + L-methionine Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate. Cofactor biosynthesis; molybdopterin biosynthesis. Monomer and homodimer. Belongs to the radical SAM superfamily. MoaA family. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +Depressant insect beta-toxins cause a transient contraction paralysis followed by a slow flaccid paralysis. They bind voltage-independently at site-4 of sodium channels (Nav) and shift the voltage of activation toward more negative potentials thereby affecting sodium channel activation and promoting spontaneous and repetitive firing. This toxin is active only on insects. Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). LD(50) is 0.1 mg/kg in Blattella germanica. Belongs to the long (4 C-C) scorpion toxin superfamily. Sodium channel inhibitor family. Beta subfamily. +H2O + L-arginine = L-citrulline + NH4(+) Amino-acid degradation; L-arginine degradation via ADI pathway; carbamoyl phosphate from L-arginine: step 1/2. Belongs to the arginine deiminase family. +Thiolesterase that catalyzes the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid. an S-(2-hydroxyacyl)glutathione + H2O = a 2-hydroxy carboxylate + glutathione + H(+) Binds 2 Zn(2+) ions per subunit. Secondary metabolite metabolism; methylglyoxal degradation; (R)-lactate from methylglyoxal: step 2/2. Monomer. Belongs to the metallo-beta-lactamase superfamily. Glyoxalase II family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +Modifies, by uridylylation and deuridylylation, the PII regulatory proteins (GlnB and homologs), in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen assimilation and metabolism. [protein-PII]-L-tyrosine + UTP = [protein-PII]-uridylyl-L-tyrosine + diphosphate [protein-PII]-uridylyl-L-tyrosine + H2O = [protein-PII]-L-tyrosine + H(+) + UMP Uridylyltransferase (UTase) activity is inhibited by glutamine, while glutamine activates uridylyl-removing (UR) activity. Has four distinct domains: an N-terminal nucleotidyltransferase (NT) domain responsible for UTase activity, a central HD domain that encodes UR activity, and two C-terminal ACT domains that seem to have a role in glutamine sensing. Belongs to the GlnD family. +Seed lectin. Homotetramer. Expressed in seed. Mostly found in non-glycosylated form. Belongs to the leguminous lectin family. +Part of a heterotetrameric complex that catalyzes the two-step biosynthesis of anthranilate, an intermediate in the biosynthesis of L-tryptophan. In the first step, the glutamine-binding beta subunit (TrpG) of anthranilate synthase (AS) provides the glutamine amidotransferase activity which generates ammonia as a substrate that, along with chorismate, is used in the second step, catalyzed by the large alpha subunit of AS (TrpE) to produce anthranilate. In the absence of TrpG, TrpE can synthesize anthranilate directly from chorismate and high concentrations of ammonia (By similarity). chorismate + L-glutamine = anthranilate + H(+) + L-glutamate + pyruvate Binds 1 Mg(2+) ion per subunit. Feedback inhibited by tryptophan. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 1/5. Heterotetramer consisting of two non-identical subunits: a beta subunit (TrpG) and a large alpha subunit (TrpE). Belongs to the anthranilate synthase component I family. +Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. This function is generally fulfilled by the C-terminal part of HisG, which is missing in some bacteria such as this one. Belongs to the class-II aminoacyl-tRNA synthetase family. HisZ subfamily. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP. GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 4/4. Belongs to the class I fructose-bisphosphate aldolase family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged tRNA(Thr) via its editing domain, at the post-transfer stage. ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Homodimer. ISGylated. Belongs to the class-II aminoacyl-tRNA synthetase family. +Plays an essential role in cytoplasmic secondary envelopment during viral egress. Interacts with the capsid via the large tegument protein/LTP and participates in its transport to the host trans-Golgi network (TGN) where secondary envelopment occurs. Modulates tegumentation and capsid accumulation at the viral assembly complex. Interacts (via C-terminus) with the large tegument protein/LTP (via N-terminus). Belongs to the herpesviridae inner tegument protein family. +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Binds 2 nickel ions per subunit. Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Carboxylation allows a single lysine to coordinate two nickel ions. Belongs to the metallo-dependent hydrolases superfamily. Urease alpha subunit family. +Positively regulates the activity of the minus-end directed microtubule motor protein dynein. Plays a central role in positioning the mitotic spindle at the bud neck during cell division. Targets cytoplasmic dynein to microtubule plus ends, thereby promoting dynein-mediated microtubule sliding along the bud cortex and consequently the movement of the mitotic spindle to the bud neck. Self-associates. Interacts with NDL1 and dynein. Localizes to the plus ends of microtubules and the mitotic spindle poles. Dimerization mediated by the LisH domain may be required to activate dynein. Belongs to the WD repeat LIS1/nudF family. +Belongs to the cysteine-rich repeat secretory protein family. +Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit. S-adenosyl-L-methionine + uridine(2552) in 23S rRNA = 2'-O-methyluridine(2552) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase RlmE family. +Involved in metal homeostasis. Specifically binds Cu(2+). The truncated isoform has less specificity in metal binding. Homotetramer. Expressed in flowers, leaves, stems and roots. A central prokaryotic signal-sequence-like domain may be used to export the protein to the chloroplast envelope after import into the stroma. Knockout lines indicate that CUTA is not essential for copper tolerance or accumulation. Belongs to the CutA family. +May activate cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion. Interacts with CDKA-1, CDKB2-1, KRP4/ICK7, KRP5/ICK3, KRP6/ICK4 and KRP7/ICK5. A number of isoforms are produced. According to EST sequences. Expressed in shoot apical meristem, leaf primordia vascular tissues and tapetum of anthers. Expressed throughout the cell cycle. Transiently expressed in the root tip during seed germination up to about 21 hours after stratification. Expressed during lateral root primordia formation, vascular tissue development, in fertilized ovules, and torpedo- and heart-stage embryos. By sucrose. Belongs to the cyclin family. Cyclin D subfamily. +Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate. ATP + formate + N(1)-(5-phospho-beta-D-ribosyl)glycinamide = ADP + H(+) + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (formate route): step 1/1. Homodimer. Belongs to the PurK/PurT family. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 4L family. +Belongs to the PPR family. P subfamily. +Metalloendoprotease which functions in fertility and memory formation (PubMed:24395329, PubMed:27629706). Required in the dorsal paired medial neurons and alpha/beta mushroom body neurons for the proper formation of long-term and middle-term memories (PubMed:27629706). Required in males to maximise egg-laying in female mates and is also required in females for their fertility (PubMed:24395329). Preferential cleavage of polypeptides between hydrophobic residues, particularly with Phe or Tyr at P1'. Binds 1 zinc ion per subunit. Expressed in the testicular tube, near and in the seminal vesicles. In adults and third-instar larvae, expressed in the midgut and in the mushroom bodies of the brain and neurons in the pars intercerebralis. Also expressed in neurons of the ventral ganglion and imaginal disks (wing and leg) of third-instar larvae. In stage 17 embryos, expressed in the peripheral nervous system, pharynx and midgut. RNAi-mediated knockdown females lay fewer eggs and display a reduced hatch rate when mated to wild-type males, and wild-type females lay fewer eggs when mated to RNAi-mediated knockdown males (PubMed:24395329). RNAi-mediated knockdown in the dorsal paired medial neurons impairs middle-term (MTM) and long-term memory (LTM), but has no effect on normal aversion learning and anesthesia-resistant memory (ARM) (PubMed:27629706). RNAi-mediated knockdown in alpha/beta mushroom body neurons impairs MTM and LTM (PubMed:27629706). RNAi-mediated knockdown in all mushroom body neurons has no effect on learning and ARM (PubMed:27629706). Belongs to the peptidase M13 family. +Essential for the development of polarized epithelia, for cell polarity associated with asymmetric cell division of neuroblasts during development, and for oocyte polarity formation. Promotes the formation of actin-rich projections at the oocyte cortex and the posterior enrichment of par-1 which is required for oocyte polarization. Regulates the localization of axis-specifying morphogens such as stau and grk. Has an essential role in control of cell proliferation and differentiation during development and could act as a tumor suppressor. Has an accessory function in control of cell proliferation and differentiation during development. May form multimeric complexes. Interacts with mahj. Interacts with aPKC; leading to phosphorylation (PubMed:18094021, PubMed:20644714). Interacts with ball (PubMed:31735666). In larval and embryonic neuroblasts, detected in the cortex with apical enrichment from late interphase to metaphase, and uniform cortical localization during anaphase and telophase. Expressed in the epithelial cells of the digestive tract and in gonads. Expressed abundantly in early embryogenesis. Moderate expression is found in larval and adult stages. The phospho-regulated basic and hydrophobic (PRBH) motif is necessary and sufficient for interaction with phospholipids permitting cortical localization (PubMed:26481050). Phosphorylation of the PRBH motif by aPKC inhibits the association of the protein with the cortical membrane (PubMed:26481050). Phosphorylated by aPKC which lowers lipid affinity and promotes dissociation from the cell cortex (PubMed:26481050). In developing oocytes, aPKC-mediated phosphorylation restricts activity to the oocyte posterior and is required for oocyte polarity formation (PubMed:18094021, PubMed:18327897). Belongs to the WD repeat L(2)GL family. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +General factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Binds specifically to the TATA box promoter element which lies close to the position of transcription initiation. Belongs to the TBP family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Catalyzes the first step in the D-alanylation of lipoteichoic acid (LTA), the activation of D-alanine and its transfer onto the D-alanyl carrier protein (Dcp) DltC. In an ATP-dependent two-step reaction, forms a high energy D-alanyl-AMP intermediate, followed by transfer of the D-alanyl residue as a thiol ester to the phosphopantheinyl prosthetic group of the Dcp. D-alanylation of LTA plays an important role in modulating the properties of the cell wall in Gram-positive bacteria, influencing the net charge of the cell wall. ATP + D-alanine + holo-[D-alanyl-carrier protein] = AMP + D-alanyl-[D-alanyl-carrier protein] + diphosphate Cell wall biogenesis; lipoteichoic acid biosynthesis. Belongs to the ATP-dependent AMP-binding enzyme family. DltA subfamily. +Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein. Monomer. Belongs to the LolB family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression. Required for nonsense-mediated mRNA decay (NMD); may act in conjunction with UPF2 to divert mRNAs from translation to the NMD pathway. May interact with MCM7 and EPAS1 and regulate the proteasome-mediated degradation of these proteins. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is composed of 13 subunits: EIF3A, EIF3B, EIF3C, EIF3D, EIF3E, EIF3F, EIF3G, EIF3H, EIF3I, EIF3J, EIF3K, EIF3L and EIF3M. The eIF-3 complex appears to include 3 stable modules: module A is composed of EIF3A, EIF3B, EIF3G and EIF3I; module B is composed of EIF3F, EIF3H, and EIF3M; and module C is composed of EIF3C, EIF3D, EIF3E, EIF3K and EIF3L. EIF3C of module C binds EIF3B of module A and EIF3H of module B, thereby linking the three modules. EIF3J is a labile subunit that binds to the eIF-3 complex via EIF3B. The eIF-3 complex interacts with RPS6KB1 under conditions of nutrient depletion. Mitogenic stimulation leads to binding and activation of a complex composed of MTOR and RPTOR, leading to phosphorylation and release of RPS6KB1 and binding of EIF4B to eIF-3. Interacts with COPS3, COPS6, COPS7 (COPS7A or COPS7B), EIF4G1, EPAS1, MCM7, NCBP1, PSMC6, TRIM27 and UPF2 (By similarity). Interacts with IFIT1 and IFIT2 (By similarity). Interacts with BZW2/5MP1 (By similarity). Belongs to the eIF-3 subunit E family. +General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Belongs to the TFIID complex together with the TBP-associated factors (TAFs). Binds DNA as monomer. Belongs to the TBP family. +May catalyze the transamination reaction in phenylalanine biosynthesis. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Can be acetylated to form H2BK6ac, H2BK33ac and H2BK34ac. Monoubiquitinated by BRE1 to form H2BK143ub1 and deubiquitinated by UBP26. Required for heterochromatic histone H3 di- and trimethylation at H3K4me. May give a specific tag for epigenetic transcriptional activation. Belongs to the histone H2B family. To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-20; H2BK34ac = acetylated Lys-21; H2BK143ub1 = monoubiquitinated Lys-128. +Catalyzes the isomerization of 5-dehydro-4-deoxy-D-glucuronate to 3-deoxy-D-glycero-2,5-hexodiulosonate. 5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate Binds 1 zinc ion per subunit. Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-gluconate from pectin: step 4/5. Belongs to the KduI family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homodimer. Belongs to the ThiC family. +Mediates apoptosis and actin stress fiber dissolution. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Ubiquitously expressed. Proteolytically cleaved by caspase-3. Autophosphorylated. Belongs to the protein kinase superfamily. STE Ser/Thr protein kinase family. STE20 subfamily. +Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones. Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines. 2 a quinone + H(+) + NADH = 2 a 1,4-benzosemiquinone + NAD(+) anthranilate + N,N-dimethyl-1,4-phenylenediamine + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 H(+) + 2 NADH Binds 1 FMN per subunit. Homodimer. Belongs to the azoreductase type 1 family. +dGTPase preferentially hydrolyzes dGTP over the other canonical NTPs. dGTP + H2O = 2'-deoxyguanosine + H(+) + triphosphate Homotetramer. Belongs to the dGTPase family. Type 1 subfamily. +The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. Belongs to the RecF family. +May be involved in recombination. Belongs to the RdgC family. +Involved in cytoplasm to vacuole transport (Cvt) and autophagic vesicle formation. Autophagy is essential for maintenance of amino acid levels and protein synthesis under nitrogen starvation. Required for selective autophagic degradation of the nucleus (nucleophagy). Also required for mitophagy, which eliminates defective or superfluous mitochondria in order to fulfill cellular energy requirements and prevent excess ROS production. Conjugation with atg12, through a ubiquitin-like conjugating system involving atg7 as an E1-like activating enzyme and atg10 as an E2-like conjugating enzyme, is essential for its function. The atg12-atg5 conjugate acts as an E3-like enzyme which is required for lipidation of atg8 and atg8 association to the vesicle membranes (By similarity). Conjugated with atg12. Conjugated to atg12; which is essential for autophagy. Belongs to the ATG5 family. +Belongs to the YejK family. +Protein modifier that is covalently attached to lysine residues of substrate proteins, thereby targeting them for proteasomal degradation. The tagging system is termed pupylation. Protein degradation; proteasomal Pup-dependent pathway. Strongly interacts with the proteasome-associated ATPase ARC through a hydrophobic interface; the interacting region of Pup lies in its C-terminal half. There is one Pup binding site per ARC hexamer ring. The N-terminal unstructured half of Pup provides a signal required to initiate unfolding and degradation by the proteasome but is not needed for pupylation, while the C-terminal helical half of Pup interacts with ARC to target proteins to the proteasome. Belongs to the prokaryotic ubiquitin-like protein family. +Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + H(+) + holo-[ACP] Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxD subfamily. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Exhibits antimicrobial activity against Gram-negative bacteria and Gram-positive bacteria. May act as a ligand for C-C chemokine receptor CCR6. Can bind to mouse (but not human) CCR6 and induce chemotactic activity of CCR6-expressing cells (PubMed:20068036). Tongue, esophagus and trachea. Belongs to the beta-defensin family. +Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12. [sulfur carrier]-SH + AH2 + L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 2 S-adenosyl-L-methionine = 3-methylsulfanyl-L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Belongs to the methylthiotransferase family. RimO subfamily. +Mating type proteins are sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. Transcriptional coactivator that, in alpha-cells, binds cooperatively with MCM1 and STE12 to a DNA sequence termed the QP' element, to activate the transcription of alpha-specific genes. Binds DNA with a high specificity in complex with an MCM1 dimer. Interacts with STE12. Only present in alpha-cells. Repressed in a/alpha diploid cells by A1/ALPHA2. There are three genetic loci for mating type genes in S.cerevisiae. MAT is the expression locus that determines the mating type of the cell, whereas HML (containing HMLALPHA1 and HMLALPHA2) and HMR (containing HMRA1 and HMRA2) represent silenced repositories of mating type information. The mating type is determined by the MAT locus, which contains either a copy of HML or of HMR. Diploid cells are usually heterozygous for the MAT locus. Belongs to the MATALPHA1 family. +Xenophagy-specific receptor required for autophagy-mediated intracellular bacteria degradation. Acts as an effector protein of galectin-sensed membrane damage that restricts the proliferation of infecting pathogens such as Salmonella typhimurium upon entry into the cytosol by targeting LGALS8-associated bacteria for autophagy (PubMed:22246324). Initially orchestrates bacteria targeting to autophagosomes and subsequently ensures pathogen degradation by regulating pathogen-containing autophagosome maturation (PubMed:23022382, PubMed:25771791). Bacteria targeting to autophagosomes relies on its interaction with MAP1LC3A, MAP1LC3B and/or GABARAPL2, whereas regulation of pathogen-containing autophagosome maturation requires the interaction with MAP3LC3C (PubMed:23022382, PubMed:25771791). May play a role in ruffle formation and actin cytoskeleton organization and seems to negatively regulate constitutive secretion (PubMed:17635994). Dimer (PubMed:23511477). Part of a complex consisting of CALCOCO2, TAX1BP1 and MYO6 (PubMed:17635994). Interacts with GEMIN4 (PubMed:12869526). Interacts with ATG8 family members MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2 (PubMed:25771791). Interacts with ATG8 family member MAP1LC3C (PubMed:23022382). Interacts with LGALS8 (PubMed:22246324, PubMed:25771791, PubMed:23511477, PubMed:23386746). According to PubMed:7540613, localizes to nuclear dots. According to PubMed:9230084 and PubMed:12869526, it is not a nuclear dot-associated protein but localizes predominantly in the cytoplasm with a coarse-grained distribution preferentially close to the nucleus. Expressed in all tissues tested with highest expression in skeletal muscle and lowest in brain. Treatment with IFNB1/IFN-beta and IFNG/IFN-gamma show an increase in number and size of CALCOCO2-specific dots and partial redistribution to the cytoplasm (PubMed:7540613). IFNG/IFN-gamma increases gene expression only slightly and IFNB does not increase expression (PubMed:9230084). The MYO6-binding domain is required for autophagy-mediated degradation of infecting bacteria such as Salmonella typhimurium, but not for bacteria targeting to autophagosomes. The CLIR (LC3C-interacting region) motif is required for interaction with MAP1LC3C, but dispensable for CALCOCO2-mediated autophagosome maturation. The LIR-like motif is required for interaction with MAP1LC3A, MAP1LC3B and GABARAPL2, as well as for CALCOCO2-mediated autophagosome maturation. The LGALS8-binding domain is essential for the recruitment to cytosol-exposed infecting bacteria. Belongs to the CALCOCO family. +Essential cell division protein. May link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic. Part of a complex composed of FtsB, FtsL and FtsQ. Localizes to the division septum. Belongs to the FtsB family. +Transcription termination factor that is transcriptionally active in chloroplasts. Belongs to the mTERF family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +Early post-infection, the reverse transcriptase converts the viral RNA genome into double-stranded viral DNA. The RNase H domain of the reverse transcriptase performs two functions. It degrades the RNA template and specifically removes the RNA primer from the RNA/DNA hybrid. Following nuclear import, the integrase catalyzes the insertion of the linear, double-stranded viral DNA into the host cell chromosome. Endogenous Pol proteins may have kept, lost or modified their original function during evolution (By similarity). a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Endonucleolytic cleavage to 5'-phosphomonoester. This protein is synthesized as Gag-Pro and Gag-Pro-Pol polyprotein precursors. These polyproteins are thought, by similarity with type-B retroviruses, to be generated by -1 frameshifts occurring at the Gag-Pro and Pro-Pol genes boundaries. The LPQG and YXDD motifs are catalytically important and conserved among many retroviruses. Exact N-terminus of this protein has not been formally described. The 102 C-terminal amino acids differ from HERV-K(HML-2) Pol prototype due to a frameshift in position 867. Belongs to the beta type-B retroviral polymerase family. HERV class-II K(HML-2) pol subfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Abundant tegument protein. Trans-activates the immediate early genes (By similarity). Belongs to the herpesviridae HHV-1 VP11/12 protein family. +Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit binds the periplasmic potassium ions and delivers the ions to the membrane domain of KdpB through an intramembrane tunnel. The system is composed of three essential subunits: KdpA, KdpB and KdpC. Belongs to the KdpA family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvP family. +Belongs to the adhesin P1 family. Could be the product of a pseudogene. +Component of the BLOC-1 complex, a complex that is required for normal biogenesis of lysosome-related organelles (LRO), such as platelet dense granules and melanosomes. Plays a role in intracellular vesicle trafficking (By similarity). Component of the biogenesis of lysosome-related organelles complex 1 (BLOC-1). Belongs to the BLOC1S5 family. +Actins are highly conserved proteins that are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells. Polymerization of globular actin (G-actin) leads to a structural filament (F-actin) in the form of a two-stranded helix. Each actin can bind to 4 others. Belongs to the actin family. +Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is responsible for the expression of sporulation specific genes in the mother cell. DNA rearrangement occurs at the third hour of sporulation. Selectively expressed in the mother cell chamber of sporulating cells. The spoIVCB gene is an incomplete structural gene that is capable of encoding only the N-terminal half of sigma-K. The remainder of sigma-K is specified by another gene, spoIIIC, that is about 10 kb from spoIVCB on the chromosome. The intervening fragment, called skin, is excised at an intermediate stage of sporulation thus allowing a full coding gene to be produced. Belongs to the sigma-70 factor family. +Lysophosphatidic acid acyltransferase which functions in phosphatidic acid biosynthesis. May regulate neutral lipid accumulation and participate in the regulation of lipid turnover in vegetative cells. May possess additional triacylglycerol lipase and phospholipase A2 activities in vitro (By similarity). a 1-acyl-sn-glycero-3-phosphate + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phosphate + CoA The HXXXXD motif is essential for acyltransferase activity and may constitute the binding site for the phosphate moiety of the glycerol-3-phosphate. Belongs to the peptidase S33 family. ABHD4/ABHD5 subfamily. +Catalyzes the transfer of adenosine 5'-monophosphate (AMP) to Ser, Thr or Tyr residues of target proteins (AMPylation). ATP + L-tyrosyl-[protein] = diphosphate + O-(5'-adenylyl)-L-tyrosyl-[protein] ATP + L-threonyl-[protein] = 3-O-(5'-adenylyl)-L-threonyl-[protein] + diphosphate ATP + L-seryl-[protein] = 3-O-(5'-adenylyl)-L-seryl-[protein] + diphosphate Belongs to the SELO family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Product of a dubious CDS prediction. May be a non-coding RNA. +May be involved in the transport of sterols. Expressed in flowers. Belongs to the OSBP family. +Belongs to the EfeM/EfeO family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved. Distribution is 50-50. Belongs to the SecA family. +Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I. di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine = Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + UMP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 4 family. MraY subfamily. +Binds with high affinity to muscular (tested on Torpedo marmorata, Kd=0.4 nM) and neuronal (tested on chimeric alpha-7/CHRNA7, Kd=0.95 nM) nicotinic acetylcholine receptor (nAChR) and inhibits acetylcholine from binding to the receptor, thereby impairing neuromuscular and neuronal transmission. It also shows an activity on GABA(A) receptors. It antagonises GABA-activated currents with high potency when tested on primary hippocampal neurons. It inhibits recombinantly expressed GABA(A) receptors composed of alpha-2-beta-2-gamma-2 (GABRA2-GABRB2-GABRG2) subunits with high potency (62.3% inhibition at 20 uM of toxin). It also shows a weaker inhibition on GABA(A) receptors composed of alpha-1-beta-2-gamma-2 (GABRA1-GABRB2-GABRG2) subunits, alpha-4-beta-2-gamma-2 (GABRA4-GABRB2-GABRG2) subunits, and alpha-5-beta-2-gamma-2 (GABRA5-GABRB2-GABRG2) subunits. A very weak inhibition is also observed on GABA(A) receptor composed of alpha-1-beta-3-gamma-2 (GABRA1-GABRB3-GABRG2). It has also been shown to bind and inhibit recombinant GABA(A) receptor beta-3/GABRB3 subunit (Kd=about 50 nM). In addition, it blocks the extracellular increase of dopamine evoked by nicotine only at the higher dose (4.2 uM). In vivo, when intraperitoneally injected into mice, induces flaccid paralysis of the limbs and respiratory distress, and causes death in a dose-dependent manner (PubMed:14505938). Monomer in solution, homodimer in crystal state. Expressed by the venom gland. LD(50) is 230 ug/kg by intraperitoneal injection into mice. Is identical to Alpha-bungarotoxin (A31) from B.multicinctus (AC P60615). Belongs to the snake three-finger toxin family. Long-chain subfamily. Type II alpha-neurotoxin sub-subfamily. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +Belongs to the 2H phosphoesterase superfamily. YjcG family. +Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate. ATP + formate + N(1)-(5-phospho-beta-D-ribosyl)glycinamide = ADP + H(+) + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (formate route): step 1/1. Homodimer. Belongs to the PurK/PurT family. +Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. Binds 1 zinc ion. Belongs to the NrdR family. +Belongs to the SlyX family. +Involved in the degradation of cholesterol. Catalyzes the introduction of a 9a-hydroxyl moiety into 1,4-androstadiene-3,17-dione (ADD) to yield the 9alpha-hydroxy-1,4-androstadiene-3,17-dione (9OHADD) intermediate which spontaneously form 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione (HSA) via the meta-cleavage of ring B with concomitant aromatization of ring A. KSH is also able to use 4-androstene-3,17-dione (AD), 3-oxo-23,24-bisnorcholesta-4-en-22-oate (4-BNC), 3-oxo-23,24-bisnorcholesta-1,4-dien-22-oate (1,4-BNC), 3-oxo-23,24-bisnorcholesta-4-en-22-oyl-coenzyme A thioester (4-BNC-CoA) and 3-oxo-23,24-bisnorcholesta-1,4-dien-22-oyl-coenzyme A thioester (1,4-BNC-CoA) as substrates. androsta-1,4-diene-3,17-dione + 2 H(+) + O2 + 2 reduced [2Fe-2S]-[ferredoxin] = 9alpha-hydroxyandrosta-1,4-diene-3,17-dione + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Binds 1 2Fe-2S cluster. kcat is 2.7 sec(-1) for 1,4-BNC-CoA as substrate (at pH 7 and at 22 degrees Celsius) (PubMed:21987574). kcat is 0.8 sec(-1) for ADD as substrate (at pH 7 and at 25 degrees Celsius) (PubMed:19234303). kcat is 0.61 sec(-1) for 4-BNC-CoA as substrate (at pH 7 and at 22 degrees Celsius) (PubMed:21987574). kcat is 0.25 sec(-1) for 1,4-BNC as substrate (at pH 7 and at 22 degrees Celsius) (PubMed:21987574). kcat is 0.08 sec(-1) for 4-BNC as substrate (at pH 7 and at 22 degrees Celsius) (PubMed:21987574). kcat is 0.07 sec(-1) for AD as substrate (at pH 7 and at 25 degrees Celsius) (PubMed:19234303). Lipid metabolism; steroid biosynthesis. Monomer. The two-component system 3-ketosteroid-9-alpha-monooxygenase is composed of an oxygenase component KshA and a reductase component KshB. Induced by KstR. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The NB-protein (BchN-BchB) is the catalytic component of the complex. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per heterodimer. The cluster is bound at the heterodimer interface by residues from both subunits. Porphyrin-containing compound metabolism; bacteriochlorophyll biosynthesis (light-independent). Protochlorophyllide reductase is composed of three subunits; BchL, BchN and BchB. Forms a heterotetramer of two BchB and two BchN subunits. Belongs to the ChlB/BchB/BchZ family. +Belongs to the UPF0738 family. +H(+) + NADP(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADPH + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Homodimer. Belongs to the ferredoxin--NADP reductase type 2 family. +Probable ion channel inhibitor. Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 14 (magi-1) family. 01 (HNTX-16) subfamily. +With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS5 family. +Involved in mercuric transport. Passes a mercury ion from the MerP protein to the mercuric reductase MerA. +Chaperone that acts in assembly of the long tail fibers. Homodimer. Belongs to the tfa family. +Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the retrotransposons dimeric RNA genome. The particles are assembled from trimer-clustered units and there are holes in the capsid shells that allow for the diffusion of macromolecules. CA has also nucleocapsid-like chaperone activity, promoting primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty2 RNA and initiation of reverse transcription (By similarity). Homotrimer. The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift. The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities. Retrotransposons are mobile genetic entities that are able to replicate via an RNA intermediate and a reverse transcription step. In contrast to retroviruses, retrotransposons are non-infectious, lack an envelope and remain intracellular. Ty2 retrotransposons belong to the copia elements (pseudoviridae). Produced by conventional translation. +The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The enzyme II UlaABC PTS system is involved in ascorbate transport. L-ascorbate(out) + N(pros)-phospho-L-histidyl-[protein] = L-ascorbate 6-phosphate(in) + L-histidyl-[protein] Induced by L-ascorbate. Repressed by UlaR. The PTS EIIB type-2 domain is phosphorylated by phospho-EIIA on a cysteinyl residue. Then, it transfers the phosphoryl group to the sugar substrate concomitantly with the sugar uptake processed by the PTS EIIC type-2 domain. +Involved in the synthesis of meso-diaminopimelate (m-DAP or DL-DAP), required for both lysine and peptidoglycan biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate. (2S,6S)-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O + L-glutamate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route): step 1/1. Homodimer. Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. LL-diaminopimelate aminotransferase subfamily. +Redox regulated molecular chaperone. Protects both thermally unfolding and oxidatively damaged proteins from irreversible aggregation. Plays an important role in the bacterial defense system toward oxidative stress. Under oxidizing conditions two disulfide bonds are formed involving the reactive cysteines. Under reducing conditions zinc is bound to the reactive cysteines and the protein is inactive. Belongs to the HSP33 family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Allosteric enzyme that catalyzes the rate-limiting step in glycogen catabolism, the phosphorolytic cleavage of glycogen to produce glucose-1-phosphate, and plays a central role in maintaining cellular and organismal glucose homeostasis. [(1->4)-alpha-D-glucosyl](n) + phosphate = [(1->4)-alpha-D-glucosyl](n-1) + alpha-D-glucose 1-phosphate Allosterically regulated through the non-covalent binding of metabolites, being activated by AMP and inhibited by ATP, ADP, and glucose-6-phosphate. The activity is also controlled by post-translational modifications including phosphorylation and acetylation. Homodimer; enzymatically active. Interacts with PPP1R3B; recruits the phosphatase PP1 which dephosphorylates and inactivates PYGL/glycogen phosphorylase. Acetylation, which is up-regulated by glucose and insulin and down-regulated by glucagon, inhibits the glycogen phosphorylase activity by promoting PPP1R3B-mediated recruitment of phosphatase PP1 and Ser-15 dephosphorylation. Phosphorylation at Ser-15 converts inactive phosphorylase b into active phosphorylase a. Dephosphorylation of Ser-15 by phosphatase PP1 inactivates the enzyme. Belongs to the glycogen phosphorylase family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short-lived. The second step is the nonenzymatic hydrolysis of the enamine/imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA (By similarity). L-threonine = 2-oxobutanoate + NH4(+) Each protein molecule can bind up to four molecules of AMP, which act as an allosteric activator to the enzyme. Amino-acid degradation; L-threonine degradation via propanoate pathway; propanoate from L-threonine: step 1/4. In the native structure, TdcB is in a dimeric form, whereas in the TdcB-AMP complex, it exists in a tetrameric form (dimer of dimers). Belongs to the serine/threonine dehydratase family. +Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III. 4 H(+) + uroporphyrinogen III = 4 CO2 + coproporphyrinogen III Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 4/4. Homodimer. Belongs to the uroporphyrinogen decarboxylase family. +Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively. Also cleaves 5'-deoxyadenosine, a toxic by-product of radical S-adenosylmethionine (SAM) enzymes, into 5-deoxyribose and adenine. Thus, is required for in vivo function of the radical SAM enzymes biotin synthase and lipoic acid synthase, that are inhibited by 5'-deoxyadenosine accumulation. H2O + S-adenosyl-L-homocysteine = adenine + S-(5-deoxy-D-ribos-5-yl)-L-homocysteine H2O + S-methyl-5'-thioadenosine = 5-(methylsulfanyl)-D-ribose + adenine 5'-deoxyadenosine + H2O = 5-deoxy-D-ribose + adenine Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; S-methyl-5-thio-alpha-D-ribose 1-phosphate from S-methyl-5'-thioadenosine (hydrolase route): step 1/2. Homodimer. Belongs to the PNP/UDP phosphorylase family. MtnN subfamily. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the proton channel; it may play a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Component of an ATP synthase complex composed of ATP5PB, ATP5MC1, ATP5F1E, ATP5PD, ATP5ME, ATP5PF, ATP5MF, MT-ATP6, MT-ATP8, ATP5F1A, ATP5F1B, ATP5F1D, ATP5F1C, ATP5PO, ATP5MG, ATP5MK and ATP5MJ (By similarity). Interacts with DNAJC30; interaction is direct (By similarity). Belongs to the ATPase A chain family. +Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I. di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 4 family. MraY subfamily. +Converts the preformed base xanthine, a product of nucleic acid breakdown, to xanthosine 5'-monophosphate (XMP), so it can be reused for RNA or DNA synthesis. diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine Purine metabolism; XMP biosynthesis via salvage pathway; XMP from xanthine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. Xpt subfamily. +Belongs to the TACO1 family. +Catalyzes a trans-dehydration via an enolate intermediate. 3-dehydroquinate = 3-dehydroshikimate + H2O Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 3/7. Homododecamer. Belongs to the type-II 3-dehydroquinase family. +ATPase. Has a role at an early stage in the morphogenesis of the spore coat outer layers. Its ATP hydrolysis is required for proper assembly of the spore coat. Forms a basement layer around the outside surface of the forespore and self-assembles irreversibly into higher order structures by binding and hydrolyzing ATP thus creating a durable and stable platform upon which thereafter morphogenesis of the coat can take place. Required for proper localization of spore coat protein CotE and sporulation-specific proteins including SpoVM. ATP + H2O = ADP + H(+) + phosphate The turnover rate is 2.7 pmol/min/pmol of SpoIVA at Vmax (PubMed:18691972). The turnover rate is 1.0 pmol/min/pmol of SpoIVA at Vmax (PubMed:23267091). Polymerizes to self-assemble into static filaments. ATP hydrolysis is required by every subunit for incorporation into the growing polymer by inducing a conformational change that drives polymerization of a nucleotide-free filament. Polymerization requires a critical concentration of the protein and only occurs after it is localized to the surface of the developing spore. Interacts (via extreme C-terminus Gly-486) with SpoVM (via Ile-6). Interacts (via full-length) with SpoVID (via C-terminus 499-575 AA). Interacts with SafA. Uniformly distributed on the membrane around the forespore, lying close to or on its outer surface. Expression only necessary in the mother cell chamber of the sporangium for the formation of a mature spore. According to PubMed:8299942, not a coat protein of the mature spore, is only transiently associated with the assembling coat. According to PubMed:9922240, present as a component of the fully mature spore. Proper localization requires the expression of a gene spoVM which is under the control of the mother cell transcription factor sigma E. Expressed soon after the formation of the asymmetric septum during sporulation. Expression commences about 2 hours after the onset of sporulation. Assembly around the developing forespore commences at the time of polar division and seems to continue after engulfment of the forespore is complete. Remains present throughout the late stages of morphogenesis and during this accumulation process preferentially collects on the mother cell side of the engulfed forespore, but eventually is deposited equally all around the forespore. Extreme C-terminal region (AA 487-492) is required for its proper localization into a spherical shell around the developing forespore. N-terminus (AA 1-64) is functionally important although largely dispensable for proper localization. Seems to be cleaved by the YabG protease. Forespores lack a well-defined cortex, and the coat is present as swirls in the mother cell compartment of the sporangia rather than having been deposited around the forespore protoplasts. According to PubMed:18691972, unable to sporulate. Present in an increased level in yabG mutant spores. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +High affinity receptor for the C-C type chemokines CCL17/TARC and CCL22/MDC. The activity of this receptor is mediated by G(i) proteins which activate a phosphatidylinositol-calcium second messenger system. Could play a role in lipopolysaccharide (LPS)-induced endotoxic shock. In the CNS, could mediate hippocampal-neuron survival (By similarity). Expressed in thymus, spleen, heart, small intestine and lymph node. In natural killer cells, CCL22 binding induces phosphorylation on yet undefined Ser/Thr residues, most probably by beta-adrenergic receptor kinases 1 and 2. Belongs to the G-protein coupled receptor 1 family. +Belongs to the rickettsiale 17 kDa surface antigen family. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. 3 H2O + hydrogen sulfide + 3 NADP(+) = 4 H(+) + 3 NADPH + sulfite Binds 1 siroheme per subunit. Binds 1 [4Fe-4S] cluster per subunit. Sulfur metabolism; hydrogen sulfide biosynthesis; hydrogen sulfide from sulfite (NADPH route): step 1/1. Alpha(8)-beta(8). The alpha component is a flavoprotein, the beta component is a hemoprotein. Belongs to the nitrite and sulfite reductase 4Fe-4S domain family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). Belongs to the long (3 C-C) scorpion toxin superfamily. +Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel. Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL. Belongs to the GroES chaperonin family. +Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). H(+) + orotidine 5'-phosphate = CO2 + UMP Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. Homodimer. Belongs to the OMP decarboxylase family. Type 1 subfamily. +Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) Binds 1 zinc ion per subunit. Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. Belongs to the class-II aminoacyl-tRNA synthetase family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of 3 enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3). (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + NAD(+) = (R)-N(6)-lipoyl-L-lysyl-[protein] + H(+) + NADH Binds 1 FAD per subunit. Homodimer. The active site is a redox-active disulfide bond. Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family. +Belongs to the bacterial ribosomal protein bL32 family. +H2O + O-phospho-L-serine = L-serine + phosphate H2O + O-phospho-D-serine = D-serine + phosphate Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 3/3. Belongs to the HAD-like hydrolase superfamily. SerB family. +Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs. uridine(55) in tRNA = pseudouridine(55) in tRNA Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +DEAD-box RNA helicase involved in RNA degradation. Has RNA-dependent ATPase activity and unwinds double-stranded RNA. ATP + H2O = ADP + H(+) + phosphate Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Belongs to the DEAD box helicase family. RhlB subfamily. +Belongs to the bacterial ribosomal protein bL27 family. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell. Belongs to the MinE family. +Specific component of the STT3A-containing form of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation. N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity. May be involved in N-glycosylation of APP (amyloid-beta precursor protein). Can modulate gamma-secretase cleavage of APP by enhancing endoprotelysis of PSEN1. Protein modification; protein glycosylation. Specific component of the STT3A-containing form of the oligosaccharyltransferase (OST) complex. OST exists in two different complex forms which contain common core subunits RPN1, RPN2, OST48, OST4, DAD1 and TMEM258, either STT3A or STT3B as catalytic subunits, and form-specific accessory subunits (PubMed:15835887). STT3A complex assembly occurs through the formation of 3 subcomplexes. Subcomplex 1 contains RPN1 and TMEM258, subcomplex 2 contains the STT3A-specific subunits STT3A, DC2/OSTC, and KCP2 as well as the core subunit OST4, and subcomplex 3 contains RPN2, DAD1, and OST48. The STT3A complex can form stable complexes with the Sec61 complex or with both the Sec61 and TRAP complexes (PubMed:15835887, PubMed:29519914). Interacts with PSEN1 and NCSTN; indicative for an association with the gamma-secretase complex (By similarity). Belongs to the OSTC family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +The primary product of this enzyme is 4,2',4',6'-tetrahydroxychalcone (also termed naringenin-chalcone or chalcone) which can under specific conditions spontaneously isomerize into naringenin. 4-coumaroyl-CoA + 2 H(+) + 3 malonyl-CoA = 2',4,4',6'-tetrahydroxychalcone + 3 CO2 + 4 CoA Secondary metabolite biosynthesis; flavonoid biosynthesis. Belongs to the thiolase-like superfamily. Chalcone/stilbene synthases family. +Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). 3-methyl-2-oxobutanoate + acetyl-CoA + H2O = (2S)-2-isopropylmalate + CoA + H(+) Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 1/4. Homotetramer. Belongs to the alpha-IPM synthase/homocitrate synthase family. LeuA type 1 subfamily. +Substrate recognition component of a DCX (DDB1-CUL4-X-box) E3 protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Has an essential role in mediating growth by negatively regulating insulin signaling. It also has a role in maintaining presynaptic function in the neuromuscular junction synapses of third-instar larvae. Protein modification; protein ubiquitination. Likely a component of a DCX (DDB1-CUL4-X-box) protein ligase complex (By similarity). May interact with pic/DDB1 (By similarity). Ubiquitinated. Belongs to the CRBN family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +Component of the spindle pole body (SPB) required for the proper execution of spindle pole body (SPB) duplication. Potential role in cross-linking filaments or anchoring other molecules. It is essential for growth (By similarity). Homodimer. Tightly associated with the nucleus. It is present in a granular pattern that excludes the nucleolus. Belongs to the SPC110 family. +Secreted subtilisin-like serine protease with keratinolytic activity that contributes to pathogenicity. Belongs to the peptidase S8 family. +Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate. (S)-dihydroorotate + H2O = H(+) + N-carbamoyl-L-aspartate Binds 2 Zn(2+) ions per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 3/3. Homodimer. Belongs to the metallo-dependent hydrolases superfamily. DHOase family. Class II DHOase subfamily. +Envelope glycoprotein that forms spikes at the surface of virion envelope. Essential for the initial attachment to heparan sulfate moieties of the host cell surface proteoglycans. Involved in fusion of viral and cellular membranes leading to virus entry into the host cell. Following initial binding to its host receptors, membrane fusion is mediated by the fusion machinery composed at least of gB and the heterodimer gH/gL. May be involved in the fusion between the virion envelope and the outer nuclear membrane during virion egress. Homotrimer; disulfide-linked. Binds to heparan sulfate proteoglycans. Interacts with gH/gL heterodimer. During virion morphogenesis, this protein probably accumulates in the endosomes and trans-Golgi where secondary envelopment occurs. It is probably transported to the cell surface from where it is endocytosed and directed to the trans-Golgi network (TGN). Belongs to the herpesviridae glycoprotein B family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase C chain family. +Chaperone that confers thermal protection to other proteins. Homooligomer of 24 subunits. Forms a spherical shape. Belongs to the small heat shock protein (HSP20) family. +Involved in the biosynthesis of mycinamicin, a 16-membered macrolide antibiotic. Catalyzes consecutive hydroxylation (at C14) and epoxidation (at C12-C13) reactions with mycinamicin IV as initial substrate, leading to mycinamicin II. These reactions require prior dimethylation of 6-deoxyallose to mycinose for effective conversion by the dual function MycG enzyme. kcat is 415.7 min(-1) for the epoxydation of mycinamicin V. Antibiotic biosynthesis; mycinamicin biosynthesis. Cells lacking this gene do not produce mycinamicin I, mycinamicin II and mycinamicin V, and accumulate mycinamicin IV. Belongs to the cytochrome P450 family. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +Produces cycloisomaltooligosaccharide from dextran containing 7, 8 or 9 glucose units. The enzyme is specific for (1->6)-alpha-D-glucans (dextrans) and, without activity toward (1->4)-alpha-D-glucans, such as amylose. It also has no activity on oligosaccharides, such as amylopectin and pullulan, containing (1->6)-alpha-D-glucosidic linkages at branch points. cyclizes part of a (1->6)-alpha-D-glucan chain by formation of a (1->6)-alpha-D-glucosidic bond. Optimum pH is 5.5. Monomer. Belongs to the glycosyl hydrolase 66 family. +Binds 2 magnesium or manganese ions per subunit. Belongs to the RimK family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the synthesis of IGP and AICAR. The resulting ammonia molecule is channeled to the active site of HisF. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate H2O + L-glutamine = L-glutamate + NH4(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. +H(+)-stimulated, divalent metal cation uptake system. Belongs to the NRAMP family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Homodimer. Belongs to the GrpE family. +Belongs to the DCC thiol-disulfide oxidoreductase family. +Specifically methylates the guanine in position 1207 of 16S rRNA in the 30S particle. guanosine(1207) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(2)-methylguanosine(1207) in 16S rRNA + S-adenosyl-L-homocysteine Monomer. Belongs to the methyltransferase superfamily. RsmC family. +Myoactive. Expressed in the brain, subesophageal ganglion and in the retrocerebral complex (mainly corpora cardiaca). Belongs to the pyrokinin family. +Coagulogen is a gel-forming protein of hemolymph; it hinders the spread of invaders by immobilizing them. Coagulogen is cleaved after Arg-18 and Arg-46 by a clotting enzyme contained in the hemocyte and activated by a bacterial endotoxin (lipopolysaccharide). This cleavage releases the peptide C and leaves 2 chains of coagulin, A and B, linked by two disulfide bonds. Coagulin molecules interlink to form a gel. Hemolymph. Belongs to the coagulin family. +Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate. ATP + shikimate = 3-phosphoshikimate + ADP + H(+) Binds 1 Mg(2+) ion per subunit. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 5/7. Monomer. Belongs to the shikimate kinase family. +Hydrolyzes a wide range of dipeptides. an L-aminoacyl-L-amino acid + H2O = 2 an L-alpha-amino acid Belongs to the metallo-dependent hydrolases superfamily. Peptidase M19 family. +Self-assembles to form an icosahedral capsid with a T=16 symmetry, about 200 nm in diameter, and consisting of 150 hexons and 12 pentons (total of 162 capsomers). Hexons form the edges and faces of the capsid and are each composed of six MCP molecules. In contrast, one penton is found at each of the 12 vertices. Eleven of the pentons are MCP pentamers, while the last vertex is occupied by the portal complex. The capsid is surrounded by a layer of proteinaceous material designated the tegument which, in turn, is enclosed in an envelope of host cell-derived lipids containing virus-encoded glycoproteins. Homomultimer. Makes the hexons and eleven out of twelve pentons. Interacts with triplex proteins 1/TRX1 and 2/TRX2; adjacent capsomers are linked together in groups of three by triplexes, heterotrimeric complexes composed of one molecule of TRX1 and two molecules of TRX2. Interacts with scaffold protein; this interaction allows efficient MCP transport to the host nucleus. Interacts with capsid vertex component 2/CVC2. Interacts with the small capsomere-interacting protein/SCP. Belongs to the herpesviridae major capsid protein family. +To E.coli YecT. +Catalyzes the NADPH-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5-carboxylate. L-glutamate 5-semialdehyde + NADP(+) + phosphate = H(+) + L-glutamyl 5-phosphate + NADPH Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 2/2. Belongs to the gamma-glutamyl phosphate reductase family. +Nucleoside transporter that can mediate uptake of adenosine, uridine, guanosine or cytidine when expressed in a heterologous system (yeast). Plasma membrane. Expressed in leaves and siliques. By nitrogen deficiency and 5-fluorouracil plus methotrexate. Belongs to the SLC29A/ENT transporter (TC 2.A.57) family. +Belongs to the bacterial ribosomal protein bS16 family. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain. +Hydrolyzes ureidoacrylate to form aminoacrylate and carbamate. The carbamate hydrolyzes spontaneously, thereby releasing one of the nitrogen atoms of the pyrimidine ring as ammonia and one of its carbon atoms as CO2. (Z)-3-ureidoacrylate + H(+) + H2O = (Z)-3-aminoacrylate + CO2 + NH4(+) (Z)-3-ureidoacrylate + H2O = (Z)-3-aminoacrylate + carbamate + H(+) (Z)-2-methylureidoacrylate + H(+) + H2O = (Z)-2-methylaminoacrylate + CO2 + NH4(+) Belongs to the isochorismatase family. RutB subfamily. +May be involved in transcriptional regulation. Shows widespread expression throughout the nucleus, but appears to be excluded from nucleoli. Belongs to the krueppel C2H2-type zinc-finger protein family. +Nuclear transcriptional activator of viral gene expression, that is essential for viral transcription from the LTR promoter and replication. Acts as a sequence-specific molecular adapter, directing components of the cellular transcription machinery to the viral RNA to promote processive transcription elongation by the RNA polymerase II (RNA pol II) complex, thereby increasing the level of full-length transcripts. In the absence of Tat, the RNA Pol II generates short or non-processive transcripts that terminate at approximately 60 bp from the initiation site. Tat associates with the CCNT1/cyclin-T1 component of the P-TEFb complex (CDK9 and CCNT1), which promotes RNA chain elongation. This binding increases Tat's affinity for a hairpin structure at the 5'-end of all nascent viral mRNAs referred to as the transactivation responsive RNA element (TAR RNA) and allows Tat/P-TEFb complex to bind cooperatively to TAR RNA. The CDK9 component of P-TEFb and other Tat-activated kinases hyperphosphorylate the C-terminus of RNA Pol II that becomes stabilized and much more processive (By similarity). Extracellular circulating Tat can be endocytosed by surrounding uninfected cells via the binding to several surface receptors. Endosomal low pH allows Tat to cross the endosome membrane to enter the cytosol and eventually further translocate into the nucleus, thereby inducing severe cell dysfunctions ranging from cell activation to cell death. Through (By similarity). Interacts with host CCNT1. Associates with the P-TEFb complex composed at least of Tat, P-TEFb (CDK9 and CCNT1), TAR RNA, RNA Pol II. Interacts with CCNT2; the resulting complex is unable to bind to TAR RNA (By similarity). The Arg-rich RNA-binding region binds the TAR RNA. This region also mediates the nuclear localization (By similarity). The phosphorylation by CDK9 does not seem to be important for transactivation function. Expressed in the late stage of the infection cycle, when unspliced viral RNAs are exported to the cytoplasm by the viral Rev protein. Belongs to the lentiviruses Tat family. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the cyclophilin-type PPIase family. PPIase D subfamily. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 2 subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 2 family. +Regulatory subunit of a potassium efflux system that confers protection against electrophiles. Required for full activity of KefC. Shows redox enzymatic activity, but this enzymatic activity is not required for activation of KefC. a quinone + H(+) + NADH = a quinol + NAD(+) a quinone + H(+) + NADPH = a quinol + NADP(+) Homodimer. Interacts with KefC. Belongs to the NAD(P)H dehydrogenase (quinone) family. KefF subfamily. +D-glyceraldehyde 3-phosphate + NADP(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADPH D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5. Homotetramer. Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. +Brain peptide responsible for activation of prothoracic glands to produce ecdysone in insects. Heterodimer of a B chain and an A chain linked by two disulfide bonds. Silk worm has two kinds of PTTH: 4K-PTTH and 22K-PTTH; there are many forms of 4K-PTTH. Belongs to the insulin family. +Belongs to the kinesin light chain family. +carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Catalyzes the dehydration of methylthioribulose-1-phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P). S-methyl-5-thio-D-ribulose 1-phosphate = 5-methylsulfanyl-2,3-dioxopentyl phosphate + H2O Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 2/6. Belongs to the aldolase class II family. MtnB subfamily. +May be a component of the linker structure that bridges the ciliary membrane and peripheral singlet microtubules. Expressed exclusively at the cilium tip where it localizes between the cell membrane and peripheral A-subfibers. 'Sentan' means 'tip' in Japanese. Belongs to the S-100 family. +May play a role in controlling magnetite number and size (Probable). Coexpression of mamLQRBIEMO in a deletion of the 17 gene mamAB operon restores magnetosome vesicle formation but not magnetite biosynthesis (PubMed:27286560). Part of the probable 17 gene mamAB operon. Normal magnetic response, slightly smaller, sometime scattered magnetosomes (PubMed:24816605). Deletion of approximately 80 kb of DNA, including this operon, leads to cells that are non-magnetic, lack internal membrane systems, grow poorly, have reduced mobility and take-up and accumulate iron poorly (PubMed:13129949). This bacteria makes up to 60 cubo-octahedral magnetosomes of about 45 nm in diameter which contain membrane-bound crystals of magnetite (Fe(3)O(4)). Expression of just the minimal mamAB gene cluster (MGMSRv2__2365 to MGMSRv2__2381), including this gene, is sufficient to form a minimal magnetosome chain with small magnetite particles. Belongs to the magnetosome MamR family. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. +Catalyzes the efflux of L-lysine. Belongs to the LysE/ArgO transporter (TC 2.A.75) family. Extended N-terminus. Extended N-terminus. +Required for maturation of ribosomal RNAs and formation of the large ribosomal subunit. Belongs to the WD repeat BOP1/ERB1 family. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +Hydrolyzes the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom. Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. H2O + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine = 2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl 1-phosphate + 2 H(+) + UMP Binds 2 Mn(2+) ions per subunit in a binuclear metal center. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 4/6. Belongs to the LpxH family. +DEAD-box RNA helicase involved in RNA degradation. Has RNA-dependent ATPase activity and unwinds double-stranded RNA. ATP + H2O = ADP + H(+) + phosphate Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Belongs to the DEAD box helicase family. RhlB subfamily. +Belongs to the 'phage' integrase family. +(2R)-O-phospho-3-sulfolactate + H2O = (2R)-3-sulfolactate + phosphate Belongs to the ComB family. +Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate. ATP + L-glutamate = ADP + L-glutamyl 5-phosphate Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 1/2. Belongs to the glutamate 5-kinase family. +Belongs to the cytochrome P450 family. +Serine protease inhibitor that also shows protective effect in a cytotoxicity model. It binds to all proteases tested (trypsin (Ki=52 nM), alpha-chymotrypsin, cathepsin G, kallikrein, and human neutrophil elastase). It significantly increases neuroblastoma cell viability in an in vitro neurotoxicity model (in which cytotoxicity is induced by 6-hydroxydopamine (6-OHDA)) being a consequence of an effective decrease of reactive oxygen species (ROS) level in the cells. Does not show activity on all potassium channel tested (Kv1.1/KCNA1, Kv1.2/KCNA2, Kv1.3/KCNA3, Kv1.4/KCNA4, Kv1.5/KCNA5, Kv1.6/KCNA8, Shaker IR, and Kv11.1/KCNH2/ERG1). Belongs to the venom Kunitz-type family. Sea anemone type 2 potassium channel toxin subfamily. +Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser) ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec) Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. Homodimer. The tRNA molecule binds across the dimer. Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Phosphotransfer between the C1 and C5 carbon atoms of pentose. alpha-D-ribose 1-phosphate = D-ribose 5-phosphate 2-deoxy-alpha-D-ribose 1-phosphate = 2-deoxy-D-ribose 5-phosphate Binds 1 or 2 manganese ions. Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route II): step 1/3. Belongs to the phosphopentomutase family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +Cytochrome P450 monooxygenase; part of the gene clusters that mediates the biosynthesis of lolitrems, indole-diterpene mycotoxins that are potent tremorgens in mammals, and are synthesized by clavicipitaceous fungal endophytes in association with their grass hosts (PubMed:16765617, PubMed:22750140). The geranylgeranyl diphosphate (GGPP) synthase ltmG is proposed to catalyze the first step in lolitrem biosynthesis (PubMed:16765617, PubMed:15991026). LtmG catalyzes a series of iterative condensations of isopentenyl diphosphate (IPP) with dimethylallyl diphosphate (DMAPP), geranyl diphosphate (GPP), and farnesyl diphosphate (FPP), to form GGPP (PubMed:16765617, PubMed:15991026). GGPP then condenses with indole-3-glycerol phosphate to form 3-geranylgeranylindole, an acyclic intermediate, to be incorporated into paxilline (PubMed:16765617). Either ltmG or ltmC could be responsible for this step, as both are putative prenyl transferases (PubMed:16765617). The FAD-dependent monooxygenase ltmM then catalyzes the epoxidation of the two terminal alkenes of the geranylgeranyl moiety, which is subsequently cyclized by ltmB, to paspaline (PubMed:16765617, PubMed:15991026). The cytochrome P450 monooxygenases ltmQ and ltmP can sequentially oxidize paspaline to terpendole E and terpendole F (PubMed:22750140). Alternatively, ltmP converts paspaline to an intermediate which is oxidized by ltmQ to terpendole F (PubMed:22750140). LtmF, ltmK, ltmE and ltmJ appear to be unique to the epichloe endophytes (PubMed:16765617, PubMed:15991026). The prenyltransferase ltmF is involved in the 27-hydroxyl-O-prenylation (PubMed:22750140). The cytochrome P450 monooxygenase ltmK is required for the oxidative acetal ring formation (PubMed:22750140). The multi-functional prenyltransferase ltmE is required for C20- and C21-prenylations of the indole ring of paspalanes and acts together with the cytochrome P450 monooxygenase ltmJ to yield lolitremanes by multiple oxidations and ring closures (PubMed:22750140). The stereoisomer pairs of lolitriol and lolitrem N or lolitrem B and lolitrem F may be attributed to variations in the way in which ring closure can occur under the action of ltmJ (PubMed:22750140). While the major product of this pathway is lolitrem B, the prenyl transferases and cytochrome P450 monooxygenases identified in this pathway have a remarkable versatility in their regio- and stereo-specificities to generate a diverse range of metabolites that are products of a metabolic grid rather than a linear pathway (PubMed:22750140). Secondary metabolite biosynthesis. Expression is down-regulated when the stress-activated mitogen-activated protein kinase (sakA) is deleted (PubMed:20519633). Accumulates the paspalane 13-desoxypaxilline (PubMed:22750140). Belongs to the cytochrome P450 family. +Gibberellin-regulated protein that may function in hormonal controlled steps of development such as seed germination, flowering and seed maturation. Six disulfide bonds may be present. Belongs to the GASA family. +Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in the wobble position of the QUC anticodon. Binds 1 zinc ion per subunit. Belongs to the class-I aminoacyl-tRNA synthetase family. GluQ subfamily. +Part of the Sec61 complex, which is the major component of a channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). The functional states of the translocon complex include co- and post-translational ER import, cotranslational membrane protein integration and retrograde transport of misfolded proteins out of the ER. In the cotranslational pathway, ribosomes synthesizing presecretory proteins are targeted to the translocon by the cytosolic signal recognition particle (SRP) and its ER-localized receptor. The association of the Sec61 complex with the ribosome is mediated by the 28S rRNA of the large ribosomal subunit. SRP-independent post-translational translocation requires the association of additional factors, such as the Sec62/63 complex and KAR2. In an initial step, the signal sequence seems to bind simultaneously to SEC61 and SEC62. A cycle of assembly and disassembly of Sec62/63 complex from SEC61 may govern the activity of the translocon. SEC61 mediates the association with the ribosome. Component of the heterotrimeric Sec61 complex, which is composed of SEC61, SBH1 and SSS1. Presumably three to four Sec61 heterotrimers assemble into an oligomeric ring with a central aqueous pore. In cotranslational ER import, the pore diameter varies from 9-15 A in a ribosome-free resting state to 40-60 A in a functional state when associated with the ribosome. The Sec61 complex is part of a channel-forming translocon complex whose composition seem to change dependent upon different functional states. During post-translational ER import the Sec61 complex associates with the Sec62/63 complex to form the Sec complex. SEC61 interacts with STT3, OST1, OST2, OST4, SWP1 AND WBP1 components of the OT complex. Present with 24800 molecules/cell in log phase SD medium. Belongs to the SecY/SEC61-alpha family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL30 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) In plastids the minimal PEP RNA polymerase catalytic core is composed of four subunits: alpha, beta, beta', and beta''. When a (nuclear-encoded) sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +IGF-binding proteins prolong the half-life of the IGFs and have been shown to either inhibit or stimulate the growth promoting effects of the IGFs on cell culture. They alter the interaction of IGFs with their cell surface receptors. Binds IGF2 more than IGF1. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Expressed in kidney, testis, lung, heart, stomach, intestine, pancreas, liver and salivary gland. Strongly expressed in acute pancreatitis, brain, and in peripheral endothelial cells. Among the many cysteines in the lumenal domain, most are probably involved in disulfide bonds. Belongs to the DIPK family. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. +Catalyzes the ATP- as well as the pyrophosphate-dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK/P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P-Ser-HPr). The two antagonistic activities of HprK/P are regulated by several intracellular metabolites, which change their concentration in response to the absence or presence of rapidly metabolisable carbon sources (glucose, fructose, etc.) in the growth medium. Therefore, by controlling the phosphorylation state of HPr, HPrK/P is a sensor enzyme that plays a major role in the regulation of carbon metabolism and sugar transport: it mediates carbon catabolite repression (CCR), and regulates PTS-catalyzed carbohydrate uptake and inducer exclusion. [HPr protein]-L-serine + ATP = [HPr protein]-O-phospho-L-serine + ADP + H(+) [HPr protein]-O-phospho-L-serine + H(+) + phosphate = [HPr protein]-L-serine + diphosphate Homohexamer. The Walker A ATP-binding motif also binds Pi and PPi. Both phosphorylation and phosphorolysis are carried out by the same active site and suggest a common mechanism for both reactions. Belongs to the HPrK/P family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Accepts sulfur from TusA and transfers it in turn to TusE. Heterohexamer, formed by a dimer of trimers. The hexameric TusBCD complex contains 2 copies each of TusB, TusC and TusD. The TusBCD complex interacts with TusE. Belongs to the DsrE/TusD family. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit. Belongs to the RnpA family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +This receptor is controlled by G proteins. Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it. Their voltage dependence is regulated by the concentration of extracellular potassium; as external potassium is raised, the voltage range of the channel opening shifts to more positive voltages. The inward rectification is mainly due to the blockage of outward current by internal magnesium. Can be blocked by extracellular barium (By similarity). Subunit of ATP-sensitive potassium channels (KATP). Can form cardiac and smooth muscle-type KATP channels with ABCC9. KCNJ11 forms the channel pore while ABCC9 is required for activation and regulation. Interacts with ABCC8/SUR. Interacts with ABCC9/SUR2. Phosphorylation by MAPK1 results in changes in channel gating that destabilize the closed states and reduce the ATP sensitivity. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Defects in KCNJ11 may contribute to non-insulin-dependent diabetes mellitus (NIDDM), also known as diabetes mellitus type 2. The disease is caused by variants affecting the gene represented in this entry. Belongs to the inward rectifier-type potassium channel (TC 1.A.2.1) family. KCNJ11 subfamily. Extended N-terminus. +Involved in pre-mRNA splicing. Associated with the spliceosome. Belongs to the SLU7 family. +Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine Purine metabolism; AMP biosynthesis via salvage pathway; AMP from adenine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. +May form a heterooligomeric complex that consists of seven subunits: mnhA2, mnhB2, mnhC2, mnhD2, mnhE2, mnhF2 and mnhG2. Belongs to the CPA3 antiporters (TC 2.A.63) subunit C family. +Cell division inhibitor that blocks the formation of polar Z ring septums. Rapidly oscillates between the poles of the cell to destabilize FtsZ filaments that have formed before they mature into polar Z rings. Prevents FtsZ polymerization. Interacts with MinD and FtsZ. Belongs to the MinC family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase gamma chain family. +Involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions. alpha-D-mannose 1-phosphate = D-mannose 6-phosphate Nucleotide-sugar biosynthesis; GDP-alpha-D-mannose biosynthesis; alpha-D-mannose 1-phosphate from D-fructose 6-phosphate: step 2/2. Homodimer. Belongs to the eukaryotic PMM family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +A bacterial surface lipoprotein that binds host (human) complement factor H (fH, gene CFH) (PubMed:16785547). Binding contributes to the avoidance of complement-mediated lysis by N.meningitidis (Probable). Binds to host factor H (fH from human) (PubMed:16785547). Both fHbp beta-barrels contact Sushi domains 6 and 7 in fH (also called complement control protein domains, CCP). This interaction probably mimics the normal (carbohydrate-dependent) mode of fH recruitement, regulating fH activity (By similarity). Surface exposed. Expressed at high levels in this strain (at protein level). Structures show there are 2 beta barrel domains, 51-156 and 167-274 each form an 8-stranded antiparallel beta-barrel joined by linker between 157-166. Bacteria no longer bind fH and are more sensitive to complement-mediated killing. Part of an outer membrane vesicle vaccine; antisera against this protein induce efficient complement-mediated killing of the homologous strain. Three antigenic variant groups were detected upon sequencing of group B strains; antibodies against a single variant group provide reduced protection against the other 2 groups. Recombinant protein lipidation increases its immunogenicity. One of the major antigens of group B N.meningitidis and a powerful protective antigen. It is highly variable, at least 300 protein variants have been seen (see Factor H binding protein sequence typing below). Belongs to the factor H binding-protein family. Extended N-terminus. +Nuclear transcriptional activator of viral gene expression, that is essential for viral transcription from the LTR promoter and replication. Acts as a sequence-specific molecular adapter, directing components of the cellular transcription machinery to the viral RNA to promote processive transcription elongation by the RNA polymerase II (RNA pol II) complex, thereby increasing the level of full-length transcripts. In the absence of Tat, the RNA Pol II generates short or non-processive transcripts that terminate at approximately 60 bp from the initiation site. Tat associates with the CCNT1/cyclin-T1 component of the P-TEFb complex (CDK9 and CCNT1), which promotes RNA chain elongation. This binding increases Tat's affinity for a hairpin structure at the 5'-end of all nascent viral mRNAs referred to as the transactivation responsive RNA element (TAR RNA) and allows Tat/P-TEFb complex to bind cooperatively to TAR RNA. The CDK9 component of P-TEFb and other Tat-activated kinases hyperphosphorylate the C-terminus of RNA Pol II that becomes stabilized and much more processive. Other factors such as HTATSF1/Tat-SF1, SUPT5H/SPT5, and HTATIP2 are also important for Tat's function. Besides its effect on RNA Pol II processivity, Tat induces chromatin remodeling of proviral genes by recruiting the histone acetyltransferases (HATs) CREBBP, EP300 and PCAF to the chromatin. This also contributes to the increase in proviral transcription rate, especially when the provirus integrates in transcriptionally silent region of the host genome. To ensure maximal activation of the LTR, Tat mediates nuclear translocation of NF-kappa-B by interacting with host RELA. Through its interaction with host TBP, Tat may also modulate transcription initiation. Tat can reactivate a latently infected cell by penetrating in it and transactivating its LTR promoter. In the cytoplasm, Tat is thought to act as a translational activator of HIV-1 mRNAs. Extracellular circulating Tat can be endocytosed by surrounding uninfected cells via the binding to several surface receptors such as CD26, CXCR4, heparan sulfate proteoglycans (HSPG) or LDLR. Neurons are rarely infected, but they internalize Tat via their LDLR. Through its interaction with nuclear HATs, Tat is potentially able to control the acetylation-dependent cellular gene expression. Modulates the expression of many cellular genes involved in cell survival, proliferation or in coding for cytokines or cytokine receptors. Tat plays a role in T-cell and neurons apoptosis. Tat induced neurotoxicity and apoptosis probably contribute to neuroAIDS. Circulating Tat also acts as a chemokine-like and/or growth factor-like molecule that binds to specific receptors on the surface of the cells, affecting many cellular pathways. In the vascular system, Tat binds to ITGAV/ITGB3 and ITGA5/ITGB1 integrins dimers at the surface of endothelial cells and competes with bFGF for heparin-binding sites, leading to an excess of soluble bFGF. Interacts with host CCNT1. Associates with the P-TEFb complex composed at least of Tat, P-TEFb (CDK9 and CCNT1), TAR RNA, RNA Pol II. Recruits the HATs CREBBP, TAF1/TFIID, EP300, PCAF and GCN5L2. Interacts with host KAT5/Tip60; this interaction targets the latter to degradation. Interacts with the host deacetylase SIRT1. Interacts with host capping enzyme RNGTT; this interaction stimulates RNGTT. Binds to host KDR, and to the host integrins ITGAV/ITGB3 and ITGA5/ITGB1. Interacts with host KPNB1/importin beta-1 without previous binding to KPNA1/importin alpha-1. Interacts with EIF2AK2. Interacts with host nucleosome assembly protein NAP1L1; this interaction may be required for the transport of Tat within the nucleus, since the two proteins interact at the nuclear rim. Interacts with host C1QBP/SF2P32; this interaction involves lysine-acetylated Tat. Interacts with the host chemokine receptors CCR2, CCR3 and CXCR4. Interacts with host DPP4/CD26; this interaction may trigger an anti-proliferative effect. Interacts with host LDLR. Interacts with the host extracellular matrix metalloproteinase MMP1. Interacts with host PRMT6; this interaction mediates Tat's methylation. Interacts with, and is ubiquitinated by MDM2/Hdm2. Interacts with host PSMC3 and HTATIP2. Interacts with STAB1; this interaction may overcome SATB1-mediated repression of IL2 and IL2RA (interleukin) in T cells by binding to the same domain than HDAC1. Interacts (when acetylated) with human CDK13, thereby increasing HIV-1 mRNA splicing and promoting the production of the doubly spliced HIV-1 protein Nef.Interacts with host TBP; this interaction modulates the activity of transcriptional pre-initiation complex. Interacts with host RELA. Probably localizes to both nuclear and nucleolar compartments. Nuclear localization is mediated through the interaction of the nuclear localization signal with importin KPNB1. Secretion occurs through a Golgi-independent pathway. Tat is released from infected cells to the extracellular space where it remains associated to the cell membrane, or is secreted into the cerebrospinal fluid and sera. Extracellular Tat can be endocytosed by surrounding uninfected cells via binding to several receptors depending on the cell type. The cell attachment site mediates the interaction with ITGAV/ITGB3 and ITGA5/ITGB1 integrins, leading to vascular cell migration and invasion. This interaction also provides endothelial cells with the adhesion signal they require to grow in response to mitogens. The Cys-rich region may bind 2 zinc ions. This region is involved in binding to KAT5. The transactivation domain mediates the interaction with CCNT1, GCN5L2, and MDM2. The Arg-rich RNA-binding region binds the TAR RNA. This region also mediates the nuclear localization through direct binding to KPNB1 and is involved in Tat's transfer across cell membranes (protein transduction). The same region is required for the interaction with EP300, PCAF, EIF2AK2 and KDR. Asymmetrical arginine methylation by host PRMT6 seems to diminish the transactivation capacity of Tat and affects the interaction with host CCNT1. Acetylation by EP300, CREBBP, GCN5L2/GCN5 and PCAF regulates the transactivation activity of Tat. EP300-mediated acetylation of Lys-50 promotes dissociation of Tat from the TAR RNA through the competitive binding to PCAF's bromodomain. In addition, the non-acetylated Tat's N-terminus can also interact with PCAF. PCAF-mediated acetylation of Lys-28 enhances Tat's binding to CCNT1. Lys-50 is deacetylated by SIRT1. Polyubiquitination by host MDM2 does not target Tat to degradation, but activates its transactivation function and fosters interaction with CCNT1 and TAR RNA. Phosphorylated by EIF2AK2 on serine and threonine residues adjacent to the basic region important for TAR RNA binding and function. Phosphorylation of Tat by EIF2AK2 is dependent on the prior activation of EIF2AK2 by dsRNA. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Expressed in the late stage of the infection cycle, when unspliced viral RNAs are exported to the cytoplasm by the viral Rev protein. Belongs to the lentiviruses Tat family. +Binds the poly(A) tail of mRNA, including that of its own transcript, and regulates processes of mRNA metabolism such as pre-mRNA splicing and mRNA stability. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Binds to N6-methyladenosine (m6A)-containing mRNAs and contributes to MYC stability by binding to m6A-containing MYC mRNAs. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. By binding to long poly(A) tails, may protect them from uridylation by ZCCHC6/ZCCHC11 and hence contribute to mRNA stability. May form homodimers. Component of a multisubunit autoregulatory ribonucleoprotein complex (ARC), at least composed of IGF2BP1, PABPC1 and CSDE1. Directly interacts with IGF2BP1. Part of a complex associated with the FOS mCRD domain and consisting of HNRPD, SYNCRIP, PAIP1 and CSDE1/UNR. Interacts with PAIP1 and PAIP2 (via the PABPC1-interacting motifs PAM1 and PAM2). Interacts with PAIP1 with a 1:1 stoichiometry and with PAIP2 with a 1:2 stoichiometry. The interaction with CSDE1 is direct and RNA-independent (By similarity). Found in a mRNP complex with YBX2. Interacts with TENT2/GLD2 (By similarity). Identified in the spliceosome C complex. Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. The interaction with DDX3X is direct and RNA-independent. This interaction increases in stressed cells and decreases during cell recovery. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with NXF1/TAP (By similarity). Interacts with PIWIL1 (By similarity). Interacts with AGO1, AGO2, GSPT1 and GSPT2. Interacts with LARP4B. Interacts (via the second and third RRM domains and the C-terminus) with PAIP2B (via central acidic portion and C-terminus). Forms a complex with LARP1 and SHFL. Interacts with LARP4. Interacts with ZFC3H1 in a RNase-sensitive manner. Interacts with TRIM71 (via NHL repeats) in an RNA-dependent manner. Interacts with TENT5C; the interaction has no effect on TENT5C poly(A) polymerase function. Interacts with G3BP1 and G3BP2 (By similarity). Interacts with ENDOV; the interaction is RNA-dependent and stimulates ENDOV activity (By similarity). Interacts with UPF1; the interaction is RNA-dependent (By similarity). Interacts with IGF2BP2 and IGF2BP3. May interact with SETX. Localized in cytoplasmic mRNP granules containing untranslated mRNAs (By similarity). Shuttles between the cytoplasm and the nucleus (By similarity). During stress and in the absence of DDX3X, localizes to the nucleus (By similarity). At the leading edge of migrating fibroblasts, colocalizes with DDX3X (By similarity). Relocalizes to cytoplasmic stress granules upon cellular stress where it colocalizes with ENDOV (By similarity). The RNA-binding domains RRM1 and RRM2 and the C-terminus (last 138 amino acids) regions interact with the PABPC1-interacting motif-1 (PAM1) and -2 (PAM2) of PAIP1, respectively. The RNA-binding domains RRM2 and RRM3 and the C-terminus (last 138 amino acids) regions interact with the PABPC1-interacting motif-1 (PAM1) and -2 (PAM2) of PAIP2, respectively. Phosphorylated by MAPKAPK2. Methylated by CARM1. Arg-493 is dimethylated, probably to asymmetric dimethylarginine (By similarity). Belongs to the polyadenylate-binding protein type-1 family. +Catalyzes the rearrangement of 1-deoxy-D-xylulose 5-phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S. 1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + [sulfur-carrier protein ThiS]-C-terminal Gly-Gly + 2 H(+) + 2 H2O Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homotetramer. Forms heterodimers with either ThiH or ThiS. Belongs to the ThiG family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Provides the (R)-glutamate required for cell wall biosynthesis. L-glutamate = D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the aspartate/glutamate racemases family. +Transcription factor. Does not translocate to the nucleus upon phosphorylation. +Catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG. D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5. Homotetramer. Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. +One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. Binds multiple chlorophylls. PSII binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbB/PsbC family. PsbB subfamily. +Carrier protein involved in the D-alanylation of lipoteichoic acid (LTA). The loading of thioester-linked D-alanine onto DltC is catalyzed by D-alanine--D-alanyl carrier protein ligase DltA. The DltC-carried D-alanyl group is further transferred to cell membrane phosphatidylglycerol (PG) by forming an ester bond, probably catalyzed by DltD. D-alanylation of LTA plays an important role in modulating the properties of the cell wall in Gram-positive bacteria, influencing the net charge of the cell wall. Cell wall biogenesis; lipoteichoic acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-DCP. Belongs to the DltC family. +Probable receptor which is required for the oocyte-to-zygote transition although its exact function is controversial (By similarity). Seems to be required for fertilization probably by promoting the interaction or fusion between sperm and oocyte (PubMed:16360684). Conversely, shown to be dispensable for fertilization but required for the formation of a continuous and cohesive eggshell chitin layer by maintaining a homogenous distribution of chitin synthase chs-1 at the unfertilized oocyte cell membrane (By similarity). Appears to recruit or maintain together to the unfertilized oocyte cortex several proteins including chs-1, kinase mbk-2 and pseudophosphatases egg-3, and possibly egg-4 and egg-5 (By similarity). Localizes to the cell membrane of developing oocytes. Plasma membrane localization requires extracellular matrix protein cbd-1. After fertilization, localizes to endosomes in zygotes. RNAi-mediated knockdown results in sterility due to the loss of oocyte fertilization. +Proton-coupled amino-acid transporter that transports oligopeptides of 2 to 4 amino acids with a preference for dipeptides (PubMed:8139693). Primarily responsible for the absorption of dietary di- and tripeptides from the small intestinal lumen (PubMed:8139693). a dipeptide(out) + H(+)(out) = a dipeptide(in) + H(+)(in) an L-amino acid tripeptide(out) + H(+)(out) = an L-amino acid tripeptide(in) + H(+)(in) glycyl-sarcosine(out) + H(+)(out) = glycyl-sarcosine(in) + H(+)(in) H(+)(out) + L-alanyl-L-proline(out) = H(+)(in) + L-alanyl-L-proline(in) H(+)(out) + L-leucyl-L-proline(out) = H(+)(in) + L-leucyl-L-proline(in) glycyl-L-proline(out) + H(+)(out) = glycyl-L-proline(in) + H(+)(in) H(+)(out) + L-alanyl-L-prolylglycine(out) = H(+)(in) + L-alanyl-L-prolylglycine(in) glycylglycyl-L-isoleucine(out) + H(+)(out) = glycylglycyl-L-isoleucine(in) + H(+)(in) glycylglycyl-L-proline(out) + H(+)(out) = glycylglycyl-L-proline(in) + H(+)(in) Interacts (via extracellular domain region) with trypsin. Intestine, kidney, liver and low in brain. The extracellular domain (ECD) region specifically binds trypsin. Belongs to the major facilitator superfamily. Proton-dependent oligopeptide transporter (POT/PTR) (TC 2.A.17) family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Hormone which plays a role in endochondral ossification through regulation of cartilaginous growth plate chondrocytes proliferation and differentiation. May also be vasoactive and natriuretic. May be important for freshwater adaptation (By similarity). Belongs to the natriuretic peptide family. +The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. Binds 1 lipoyl cofactor covalently. The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvH family. +Belongs to the UPF0301 (AlgH) family. +Belongs to the universal ribosomal protein uS9 family. +Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis. ATP + beta-D-fructose 6-phosphate = ADP + beta-D-fructose 1,6-bisphosphate + H(+) Allosterically activated by ADP and other diphosphonucleosides, and allosterically inhibited by phosphoenolpyruvate. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 3/4. Homotetramer. Belongs to the phosphofructokinase type A (PFKA) family. ATP-dependent PFK group I subfamily. Prokaryotic clade 'B1' sub-subfamily. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL30 family. +Farnesyl pyrophosphate synthase involved in murgantiol biosynthesis, a male-released aggregation pheromone, by catalyzing the formation of (2E,6E)-farnesyl diphosphate. (2E)-geranyl diphosphate + isopentenyl diphosphate = (2E,6E)-farnesyl diphosphate + diphosphate Binds 2 Mg(2+) ions per subunit. Pheromone biosynthesis. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg(2+). Belongs to the FPP/GGPP synthase family. +Belongs to the UPF0260 family. +Involved in membrane organization. Required for the formation of membrane compartments of CAN1 (MCCs), localization of CAN1 at the MCCs and subsequent invagination of the plasma membrane at the MCCs sites. Involved in eisosome organization and might act as a sensor of sphingolipids that regulates plasma membrane function. Involved in a novel pathway of export of proteins that lack a cleavable signal sequence. Non-classical export pathway functions also as an alternative clearance/detoxification pathway to eliminate damaged material, when the basic repair pathway is not sufficient. Associates with the ergosterol-rich membrane compartment of CAN1 (MCC). Accumulates in membrane domains at eisosomes. By ketoconazole. the promoter contains a sterol regulatory element motif, which has been identified as a UPC2-binding site. Belongs to the NCE102 family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the synthesis of IGP and AICAR. The resulting ammonia molecule is channeled to the active site of HisF. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate H2O + L-glutamine = L-glutamate + NH4(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. +Regulates arginine biosynthesis genes. Amino-acid biosynthesis; L-arginine biosynthesis [regulation]. Belongs to the ArgR family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Belongs to the UPF0051 (ycf24) family. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +This b-type cytochrome is tightly associated with the reaction center of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. With its partner (PsbE) binds heme. PSII binds additional chlorophylls, carotenoids and specific lipids. Heterodimer of an alpha subunit and a beta subunit. Cyanobacterial PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins PsbO, PsbU, PsbV and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbE/PsbF family. +NADPH-dependent alpha,beta-unsaturated oxoene reductase reducing the double bond of medium-chain (C9) to long-chain (C18) reactive electrophile species deriving from poly-unsaturated fatty acid peroxides. The best substrates are 13-lipoxygenase-derived gamma-ketols, but is unable to reduce the double bond of short-chain alkenals and alkenones such as acrolein, crotonaldehyde, 3-buten-2-one, 4-hexen-3-one and trans-2-hexenal, or quinones such as duroquinone, decylubiquinone, coenzyme Q0, menadione, menaquinone and phylloquinone. Can use trans-2-nonenal, trans-3-decen-2-one, 4-hydroxynonenal, 12-oxo-10(E) dodecanoate (traumatin), 4-oxononenal, trans-1,3 diphenyl-2-propenone, trans-1,4-diphenyl-2-butene-1,4-dione, 9-oxo-12,13-epoxy-(10E)-octadecenoic acid (trans-EKODE-1b), 9-hydroxy-12-oxo-10(E)-octadecenoic acid, 9-Hydroxy-12-oxo-10(E),15(Z)-octadecadienoic acid and 9,13-dihydroxy-10-oxo-11-octadecenoic acid as substrates, but has no activity with 13(R,S)-hydroperoxy-9(Z),11(E)-octadecadienoic acid (13-HPOD), 9(S),12(S),13(S)-trihydroxy-10(E)-octadecenoic acid, 13-hydroxy-12-oxo-9(Z)-octadecenoic acid, 9-oxo-10(E),12(Z)-octadecadienoic acid (9-KODE), 13-oxo-9(Z),11(E)-octadecadienoic acid (13-KODE) and 12-oxo-10,15(Z)-phytodienoic acid (12-OPDA). kcat is 14 sec(-1) for 4-oxo-nonenal. kcat is 4.5 sec(-1) for trans-1,4-diphenyl-2-butene-1,4-dione. kcat is 6 sec(-1) for 9-hydroxy-12-oxo-10(E)-octadecenoic acid. kcat is 3 sec(-1) for 9-Hydroxy-12-oxo-10(E),15(Z)-octadecadienoic acid. Homodimer or homotetramer (PubMed:25849509). Transition to monomer upon NADPH binding (PubMed:25849509). Interacts with calmodulin (PubMed:23549413). Interacts with HP30-1, HP30-2 and HP20 (PubMed:24248378). Faces the stroma side of the membrane (PubMed:20424175). Targeting to the chloroplast inner membrane is mediated by HP30-1, HP30-2 and HP20 (PubMed:24248378). Not regulated by 2,6-dimethoxy-p-benzoquinone (DMBQ). A nonterminal hydrophilic domain (59-100) is essential for targeting to the chloroplast. The C-terminal part (101-329) is necessary and sufficient to select for the import site. The trimeric TOC159/75/34 complex is not involved in chloroplast import of CEQORH. Belongs to the zinc-containing alcohol dehydrogenase family. Quinone oxidoreductase subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS7 family. +Intracellular vesicle trafficking and protein transport. May play a role in adaptation to stress by recylcing macromolecules in specific cellular compartments. By hydrogen peroxide and infection with an incompatible race of P.syringae and B.cinerea. Plants overexpressing RABG3E exhibit accelerated endocytosis, increased tolerance to salt and osmotic stresses and reduced accumulation of reactive oxygen species during salt stress. Belongs to the small GTPase superfamily. Rab family. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. Protein modification; protein ubiquitination. Part of a SCF (ASK-cullin-F-box) protein ligase complex (By similarity). Interacts with SKP1A/ASK1, SKP1B/ASK2 and ASK11. The F-box is necessary for the interaction with ASK proteins. +Involved in the targeting and/or fusion of transport vesicles to their target membrane during transport of proteins from the early endosome to the lysosome. Required for heterotypic fusion of late endosomes with lysosomes and homotypic lysosomal fusion. Required for calcium regulated lysosomal exocytosis. Involved in the export of chylomicrons from the endoplasmic reticulum to the cis Golgi. Required for focal exocytosis of late endocytic vesicles during phagosome formation (By similarity). Belongs to the synaptobrevin family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase epsilon chain family. +Up-regulated during co-cultivation with L.plantarum. +Snake venom natriuretic peptide that exhibits hypotensive and vasodepressor activity. Acts by activating natriuretic receptors (NPR1 and/or NPR2 and/or NPR3) (By similarity). Expressed by the venom gland. Belongs to the natriuretic peptide family. +Controls wing pigmentation patterning, possibly by regulating scale cell development (PubMed:27251284). Probably acts as an activator of the anaphase promoting complex/cyclosome (APC/C) that promotes the ubiquitin ligase activity and substrate specificity of the APC/C (By similarity). Highly expressed between the sixth larval instar (La6) and day 4 prepupa (Cr4), coinciding with a phase of rapid wing disk morphogenesis. Expression drops to a low level by day 6 prepupa (Cr6). Variations in cort gene cortex directly affect wing pigmentation patterning and are the cause of the darkening of the wing in the f. carbonaria strain. This phenomenon, known as industrial melanism, is a classroom example of evolution: during industrial revolution, the common pale B.betularia strain (f. typica) was replaced by a previously unknown black strain (f. carbonaria), driven by the interaction between bird predation and coal pollution. The variation is caused by insertion of a transposable element into the first intron of cort gene, which occured around 1819, in the early years of the industrial revolution. Belongs to the WD repeat CORT family. You want it darker - Issue 183 of September 2016 +Uptake of L-rhamnose across the cytoplasmic membrane with the concomitant transport of protons into the cell (symport system). H(+)(in) + L-rhamnopyranose(in) = H(+)(out) + L-rhamnopyranose(out) Belongs to the L-rhamnose transporter (TC 2.A.7.6) family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Endoplasmic reticulum 2-OH acyl-CoA lyase involved in the cleavage (C1 removal) reaction in the fatty acid alpha-oxydation in a thiamine pyrophosphate (TPP)-dependent manner. 2-hydroxyoctadecanoyl-CoA = formyl-CoA + heptadecanal (2R)-hydroxyhexadecanoyl-CoA = formyl-CoA + pentadecanal Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Belongs to the TPP enzyme family. +Component of the methyl-coenzyme M reductase (MCR) I that catalyzes the reductive cleavage of methyl-coenzyme M (CoM-S-CH3 or 2-(methylthio)ethanesulfonate) using coenzyme B (CoB or 7-mercaptoheptanoylthreonine phosphate) as reductant which results in the production of methane and the mixed heterodisulfide of CoB and CoM (CoM-S-S-CoB). This is the final step in methanogenesis. coenzyme B + methyl-coenzyme M = coenzyme M-coenzyme B heterodisulfide + methane Binds 2 coenzyme F430 non-covalently per MCR complex. Coenzyme F430 is a yellow nickel porphinoid. One-carbon metabolism; methyl-coenzyme M reduction; methane from methyl-coenzyme M: step 1/1. MCR is a hexamer of two alpha, two beta, and two gamma chains, forming a dimer of heterotrimers. There are two MCR complexes in this bacteria. MCR II is expressed in the early growth phase. Late growth cells contain mostly MCR I. Belongs to the methyl-coenzyme M reductase beta subunit family. +Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD). ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Belongs to the NadD family. +Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P). an N-acyl-D-glucosamine 6-phosphate = an N-acyl-D-mannosamine 6-phosphate Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 3/5. Belongs to the NanE family. +Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP. an acyl phosphate + sn-glycerol 3-phosphate = a 1-acyl-sn-glycero-3-phosphate + phosphate Lipid metabolism; phospholipid metabolism. Probably interacts with PlsX. Belongs to the PlsY family. +This major soluble protein in olfactory sensilla of male moths serves to solubilize the extremely hydrophobic pheromone molecules such as bombykol and to transport pheromone through the aqueous lymph to receptors located on olfactory cilia. Homodimer. Antenna. Belongs to the PBP/GOBP family. +With CysN forms the ATP sulfurylase (ATPS) that catalyzes the adenylation of sulfate producing adenosine 5'-phosphosulfate (APS) and diphosphate, the first enzymatic step in sulfur assimilation pathway. APS synthesis involves the formation of a high-energy phosphoric-sulfuric acid anhydride bond driven by GTP hydrolysis by CysN coupled to ATP hydrolysis by CysD. ATP + H(+) + sulfate = adenosine 5'-phosphosulfate + diphosphate Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 1/3. Heterodimer composed of CysD, the smaller subunit, and CysN. Belongs to the PAPS reductase family. CysD subfamily. +Catalyzes 2 different reactions between oxygen and the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene) depending upon the metal bound in the active site. Fe-containing acireductone dioxygenase (Fe-ARD) produces formate and 2-keto-4-methylthiobutyrate (KMTB), the alpha-ketoacid precursor of methionine in the methionine recycle pathway. Ni-containing acireductone dioxygenase (Ni-ARD) produces methylthiopropionate, carbon monoxide and formate, and does not lie on the methionine recycle pathway. 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2 = 3-(methylsulfanyl)propanoate + CO + formate + 2 H(+) 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2 = 4-methylsulfanyl-2-oxobutanoate + formate + 2 H(+) Binds 1 Fe(2+) cation per monomer. Binds 1 nickel ion per monomer. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 5/6. Monomer. Belongs to the acireductone dioxygenase (ARD) family. +Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the retrotransposons dimeric RNA genome. The particles are assembled from trimer-clustered units and there are holes in the capsid shells that allow for the diffusion of macromolecules. CA has also nucleocapsid-like chaperone activity, promoting primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty2 RNA and initiation of reverse transcription (By similarity). The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP. Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that catalyzes the conversion of the retro-elements RNA genome into dsDNA within the VLP. The enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes during plus-strand synthesis and hydrolyzes RNA primers. The conversion leads to a linear dsDNA copy of the retrotransposon that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase (IN) targets the VLP to the nucleus, where a subparticle preintegration complex (PIC) containing at least integrase and the newly synthesized dsDNA copy of the retrotransposon must transit the nuclear membrane. Once in the nucleus, integrase performs the integration of the dsDNA into the host genome (By similarity). a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Endonucleolytic cleavage to 5'-phosphomonoester. The capsid protein forms a homotrimer, from which the VLPs are assembled. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues (By similarity). The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift. The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities. Integrase core domain contains the D-x(n)-D-x(35)-E motif, named for the phylogenetically conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein (By similarity). Initially, virus-like particles (VLPs) are composed of the structural unprocessed proteins Gag and Gag-Pol, and also contain the host initiator methionine tRNA (tRNA(i)-Met) which serves as a primer for minus-strand DNA synthesis, and a dimer of genomic Ty RNA. Processing of the polyproteins occurs within the particle and proceeds by an ordered pathway, called maturation. First, the protease (PR) is released by autocatalytic cleavage of the Gag-Pol polyprotein, and this cleavage is a prerequisite for subsequent processing at the remaining sites to release the mature structural and catalytic proteins. Maturation takes place prior to the RT reaction and is required to produce transposition-competent VLPs (By similarity). Retrotransposons are mobile genetic entities that are able to replicate via an RNA intermediate and a reverse transcription step. In contrast to retroviruses, retrotransposons are non-infectious, lack an envelope and remain intracellular. Ty2 retrotransposons belong to the copia elements (pseudoviridae). Produced by +1 ribosomal frameshifting between codon Leu-431 and Gly-432 of the YDR034C-C ORF. +Belongs to the PsaM family. +DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (Probable). The highly mobile Rpo4/Rpo7 heterodimer stalk is conditionally required for transcription initiation (Probable). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Part of the 13-subunit RNA polymerase complex. Forms a stalk with Rpo7 that extends from the main structure. Belongs to the eukaryotic RPB4 RNA polymerase subunit family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Belongs to the G-protein coupled receptor 1 family. +Receptor tyrosine kinase involved in nervous system and probably heart development. Upon binding of its ligand NTF3/neurotrophin-3, NTRK3 autophosphorylates and activates different signaling pathways, including the phosphatidylinositol 3-kinase/AKT and the MAPK pathways, that control cell survival and differentiation. ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein] Exists in a dynamic equilibrium between monomeric (low affinity) and dimeric (high affinity) structures (By similarity). Binds SH2B2. Interacts with SQSTM1 and KIDINS220 (By similarity). Interacts with PTPRS (PubMed:25385546).Interacts with MAPK8IP3/JIP3 (By similarity). Isoform 2 expression is restricted to specific areas in adult brain. Isoform 3 transcripts are readily detected early during embryogenesis and are expressed predominantly in adult brain and gonads. Expression oscillates in a circadian manner in the liver. Ligand-mediated auto-phosphorylation. Non-catalytic. Non-catalytic. Belongs to the protein kinase superfamily. Tyr protein kinase family. Insulin receptor subfamily. +Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex, which mediates the ubiquitination of target proteins, leading to their degradation by the proteasome. Protein modification; protein ubiquitination. Forms pentamers. Component of a complex composed of 5 subunits of KCTD9 and 5 CUL3. +Multidrug efflux pump that functions probably as a Na(+)/drug antiporter. Belongs to the multi antimicrobial extrusion (MATE) (TC 2.A.66.1) family. MdtK subfamily. +The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpA family. +Attaches the virus to host cellular receptor, inducing endocytosis of the virion. In the endosome, the acidic pH induces conformational changes in the glycoprotein trimer, which trigger fusion between virus and cell membrane (By similarity). Homotrimer. Interacts with matrix protein (By similarity). Glycosylated by host. Glycosylation is crucial for glycoprotein export at the cell surface (By similarity). Belongs to the nucleorhabdovirus glycoprotein family. +Pore-forming subunit of a potassium efflux system that confers protection against electrophiles. Catalyzes K(+)/H(+) antiport. Interacts with the regulatory subunit KefG. Belongs to the monovalent cation:proton antiporter 2 (CPA2) transporter (TC 2.A.37) family. KefB subfamily. +Binds with low affinity to muscular (alpha-1-beta-1-delta-epsilon/CHRNA1-CHRNB1-CHRND-CHRNE) and very low affinity to neuronal (alpha-7/CHRNA7) nicotinic acetylcholine receptor (nAChR). Expressed by the venom gland. Belongs to the snake three-finger toxin family. Ancestral subfamily. Orphan group II sub-subfamily. +Belongs to the bacterial ribosomal protein bS16 family. +Short chain dehydrogenase; part of the gene cluster that mediates the biosynthesis of terretonin, a fungal meroterpenoid that acts as a mycotoxin (PubMed:22549923, PubMed:23116177, PubMed:25671343). The first step of the pathway is the synthesis of 3,5-dimethylorsellinic acid (DMOA) by the polyketide synthase trt4 (PubMed:22549923, PubMed:23116177). DMOA is then prenylated into farnesyl-DMOA by the polyprenyl transferase trt2 (PubMed:22549923, PubMed:22782788, PubMed:23116177). Methylation by the methyltransferase trt5 then leads to farnesyl-DMOA methyl ester which is further subject to epoxidation by the FAD-dependent monooxygenase trt8 to yield epoxyfarnesyl-DMOA methyl ester (PubMed:22549923, PubMed:22782788, PubMed:23116177). Cyclization of epoxyfarnesyl-DMOA methyl ester by the terpene cyclase trt1 leads to a tetracycle intermediate which is in turn converted to preterretonin (PubMed:22549923, PubMed:22782788, PubMed:23116177). Dehydrogenase trt9 comes next to transform preterretonin to preterrenoid (PubMed:22549923, PubMed:23116177). The FAD-dependent monooxygenase trt3 is then required for the C-hydroxylation at C16 of preterrenoid to yield terrenoid (PubMed:22549923, PubMed:23116177). The cytochrome P450 trt6 catalyzes three successive oxidations to transform terrenoid into an unstable intermediate, which then undergoes the D-ring expansion and unusual rearrangement of the methoxy group to afford the core skeleton of terretonin (PubMed:25671343, PubMed:28759016). Trt14 catalyzes the D-ring expansion of terretonin involving intramolecular methoxy rearrangement as well as the hydrolysis of the expanded D-ring and the methyl ester moiety (PubMed:25671343, PubMed:28759016). Finally, the nonheme iron-dependent dioxygenase trt7 accomplishes the last two oxidation reactions steps to complete the biosynthesis of terretonin (PubMed:25671343). Terretonin C is produced via spontaneous decarboxylation of the terretonin precursor (PubMed:23116177). Another shunt product of the terretonin biosynthesis is dihydrofarnesyl-DMOA, derived from epoxyfarnesyl-DMOA through hydrolysis of the epoxide (PubMed:22549923, PubMed:22782788, PubMed:23116177). Secondary metabolite biosynthesis; terpenoid biosynthesis. Impairs the synthesis of terretonin (PubMed:23116177). Belongs to the short-chain dehydrogenases/reductases (SDR) family. +DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate. Belongs to the endonuclease V family. +Transcriptional activator. Seems to be essential for sexual differentiation and formation of the primary steroidogenic tissues. Binds to the Ad4 site found in the promoter region of steroidogenic P450 genes such as CYP11A, CYP11B and CYP21B. Also regulates the AMH/Muellerian inhibiting substance gene as well as the AHCH and STAR genes. 5'-YCAAGGYC-3' and 5'-RRAGGTCA-3' are the consensus sequences for the recognition by NR5A1. The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional activity. Binds phospholipids with a phosphatidylinositol (PI) headgroup, in particular PI(3,4)P2 and PI(3,4,5)P3. Activated by the phosphorylation of NR5A1 by HIPK3 leading to increased steroidogenic gene expression upon cAMP signaling pathway stimulation (By similarity). Binds DNA as a monomer (By similarity). Part of a complex consisting of SFPQ, NONO and NR5A1. Interacts with NR0B2. Interacts with DGKQ and CDK7. Binds to and activated by HIPK3 (By similarity). Acetylation stimulates the transcriptional activity. Sumoylation reduces CDK7-mediated phosphorylation on Ser-203. Phosphorylated on Ser-203 by CDK7. This phosphorylation promotes transcriptional activity (By similarity). Belongs to the nuclear hormone receptor family. NR5 subfamily. +Part of the ABC transporter complex LolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone, LolA. Responsible for the formation of the LolA-lipoprotein complex in an ATP-dependent manner. The complex is composed of two ATP-binding proteins (LolD) and two transmembrane proteins (LolC and LolE). Belongs to the ABC transporter superfamily. Lipoprotein translocase (TC 3.A.1.125) family. +Catalyzes the ATP-dependent dehydration of threonylcarbamoyladenosine at position 37 (t(6)A37) to form cyclic t(6)A37 (ct(6)A37) in tRNAs that read codons beginning with adenine. Belongs to the HesA/MoeB/ThiF family. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +ATPase subunit of a proteasome-like degradation complex; this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the ClpX chaperone family. HslU subfamily. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +Secreted effector that acts as an elicitor that induces cell death in host plant cells. Localizes to speckle-like structures within the nucleus. The RxLR-dEER motif acts to carry the protein into the host cell cytoplasm through binding to cell surface phosphatidylinositol-3-phosphate. Belongs to the RxLR effector family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has four main subunits: a(1), b(1), b'(1) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta, b and b' chains. In plastids the F-type ATPase is also known as CF(1)CF(0). Belongs to the ATPase C chain family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Pseudokinase which, in complex with CAB39/MO25 (CAB39/MO25alpha or CAB39L/MO25beta), binds to and activates STK11/LKB1. Adopts a closed conformation typical of active protein kinases and binds STK11/LKB1 as a pseudosubstrate, promoting conformational change of STK11/LKB1 in an active conformation (By similarity). Component of a trimeric complex composed of STK11/LKB1, STRAD (STRADA or STRADB) and CAB39/MO25 (CAB39/MO25alpha or CAB39L/MO25beta): the complex tethers STK11/LKB1 in the cytoplasm and stimulates its catalytic activity. The protein kinase domain is predicted to be catalytically inactive. Belongs to the protein kinase superfamily. STE Ser/Thr protein kinase family. STE20 subfamily. +Transcription factor involved in glucosinolates biosynthesis. Can form complexes with MYC2, MYC3 or MYC4. Expressed in trichomes. Low levels of indolic glucosinolates and loss of responses to brassinosteroids. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. ATP + cytidine(34) in tRNA(Ile2) + L-lysine = AMP + diphosphate + H(+) + lysidine(34) in tRNA(Ile2) The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a P-loop motif involved in ATP binding. Belongs to the tRNA(Ile)-lysidine synthase family. +Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids. acetyl-CoA + H(+) + malonyl-[ACP] = 3-oxobutanoyl-[ACP] + CO2 + CoA Lipid metabolism; fatty acid biosynthesis. Homodimer. The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH. Belongs to the thiolase-like superfamily. FabH family. +Carboxylesterase involved in the biosynthesis of the benzylisoquinoline alkaloid noscapine (PubMed:25485687). Converts 3-O-acetylpapaveroxine to narcotine hemiacetal (PubMed:25485687). 3-O-acetylpapaveroxine + H2O = acetate + H(+) + narcotine hemiacetal Alkaloid biosynthesis. Belongs to the 'GDXG' lipolytic enzyme family. +Belongs to the fuselloviridae capsid protein VP1/VP3 family. +Specifically methylates the N1 position of guanosine-37 in various cytoplasmic and mitochondrial tRNAs. Methylation is not dependent on the nature of the nucleoside 5' of the target nucleoside. This is the first step in the biosynthesis of wybutosine (yW), a modified base adjacent to the anticodon of tRNAs and required for accurate decoding. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Monomer. Predominantly in the mitochondria and in the nucleus. Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM5/TYW2 family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +Tightly binding, competitive inhibitor of different types of pancreatic-like carboxypeptidases. Belongs to the protease inhibitor I46 family. +This protein specifically catalyzes the removal of signal peptides from prolipoproteins. Release of signal peptides from bacterial membrane prolipoproteins. Hydrolyzes -Xaa-Yaa-Zaa-|-(S,diacylglyceryl)Cys-, in which Xaa is hydrophobic (preferably Leu), and Yaa (Ala or Ser) and Zaa (Gly or Ala) have small, neutral side chains. Protein modification; lipoprotein biosynthesis (signal peptide cleavage). Belongs to the peptidase A8 family. +Catalyzes the transformation of pimelate into pimeloyl-CoA with concomitant hydrolysis of ATP to AMP. ATP + CoA + heptanedioate = 6-carboxyhexanoyl-CoA + AMP + diphosphate Metabolic intermediate metabolism; pimeloyl-CoA biosynthesis; pimeloyl-CoA from pimelate: step 1/1. Homodimer. Belongs to the BioW family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs. Interacts with KDM5B. +Contributes to the efficiency of the cell division process by stabilizing the polymeric form of the cell division protein FtsZ. Acts by promoting interactions between FtsZ protofilaments and suppressing the GTPase activity of FtsZ. Interacts directly with FtsZ. Belongs to the ZapC family. +Promotes colloidosmotic lysis by binding to the midgut epithelial cells of insects. The crystal protein is produced during sporulation and is accumulated both as an inclusion and as part of the spore coat. Toxic segment of the protein is located in the N-terminus. Belongs to the delta endotoxin family. +Belongs to the TACO1 family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +Belongs to the bacterial ribosomal protein bL33 family. +Involved in inositol deacylation of GPI-anchored proteins which plays important roles in the quality control and ER-associated degradation of GPI-anchored proteins. Belongs to the GPI inositol-deacylase family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Component of the helicase/primase complex. Unwinds the DNA at the replication forks and generates single-stranded DNA for both leading and lagging strand synthesis. The primase synthesizes short RNA primers on the lagging strand that the polymerase presumably elongates using dNTPs. The primase-associated factor has no known catalytic activity in the complex and may serve to facilitate the formation of the replisome by directly interacting with the origin-binding protein and the polymerase. Associates with the primase and the helicase to form the helicase-primase complex. Interacts with the origin-binding protein. Interacts with the polymerase catalytic subunit. Belongs to the herpesviridae HEPA family. +2 ATP + H2O + hydrogencarbonate + L-glutamine = 2 ADP + carbamoyl phosphate + 2 H(+) + L-glutamate + phosphate Binds 4 Mg(2+) or Mn(2+) ions per subunit. Amino-acid biosynthesis; L-arginine biosynthesis; carbamoyl phosphate from bicarbonate: step 1/1. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 1/3. Composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate. Belongs to the CarB family. +Nonheme diiron monooxygenase involved in the biosynthesis of xanthophylls. Specific for beta-ring hydroxylations of beta-carotene. Has also a low activity toward the beta- and epsilon-rings of alpha-carotene. No activity with acyclic carotenoids such as lycopene and neurosporene. Uses ferredoxin as an electron donor. all-trans-beta-carotene + 4 H(+) + 2 O2 + 4 reduced [2Fe-2S]-[ferredoxin] = all-trans-zeaxanthin + 2 H2O + 4 oxidized [2Fe-2S]-[ferredoxin] Homodimer. Expressed in leaves, flowers, stems, roots and siliques. The histidine box domains may contain the active site and/or be involved in iron binding. No visible phenotype when grown under normal light conditions; due to the redundancy with BCH1. Bch1 and bch2 double mutant has no visible phenotype, but lower levels of beta, beta-xanthophylls and increased beta-carotene and lutein. Cyp97c1, bch1 and bch2 triple mutant is paler and smaller than wild-type. Belongs to the sterol desaturase family. +Nitric oxide-sensitive repressor of genes involved in protecting the cell against nitrosative stress. May require iron for activity. Binds 1 [2Fe-2S] cluster per subunit. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Zn(2+) ion per subunit. In plastids the minimal PEP RNA polymerase catalytic core is composed of four subunits: alpha, beta, beta', and beta''. When a (nuclear-encoded) sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. RpoC2 subfamily. +May be a proton symporter involved in the uptake of osmolytes such as proline and glycine betaine. Belongs to the major facilitator superfamily. Metabolite:H+ Symporter (MHS) family (TC 2.A.1.6) family. +Catalyzes the NADPH-dependent reduction of glyoxylate and hydroxypyruvate into glycolate and glycerate, respectively. glycolate + NADP(+) = glyoxylate + H(+) + NADPH (R)-glycerate + NAD(+) = 3-hydroxypyruvate + H(+) + NADH (R)-glycerate + NADP(+) = 3-hydroxypyruvate + H(+) + NADPH Homodimer. Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. GhrB subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Motor protein that may participate in process critical to neuronal development and function such as cell migration, neurite outgrowth and vesicular transport. Prominent expression is seen in the brain, lung and liver. It is also expressed in the heart and testis. A high level expression is seen in virtually all neurons (but not glia) in the postnatal and adult mouse brain and in neuroblasts of the cerebellar external granular layer. Belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Myosin family. Represents an unconventional myosin. This protein should not be confused with the conventional myosin-1 (MYH1). +Has flap endonuclease activity. During DNA replication, flap endonucleases cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds 2 Mg(2+) per subunit. Only one magnesium ion has a direct interaction with the protein, the other interactions are indirect. Binds 1 K(+) per subunit. The potassium ion strongly increases the affinity for DNA. Belongs to the Xni family. Extended N-terminus. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Binds the 23S rRNA. Binds 1 zinc ion per subunit. Part of the 50S ribosomal subunit. Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily. +Forms the virus contractile tail sheath. Belongs to the myoviridae tail sheath protein family. +Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate. (S)-dihydroorotate + H2O = H(+) + N-carbamoyl-L-aspartate Binds 2 Zn(2+) ions per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 3/3. Belongs to the metallo-dependent hydrolases superfamily. DHOase family. Class I DHOase subfamily. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Catalyzes the conversion of S-adenosyl-L-methionine (SAM) to carboxy-S-adenosyl-L-methionine (Cx-SAM). prephenate + S-adenosyl-L-methionine = 3-phenylpyruvate + carboxy-S-adenosyl-L-methionine + H2O Homodimer. Belongs to the class I-like SAM-binding methyltransferase superfamily. Cx-SAM synthase family. +Essential cell division protein that coordinates cell division and chromosome segregation. The N-terminus is involved in assembly of the cell-division machinery. The C-terminus functions as a DNA motor that moves dsDNA in an ATP-dependent manner towards the dif recombination site, which is located within the replication terminus region. Required for activation of the Xer recombinase, allowing activation of chromosome unlinking by recombination (By similarity). Homohexamer. Forms a ring that surrounds DNA (By similarity). Located at the septum. Consists of an N-terminal domain, which is sufficient for the localization to the septal ring and is required for cell division, followed by a linker domain, and a C-terminal domain, which forms the translocation motor involved in chromosome segregation. The C-terminal domain can be further subdivided into alpha, beta and gamma subdomains. The alpha and beta subdomains form the DNA pump, and the gamma subdomain is a regulatory subdomain (By similarity). Belongs to the FtsK/SpoIIIE/SftA family. +Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain-length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate a ribonucleoside 3'-phosphate + H2O = a ribonucleoside + phosphate [phosphate](n) + H2O = [phosphate](n-1) + H(+) + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Part of the nuclear protein complex gamma-globin promoter and enhancer binding factor (gamma-PE) composed at least by SATB1 and HOXB2. Expressed in whole embryos and fetuses at 5-9 weeks from conception. Belongs to the Antp homeobox family. Proboscipedia subfamily. +Proton-coupled monocarboxylate transporter. Catalyzes the rapid transport across the plasma membrane of many monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and the ketone bodies acetoacetate, beta-hydroxybutyrate and acetate. Depending on the tissue and on cicumstances, mediates the import or export of lactic acid and ketone bodies. Required for normal nutrient assimilation, increase of white adipose tissue and body weight gain when on a high-fat diet. Plays a role in cellular responses to a high-fat diet by modulating the cellular levels of lactate and pyruvate, small molecules that contribute to the regulation of central metabolic pathways and insulin secretion, with concomitant effects on plasma insulin levels and blood glucose homeostasis. Inhibited by stilbene disulfonates, such as di-isothiocyanostilbene disulfonate(DIDS), a cross-linking reagent that forms covalent linkages with lysine groups. Interacts with BSG. Interacts with EMB. Interaction with either BSG or EMB is required for expression at the cell membrane. Detected in erythrocytes (at protein level). Detected in brain, heart, kidney, lung, muscle, jejunum enterocytes and brain capillaries. Belongs to the major facilitator superfamily. Monocarboxylate porter (TC 2.A.1.13) family. +Required for normal contractile vacuole structure and function. Cells expressing a dominant negative rab11A exhibit a more extensive contractile vacuole network and enlarged contractile vacuole bladders. These cells exhibit a functional defect in osmotic regulation where cells immersed in water become rounded and detach from the surface, and contain swollen contractile vacuoles. Belongs to the small GTPase superfamily. Rab family. +Belongs to the bacterial ribosomal protein bL28 family. +Belongs to the UPF0344 family. +Mediates taxis toward dipeptides via an interaction with the periplasmic dipeptide-binding protein. Chemotactic-signal transducers respond to changes in the concentration of attractants and repellents in the environment, transduce a signal from the outside to the inside of the cell, and facilitate sensory adaptation through the variation of the level of methylation. Attractants increase the level of methylation while repellents decrease the level of methylation, the methyl groups are added by the methyltransferase CheR and removed by the methylesterase CheB. Found predominantly at cell poles. Belongs to the methyl-accepting chemotaxis (MCP) protein family. +Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. 2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2 The D1/D2 heterodimer binds P680, chlorophylls that are the primary electron donor of PSII, and subsequent electron acceptors. It shares a non-heme iron and each subunit binds pheophytin, quinone, additional chlorophylls, carotenoids and lipids. D1 provides most of the ligands for the Mn4-Ca-O5 cluster of the oxygen-evolving complex (OEC). There is also a Cl(-1) ion associated with D1 and D2, which is required for oxygen evolution. The PSII complex binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Tyr-161 forms a radical intermediate that is referred to as redox-active TyrZ, YZ or Y-Z. C-terminally processed by CTPA; processing is essential to allow assembly of the oxygen-evolving complex and thus photosynthetic growth. 2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water. Herbicides such as atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer. Belongs to the reaction center PufL/M/PsbA/D family. +Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes. Localizes to the plus end of microtubules and to the centrosome. Dimerization mediated by the LisH domain may be required to activate dynein. Belongs to the WD repeat LIS1/nudF family. +Belongs to the UPF0246 family. +This is a copper-containing oxidase that functions in the formation of pigments such as melanins and other polyphenolic compounds. Catalyzes the rate-limiting conversions of tyrosine to DOPA, DOPA to DOPA-quinone and possibly 5,6 dihydroxyindole to indole-5'6 quinone. 2 L-dopa + O2 = 2 H2O + 2 L-dopaquinone L-tyrosine + O2 = H2O + L-dopaquinone Binds 2 copper ions per subunit. Heterodimer. Synthesized by hemocytes and released into the hemolymph plasma. The N-terminus is blocked. Belongs to the tyrosinase family. +beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Binds 2 magnesium ions per subunit. Carbohydrate biosynthesis; gluconeogenesis. Homotetramer. Belongs to the FBPase class 1 family. +In association with ufd-1 and ATPase cdc-48.1 and/or cdc-48.2, involved in the cytoplasmic elimination of misfolded proteins exported from the ER (PubMed:16647269, PubMed:22768338). This pathway, known as ERAD, prevents the activation of the unfolded protein response (UPR) caused by the accumulation of misfolded proteins in the ER (PubMed:16647269, PubMed:22768338). During S phase and in association with ufd-1, cdc-48.1 and/or cdc-48.2 and ubxn-3, ensures the degradation of DNA licensing factor cdt-1 after the initiation of DNA replication and thus the disassembly of the DNA replication CGM helicase complex by promoting the dissociation from chromatin of several of its components including cdc-45 and sld-5 (PubMed:18728180, PubMed:21981920, PubMed:26842564, PubMed:28368371). Regulates ubxn-3 nuclear localization during S phase (PubMed:26842564). Forms a complex composed of ubxn-3, ufd-1, npl-4.1 and cdc-48.1; within the complex, interacts with ufd-1 and ubxn-3 (PubMed:20977550). Interacts with ufd-1 (PubMed:16647269). Interacts with elc-1/elongin C; the interaction may mediate the interaction between the npl-4-ufd-1-cdc-48 complex and the E3 ubiquitin ligase cul-2 complex (PubMed:19773360). Localizes to the cytoplasm during mitosis. Nuclear localization upon nuclear membrane re-assembly is cdc-48-dependent. Simultaneous RNAi-mediated knockdown of npl-4.1 and npl-4.2 causes embryonic lethality (PubMed:16647269, PubMed:26842564). In embryos, DNA replication is partially impaired causing a delay in S phase progression in P0, AB and P1 cells; simultaneous RNAi-mediated knockdown of DNA replication checkpoint kinases chk-1 or atl-1 suppresses the delay in S phase (PubMed:18728180, PubMed:26842564). During S phase, prevents DNA replication licensing factor cdt-1 down-regulation and causes cdt-1 accumulation on mitotic chromosomes (PubMed:21981920). Impairs dissociation from the chromatin of components of the DNA replication machinery, including cdc-45, GINS complex component sld-5 and CMG helicase component mcm-3, resulting in their persistent association with chromatin throughout embryonic mitosis (PubMed:21981920, PubMed:26842564, PubMed:28368371). Abnormal ubxn-3 localization into punctate structures in the nucleus (PubMed:26842564). Reduces ufd-1 expression in embryos (PubMed:21981920, PubMed:26842564). Simultaneous RNAi-mediated knockdown of npl-4.1 and npl-4.2 in adults causes a proliferation arrest of mitotic germline cells in the gonad with formation of rad-51 foci on chromatin (PubMed:18728180). Induces the unfolded protein response and increases sensitivity to tunicamycin-induced ER stress (PubMed:16647269). Causes accumulation of misfolded protein cpl-1 in the ER (PubMed:22768338). Belongs to the NPL4 family. There is another gene, npl-4.2, which has a 99% identical sequence making it difficult to identify the specific function for each protein. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +Required for the processing of the 27S pre-rRNA. Belongs to the EBP2 family. +Homotrimer (via collagen-like domain). May form higher order oligomers by supercoiling of the trimers (By similarity). May interact with ERFE. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine. L-leucyl-tRNA(Leu) + N-terminal L-lysyl-[protein] = H(+) + N-terminal L-leucyl-L-lysyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-arginyl-[protein] = H(+) + N-terminal L-leucyl-L-arginyl-[protein] + tRNA(Leu) an N-terminal L-alpha-aminoacyl-[protein] + L-phenylalanyl-tRNA(Phe) = an N-terminal L-phenylalanyl-L-alpha-aminoacyl-[protein] + tRNA(Phe) Belongs to the L/F-transferase family. +Essential for oogenesis; required for late follicle cell development. Component of the small ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains about 33 different proteins and 1 molecule of RNA (18S). The 60S subunit contains about 49 different proteins and 3 molecules of RNA (28S, 5.8S and 5S). Belongs to the eukaryotic ribosomal protein eS1 family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Repressed under conditions of excess protein secretion capacity and derepressed when protein secretion becomes limiting. This is regulated by SecM. Belongs to the SecA family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Belongs to the imidazoleglycerol-phosphate dehydratase family. +DNA helicase which seems to act as a postreplicative transcription termination factor. Involved in ATP-dependent release of nascent RNA. Forms a stable complex with single-stranded DNA, and to a lesser extent RNA (By similarity). Interacts with G2. Might be part of a transcription complex composed at least of G2, A18, and H5. Localizes to the virion core. Belongs to the helicase family. Poxviruses subfamily. +Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34. 5-aminomethyl-2-thiouridine(34) in tRNA + S-adenosyl-L-methionine = 5-methylaminomethyl-2-thiouridine(34) in tRNA + H(+) + S-adenosyl-L-homocysteine In the N-terminal section; belongs to the methyltransferase superfamily. tRNA (mnm(5)s(2)U34)-methyltransferase family. In the C-terminal section; belongs to the DAO family. +May be involved in autophagy-related processes. Unlike other Rab family members, does not interact with GDP dissociation inhibitors (GDIs), including ARHGDIA and ARHGDIB. Interacts with ZFYVE20. Only about 20-25% is recovered in the particulate fraction. By extensive retinoic acid treatment, in Ntera-2 teratoma cell line induced to differentiate into post-mitotic neurons (NTN2) (at protein level). Isoprenylation is inefficient compared to other Rab family members. The unusual Ser-67, instead of a conserved Gln in other family members, is the cause of low GTPase activity. As a result, the predominant nucleotide associated with the protein is GTP (By similarity). Belongs to the small GTPase superfamily. Rab family. +Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6-phosphate and D-lactate. H2O + N-acetyl-D-muramate 6-phosphate = (R)-lactate + N-acetyl-D-glucosamine 6-phosphate Amino-sugar metabolism; N-acetylmuramate degradation. Homodimer. A lyase-type mechanism (elimination/hydration) is suggested for the cleavage of the lactyl ether bond of MurNAc 6-phosphate, with the formation of an alpha,beta-unsaturated aldehyde intermediate with (E)-stereochemistry, followed by the syn addition of water to give product. Belongs to the GCKR-like family. MurNAc-6-P etherase subfamily. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Functions as an ATPase. May play a role in metal insertion (metal-chelatase) or as a chaperone. The complex formed with CadA represents a possible means of regulating RavA activity in response to acid stress conditions. This interaction results in an increase in RavA ATPase activity. RavA also has GTPase activity. Optimum pH is 7.5. Hexameric oligomer. Interactions of five RavA oligomers with two CadA decamers. Possible formation of a ternary complex RavA-ViaA-CadA. Expression is sigma S-dependent. Belongs to the RavA family. +Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ). 5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphooxyethyl)-thiazole + ADP + H(+) Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-methyl-5-(2-phosphoethyl)-thiazole from 5-(2-hydroxyethyl)-4-methylthiazole: step 1/1. Belongs to the Thz kinase family. +Envelope protein. Probably localizes to the membrane of mature virions (MV). Expressed in the late phase of the viral replicative cycle. Belongs to the Chordopoxvirinae I5 family. +Mediates the nuclear export of encapsidated genomic RNAs (ribonucleoproteins, RNPs). Acts as an adapter between viral RNPs complexes and the nuclear export machinery of the cell. Possesses no intrinsic RNA-binding activity, but includes a C-terminal M1-binding domain. This domain is believed to allow recognition of RNPs bound to the protein M1. Since protein M1 is not available in large quantities before late stages of infection, such an indirect recognition mechanism probably ensures that genomic RNPs are not exported from the host nucleus until sufficient quantities of viral mRNA and progeny genomic RNA have been synthesized. Furthermore, the RNPs enter the host cytoplasm only when associated with the M1 protein that is necessary to guide them to the plasma membrane. May down-regulate viral RNA synthesis when overproduced. Interacts with protein M1. May interact with host nucleoporin RAB/HRB and exportin XPO1/CRM1. Average number present in a viral particle is estimated to be 130-200 molecules. Belongs to the influenza viruses NEP family. +Probably mediates the hydrolysis of some nucleoside diphosphate derivatives. Belongs to the Nudix hydrolase family. PCD1 subfamily. +Receptor for adenosine. The activity of this receptor is mediated by G proteins which inhibits adenylyl cyclase. Phosphorylation on Ser-318 may be crucial for rapid desensitization. Belongs to the G-protein coupled receptor 1 family. +Odorant receptor. Belongs to the G-protein coupled receptor 1 family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Interleukin-16 stimulates a migratory response in CD4+ lymphocytes, monocytes, and eosinophils. Primes CD4+ T-cells for IL-2 and IL-15 responsiveness. Also induces T-lymphocyte expression of interleukin 2 receptor. Ligand for CD4. May act as a scaffolding protein that anchors ion channels in the membrane. Isoform 3 is involved in cell cycle progression in T-cells. Appears to be involved in transcriptional regulation of SKP2 and is probably part of a transcriptional repression complex on the core promoter of the SKP2 gene. May act as a scaffold for GABPB1 (the DNA-binding subunit the GABP transcription factor complex) and HDAC3 thus maintaining transcriptional repression and blocking cell cycle progression in resting T-cells. Homotetramer (Probable). According to PubMed:9699630, the formation of a homotetrameric protein complex is not required for the chemo-attractant function. Isoform 3 interacts (via PDZ 3 domain) with PPP1R12A, PPP1R12B and PPP1R12C. Isoform 1 interacts with PPP1R12B. Isoform 3 interacts with GRIN2A. Isoform 3 interacts with GABPB1. Isoform 3 interacts (via PDZ 3 domain) with HDAC3. Isoform 1 interacts with GRIN2D, KCNJ10, KCNJ15 and CACNA1C (By similarity). (Microbial infection) Isoform 3 interacts with HTLV-1 tax. Expressed in hemopoietic tissues, such as resting T-cells, but undetectable during active T-cell proliferation. Down-regulated in T-cells after TCR activation. Synthesized as a chemo-attractant inactive precursor in hemopoietic tissues, and proteolytically cleaved by caspase-3 to yield IL-16. Produced by alternative promoter usage. Is probably proteolytically processed to yield IL-16. Produced by alternative splicing of isoform 1. Is probably proteolytically processed to yield IL-16. Produced by alternative promoter usage. Is proteolytically processed to yield IL-16. +Component of the signal recognition particle (SRP) complex, a ribonucleoprotein complex that mediates the cotranslational targeting of secretory and membrane proteins to the endoplasmic reticulum (ER) (PubMed:7925282, PubMed:10573124). The SRP complex is required for the cotranslational protein translocation for ER import and preferentially recognizes strongly hydrophobic signal sequences (PubMed:10573124). It is involved in targeting the nascent chain-ribosome (RNC) complex to the ER and is proposed to participate in the arrest of nascent chain elongation during membrane targeting (PubMed:10573124). SRP14 binds scR1 RNA to form the probable Alu domain of SRP responsible for elongation arrest (PubMed:10573124). Component of a fungal signal recognition particle (SRP) complex that consists of a 7SL RNA molecule (scR1) and at least six protein subunits: SRP72, SRP68, SRP54, SEC65, SRP21 and SRP14 (PubMed:7925282). At least SRP14, SRP21, SRP68 and SRP72 are proposed to get assembled together with scR1 RNA as a pre-SRP complex in the nucleolus which is exported to the cytoplasm. SRP14 binds RNA as a homodimer (PubMed:7925282). Present with 8000 molecules/cell in log phase SD medium. Belongs to the SRP14 family. +Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway. The reaction occurs in a stepwise manner with a three-propionate intermediate. Fe-coproporphyrin III + 2 H(+) + 2 H2O2 = 2 CO2 + 4 H2O + heme b Fe-coproporphyrin III + H(+) + H2O2 = CO2 + 2 H2O + harderoheme III H(+) + H2O2 + harderoheme III = CO2 + 2 H2O + heme b Fe-coproporphyrin III acts as both substrate and redox cofactor. Porphyrin-containing compound metabolism; protoheme biosynthesis. Belongs to the ChdC family. Type 1 subfamily. +Cytochrome c2 is found mainly in purple, non-sulfur, photosynthetic bacteria where it functions as the electron donor to the oxidized bacteriochlorophyll in the photophosphorylation pathway. However, it may also have a role in the respiratory chain and is found in some non-photosynthetic bacteria. Binds 1 heme c group covalently per subunit. Belongs to the cytochrome c family. The sequence shown here has been extracted from PDB entry 1CXA. +Part of the elfADCG fimbrial operon, which could be required for adherence to host epithelial cells. Could be required for the biogenesis of the ElfA fimbriae. Induced in the presence of epithelial cells. Belongs to the periplasmic pilus chaperone family. +Chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Has a low intrinsic ATPase activity which is markedly stimulated by HscB. Belongs to the heat shock protein 70 family. +Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. H2O + IMP + NAD(+) = H(+) + NADH + XMP Mycophenolic acid (MPA) is a non-competitive inhibitor that prevents formation of the closed enzyme conformation by binding to the same site as the amobile flap. In contrast, mizoribine monophosphate (MZP) is a competitive inhibitor that induces the closed conformation. MPA is a potent inhibitor of mammalian IMPDHs but a poor inhibitor of the bacterial enzymes. MZP is a more potent inhibitor of bacterial IMPDH. Purine metabolism; XMP biosynthesis via de novo pathway; XMP from IMP: step 1/1. Homotetramer. Belongs to the IMPDH/GMPR family. +a uridine in RNA = a pseudouridine in RNA Belongs to the pseudouridine synthase RluA family. +Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation. Cleavage of peptide bonds with very broad specificity. The formation of the proteasomal ATPase ARC-20S proteasome complex, likely via the docking of the C-termini of ARC into the intersubunit pockets in the alpha-rings, may trigger opening of the gate for substrate entry. Interconversion between the open-gate and close-gate conformations leads to a dynamic regulation of the 20S proteasome proteolysis activity. Protein degradation; proteasomal Pup-dependent pathway. The 20S proteasome core is composed of 14 alpha and 14 beta subunits that assemble into four stacked heptameric rings, resulting in a barrel-shaped structure. The two inner rings, each composed of seven catalytic beta subunits, are sandwiched by two outer rings, each composed of seven alpha subunits. The catalytic chamber with the active sites is on the inside of the barrel. Has a gated structure, the ends of the cylinder being occluded by the N-termini of the alpha-subunits. Is capped by the proteasome-associated ATPase, ARC. Belongs to the peptidase T1B family. Extended N-terminus. +acetyl-CoA + L-glutamate = CoA + H(+) + N-acetyl-L-glutamate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 1/4. Belongs to the acetyltransferase family. ArgA subfamily. +Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate. (R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA + diphosphate Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 4/5. Homohexamer. Belongs to the bacterial CoaD family. +Plays a role in neurogenesis. Prevents motor neuron cell body migration out of the neural tube. Detected in boundary cap cells at 11.5 dpc, expression is strongest between 15.5 and 17.5 dpc and is barely detectable at birth. Deficient mice exhibit ectopic motor neurons that migrate out of the ventral horn and into the motor roots. +Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel. Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL. Belongs to the GroES chaperonin family. +Controls the flux of glucose into the hexosamine pathway. Most likely involved in regulating the availability of precursors for N- and O-linked glycosylation of proteins. Regulates the circadian expression of clock genes ARNTL/BMAL1 and CRY1 (By similarity). Has a role in fine tuning the metabolic fluctuations of cytosolic UDP-GlcNAc and its effects on hyaluronan synthesis that occur during tissue remodeling (PubMed:26887390). D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; alpha-D-glucosamine 6-phosphate from D-fructose 6-phosphate: step 1/1. Homotetramer (Probable), may also exist as homodimers. Isoform 1 is predominantly expressed in skeletal muscle. Not expressed in brain. Seems to be selectively expressed in striated muscle. The disease is caused by variants affecting the gene represented in this entry. +Mating type proteins are sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. Transcriptional corepressor that, in a/alpha diploid cells, binds cooperatively with the ALPHA2 protein to a 21-bp DNA sequence termed the haploid-specific gene (hsg) operator, to repress transcription of haploid-specific genes and of MATALPHA1. Binds DNA with a high specificity as a heterodimer of A1 and ALPHA2. Only present in a-cells and in a/alpha diploid cells. Was initially thought to be alternatively spliced. This gene is functional with 1, 2 or no introns, but the functional protein is produced only when both introns are spliced from the mRNA. There are three genetic loci for mating type genes in S.cerevisiae. MAT is the expression locus that determines the mating type of the cell, whereas HML (containing HMLALPHA1 and HMLALPHA2) and HMR (containing HMRA1 and HMRA2) represent silenced repositories of mating type information. The mating type is determined by the MAT locus, which contains either a copy of HML or of HMR. Diploid cells are usually heterozygous for the MAT locus. Belongs to the MATA1 family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. PetL is important for photoautotrophic growth as well as for electron transfer efficiency and stability of the cytochrome b6-f complex. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the PetL family. +Reversibly inhibits acid-sensing ion channels (ASIC) in rat dorsal root ganglia neurons. Reversibly inhibits voltage-gated potassium channels (Kv) in rat DRG neurons. +May have S-adenosyl-L-methionine-dependent methyl-transferase activity. Ubiquitous. NSUN5C is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family. Could be the product of a pseudogene. Extended N-terminus. +3-beta-HSD is a bifunctional enzyme, that catalyzes the oxidative conversion of Delta(5)-ene-3-beta-hydroxy steroid, and the oxidative conversion of ketosteroids. The 3-beta-HSD enzymatic system plays a crucial role in the biosynthesis of all classes of hormonal steroids (By similarity). a 3beta-hydroxy-Delta(5)-steroid + NAD(+) = a 3-oxo-Delta(5)-steroid + H(+) + NADH a 3-oxo-Delta(5)-steroid = a 3-oxo-Delta(4)-steroid Lipid metabolism; steroid biosynthesis. Belongs to the 3-beta-HSD family. +Hydrolyzes malto-oligosaccharides, but has a low activity toward soluble starch. Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose. By maltose. Belongs to the glycosyl hydrolase 31 family. +Belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Kinesin family. KIN-7 subfamily. Could be the product of a pseudogene. The kinesin motor domain is truncated at the N-terminus and lacks the ATP-binding site which is one of the conserved features of the KIN7 family. +Does not possess sterol isomerase activity and does not bind sigma ligands. Homodimer. Widely expressed with highest levels in liver, lung and kidney. Belongs to the EBP family. +Cleaves the propeptides of type II collagen prior to fibril assembly. Does not act on types I and III collagens. Binds 1 zinc ion per subunit. Found in cartilage and skin. The spacer domain and the TSP type-1 domains are important for a tight interaction with the extracellular matrix. The precursor is cleaved by a furin endopeptidase. Glycosylated. Can be O-fucosylated by POFUT2 on a serine or a threonine residue found within the consensus sequence C1-X(2)-(S/T)-C2-G of the TSP type-1 repeat domains where C1 and C2 are the first and second cysteine residue of the repeat, respectively. Fucosylated repeats can then be further glycosylated by the addition of a beta-1,3-glucose residue by the glucosyltransferase, B3GALTL. Fucosylation mediates the efficient secretion of ADAMTS family members. Can also be C-glycosylated with one or two mannose molecules on tryptophan residues within the consensus sequence W-X-X-W of the TPRs, and N-glycosylated. These other glycosylations can also facilitate secretion (By similarity). The disease is caused by variants affecting the gene represented in this entry. Has sometimes been referred to as ADAMTS4. +Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP. H2O + P(1),P(4)-bis(5'-adenosyl) tetraphosphate = 2 ADP + 2 H(+) Belongs to the Ap4A hydrolase family. +Belongs to the UPF0154 family. +Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP + H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA Binds 1 Fe(2+) ion per subunit. Belongs to the KAE1 / TsaD family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). Interacts with snoRNA U3. Interacts with MPP10. Component of the ribosomal small subunit (SSU) processome composed of at least 40 protein subunits and snoRNA U3. In the absence of snoRNA3, forms a complex with other t-UTPs. This complex can associate with pre-18S ribosomal RNAs. Present with 5440 molecules/cell in log phase SD medium. +This enzyme converts phytoene into lycopene via the intermediaries of phytofluene, zeta-carotene and neurosporene by the introduction of four double bonds. 15-cis-phytoene + 4 A = 4 AH2 + all-trans-lycopene Carotenoid biosynthesis; astaxanthin biosynthesis. Belongs to the carotenoid/retinoid oxidoreductase family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Catalyzes the final step of fatty acid oxidation in which acetyl-CoA is released and the CoA ester of a fatty acid two carbons shorter is formed. acetyl-CoA + an acyl-CoA = a 3-oxoacyl-CoA + CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadJ) and two beta chains (FadI). Belongs to the thiolase-like superfamily. Thiolase family. +Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA (By similarity). Plays an essential role in early embryonic development. Embryos have a reduced forebrain, kinked tail and inflated hindbrain ventricle. Belongs to the universal ribosomal protein uS13 family. +Negative regulator of replication initiation, which contributes to regulation of DNA replication and ensures that replication initiation occurs exactly once per chromosome per cell cycle. Binds to pairs of hemimethylated GATC sequences in the oriC region, thus preventing assembly of replication proteins and re-initiation at newly replicated origins. Repression is relieved when the region becomes fully methylated. Homodimer. Polymerizes to form helical filaments. Belongs to the SeqA family. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 1 family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. Interacts with UvrB in an incision complex. Belongs to the UvrC family. +Belongs to the UPF0758 family. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +Belongs to the bacterial ribosomal protein bS21 family. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbJ family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Interacts with AAK6. Belongs to the universal ribosomal protein uS11 family. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Manganese-binding polypeptide with L-arginine metabolizing enzyme activity. Component of the core of photosystem II. Belongs to the PsbY family. +Provides oxygen to the bacteroids. This role is essential for symbiotic nitrogen fixation. Monomer. Root nodules. Belongs to the plant globin family. +Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate. 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 6/7. Monomer. Belongs to the EPSP synthase family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the proton-dependent transport of sialic acid. H(+)(in) + N-acetylneuraminate(in) = H(+)(out) + N-acetylneuraminate(out) Belongs to the major facilitator superfamily. Sialate:H(+) symporter (SHS) (TC 2.A.1.12) family. +Catalyzes the ATP-dependent phosphorylation of L-homoserine to L-homoserine phosphate. ATP + L-homoserine = ADP + H(+) + O-phospho-L-homoserine Amino-acid biosynthesis; L-threonine biosynthesis; L-threonine from L-aspartate: step 4/5. Belongs to the GHMP kinase family. Homoserine kinase subfamily. +Functions in nuclear protein import as nuclear transport receptor. Serves as receptor for nuclear localization signals (NLS) in cargo substrates. Is thought to mediate docking of the importin/substrate complex to the nuclear pore complex (NPC) through binding to nucleoporin and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to the importin, the importin/substrate complex dissociates and importin is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus (By similarity). Involved in nuclear import of M9-containing proteins. In vitro, binds directly to the M9 region of the glycine-rich RNA-binding RBG7 and mediates its nuclear import. Interacts with RBG7, RBG8, RAN1 and RNP1. Shuttles continuously between the nucleus and the cytoplasm. Belongs to the importin beta family. Importin beta-2 subfamily. +Cell wall formation. ATP + L-alanine + UDP-N-acetyl-alpha-D-muramate = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Inhibitor of the activity of phosphatase RapA. Belongs to the phr family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 1 subfamily. +Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF2 (By similarity). Was identified as a high-confidence drug target. Belongs to the prokaryotic/mitochondrial release factor family. Extended N-terminus. +The specificity (S) subunit of a type I restriction enzyme; this subunit dictates DNA sequence specificity. The M and S subunits together form a methyltransferase (MTase) that methylates adenosines in the sequence 5'-RAACN(5)TAG-3'. Methylation protects against cleavage by HindI (PubMed:4591672) (Probable). In the presence of the R subunit the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance MTase modifying the DNA so that both strands become methylated (Probable) (PubMed:12654995). After locating a non-methylated recognition site, the enzyme complex serves as a molecular motor that translocates DNA in an ATP-dependent manner until a collision occurs that triggers cleavage (By similarity). The type I restriction/modification system is composed of three polypeptides R, M and S; the restriction enzyme has stoichiometry R(2)M(2)S(1) while the methyltransferase is M(2)S(1). Contains two DNA recognition domains, each specifying recognition of one of the two defined components of the target sequence. Type I restriction and modification enzymes are complex, multifunctional systems which require ATP, S-adenosyl methionine and Mg(2+) as cofactors and, in addition to their endonucleolytic and methylase activities, are potent DNA-dependent ATPases. Belongs to the type-I restriction system S methylase family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Catalyzes the transfer of succinyl-CoA to arginine to produce N(2)-succinylarginine. L-arginine + succinyl-CoA = CoA + H(+) + N(2)-succinyl-L-arginine Amino-acid degradation; L-arginine degradation via AST pathway; L-glutamate and succinate from L-arginine: step 1/5. Belongs to the arginine N-succinyltransferase family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Belongs to the GOLM family. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +Antifungal activity. Inhibits mycelial growth of F.oxysporum, M.oxysporum and P.piricola. Inhibits cell-free translation with an IC(50) of 28 uM. Antiproliferative activity against MBL2 and L1210 tumor cell lines in vitro. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Probable glucose transporter. Belongs to the major facilitator superfamily. Sugar transporter (TC 2.A.1.1) family. +Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. cyanate + 3 H(+) + hydrogencarbonate = 2 CO2 + NH4(+) Belongs to the cyanase family. +Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles. Belongs to the globin family. +Essential for the production of a quorum sensing system signal molecule, the autoinducing peptide (AIP). This quorum sensing system is responsible for the regulation of the expression of virulence factor genes. Involved in the proteolytic processing of AgrD, the precursor of AIP. Belongs to the AgrB family. +Component of the mitochondrial ribosome small subunit (28S) which comprises a 12S rRNA and about 30 distinct proteins. Belongs to the mitochondrion-specific ribosomal protein mL65 family. +Catalyzes the hydrolytic cleavage of the carbon-nitrogen bond in imidazolone-5-propanoate to yield N-formimidoyl-L-glutamate. It is the third step in the universal histidine degradation pathway. 4-imidazolone-5-propanoate + H2O = N-formimidoyl-L-glutamate Binds 1 zinc or iron ion per subunit. Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 3/3. Belongs to the metallo-dependent hydrolases superfamily. HutI family. +Belongs to the UPF0761 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. Belongs to the NAD-dependent DNA ligase family. LigA subfamily. +Part of the binding-protein-dependent transport system for sn-glycerol-3-phosphate; probably responsible for the translocation of the substrate across the membrane. The complex is composed of two ATP-binding proteins (UgpC), two transmembrane proteins (UgpA and UgpE) and a solute-binding protein (UgpB). Belongs to the binding-protein-dependent transport system permease family. UgpAE subfamily. +Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP. H2O + P(1),P(4)-bis(5'-adenosyl) tetraphosphate = 2 ADP + 2 H(+) Belongs to the Ap4A hydrolase family. +Growth hormone plays an important role in growth control and is involved in the regulation of several anabolic processes. Implicated as an osmoregulatory substance important for seawater adaptation. Belongs to the somatotropin/prolactin family. +Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. ATP + cytidine(34) in tRNA(Ile2) + L-lysine = AMP + diphosphate + H(+) + lysidine(34) in tRNA(Ile2) The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a P-loop motif involved in ATP binding. Belongs to the tRNA(Ile)-lysidine synthase family. +Belongs to the TACO1 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 4L family. +Belongs to the aerolysin family. +Belongs to the staphylococcal tandem lipoprotein family. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. Belongs to the radical SAM superfamily. Lipoyl synthase family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Molecular chaperone; binds unfolded polypeptides in vitro, and has a weak ATPase activity. Forms a Heterooligomeric complex of two stacked eight-membered rings. Belongs to the TCP-1 chaperonin family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +Efflux system for nickel and cobalt. By nickel and cobalt. Transcriptionally repressed by RcnR (By similarity). Belongs to the NiCoT transporter (TC 2.A.52) family. RcnA subfamily. +Cytidylyltransferase required for protein O-linked mannosylation (By similarity). Catalyzes the formation of CDP-ribitol nucleotide sugar from D-ribitol 5-phosphate (By similarity). CDP-ribitol is a substrate of FKTN during the biosynthesis of the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity (By similarity). Shows activity toward other pentose phosphate sugars and mediates formation of CDP-ribulose or CDP-ribose using CTP and ribulose-5-phosphate or ribose-5-phosphate, respectively. Not involved in dolichol production (By similarity). CTP + D-ribitol 5-phosphate + H(+) = CDP-L-ribitol + diphosphate CTP + D-ribose 5-phosphate + H(+) = CDP-D-ribose + diphosphate CTP + D-ribulose 5-phosphate + H(+) = CDP-D-ribulose + diphosphate Protein modification; protein glycosylation. Homodimer. Belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily. +Binds to muscle nicotinic acetylcholine receptor (nAChR) and inhibit acetylcholine from binding to the receptor, thereby impairing neuromuscular transmission. Expressed by the venom gland. Belongs to the snake three-finger toxin family. Short-chain subfamily. Type I alpha-neurotoxin sub-subfamily. +Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-cysteinyl-[prolipoprotein] = H(+) + S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[prolipoprotein] + sn-glycerol 1-phosphate Protein modification; lipoprotein biosynthesis (diacylglyceryl transfer). Belongs to the Lgt family. +Belongs to the UPF0060 family. +Acts as a receptor for hemoglobin or the hemoglobin/haptoglobin complex of the human host and is required for heme uptake. This protein is subject to phase-variable expression associated with alteration in the length of the CCAA repeat region. This mechanism is called slipped-strand mispairing. Addition or loss of CCAA repeat units would change the reading frame and result in introduction of stop codons downstream of the repeat region. This may be a mechanism of regulation and a way to avoid the immunological response of the host. Belongs to the TonB-dependent receptor family. Hemoglobin/haptoglobin binding protein subfamily. +One of the components of the core complex of photosystem II (PSII), required for its stability and/or assembly. PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, numerous small proteins, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbH family. +Protein phosphatase that dephosphorylates specifically tyrosine-phosphorylated peptides; especially active on dual-phosphorylated substrates containing a phosphothreonine-X-phosphotyrosine motif. H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate Binds 2 divalent metal cations per subunit. Inhibited by the tyrosine phosphatase inhibitor orthovanadate, but resistant to the serine/threonine phosphatase inhibitors okadaic acid and microcystin. Inhibited by phosphate analogs NaF and Na(3)VO(4), and the adenylates ATP and ADP. Inactivated by zinc ions. Optimum pH is 7-7.8. Expressed in roots, stems, leaves, flowers and siliques (at protein level). Belongs to the PPP phosphatase family. +Belongs to the YejK family. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +Catalyzes carboxymethyl transfer from carboxy-S-adenosyl-L-methionine (Cx-SAM) to 5-hydroxyuridine (ho5U) to form 5-carboxymethoxyuridine (cmo5U) at position 34 in tRNAs. 5-hydroxyuridine(34) in tRNA + carboxy-S-adenosyl-L-methionine = 5-carboxymethoxyuridine(34) in tRNA + H(+) + S-adenosyl-L-homocysteine Homotetramer. Belongs to the class I-like SAM-binding methyltransferase superfamily. CmoB family. +MFS transporter involved in the basal level of azole susceptibility (PubMed:26933209). Confers resistance to voriconazole and, to a lesser extent, to fluconazole (PubMed:26933209). Expression is up-regulated by exposure to human monocyte-derived immature dendritic cells (PubMed:21264256). Expression is increased in clinical azole-resistant isolates (PubMed:26933209). Exhibits enhanced susceptibility to voriconazole, however itraconazole susceptibility is less affected. Belongs to the major facilitator superfamily. DHA1 family. Polyamines/proton antiporter (TC 2.A.1.2.16) subfamily. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Belongs to the histone H4 family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Dual-function toxin that inhibits both serine proteases and voltage-gated potassium channels (Kv). Expressed by the venom gland. Belongs to the venom Kunitz-type family. 03 (sub-Kunitz) subfamily. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the LeuD family. LeuD type 2 subfamily. +Part of the photosystem II complex. Belongs to the Psb28 family. +Specific growth arrest protein involved in growth suppression. Blocks entry to S phase. Prevents cycling of normal and transformed cells. +Homotrimer. When expressed in mutant CS384. Encoded by the cryptic lambdoid prophage DLP12. Belongs to the Gram-negative porin family. Could be the product of a pseudogene, as in E.coli K12 the nmpC open reading frame is interrupted by an IS5 insertion and generates a hybrid open reading frame that is not expressed. In strains which have undergone selection for suppressors of ompB mutations (for example, mutant strain CS384) nmpC is expressed. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +The protein kinase domain is predicted to be catalytically inactive. Lacks the conserved Asp active site at position 645, which is replaced by a Glu residue. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +Catalyzes the oxidation of erythronate-4-phosphate to 3-hydroxy-2-oxo-4-phosphonooxybutanoate. 4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + H(+) + NADH Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 2/5. Homodimer. Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily. +Belongs to the proline racemase family. +Antimicrobial peptide. Active against a broad spectrum of Gram-positive and Gram-negative bacteria including methicillin-resistant S.aureus ATCC 43 300, S.aureus BAA-39, pathogenic strains of L.monocytogenes, K.pneumoniae, E.coli O157:H7, S.typhimurium and multidrug-resistant S.typhimurium DT104 with minimum inhibitory concentration (MIC) of 1.4 uM for all except for S.aureus BAA-39 (PubMed:18265434). Also active against Serratia marcescens (PubMed:14728663). Probably acts by disturbing membrane functions with its amphipathic alpha-helical structure (PubMed:18265434). May protect a developing embryo from bacterial infection (Probable). Monomer. Expressed at low levels in nerve tissue, salivary gland, Malpighian tubule, trachea, midgut, fat body, integument and muscle from day 3, fifth instar naive larvae. Moderate levels expressed in fat body from the 4th instar larvae (day 0), 5th instar larvae (days 3 and 6), wandering larvae (day 6), and adults in the absence of infection. A moderate level of expression in the hemocytes of the naive larvae. Expression increases substantially in fat body and hemocytes after fifth instar larvae are challenged with bacterial cells (PubMed:18265434). Constitutive low expression in naive eggs, but up-regulated in them in response to bacteria. Expressed in 24 h (predorsal closure stage) eggs in extra-embryonic tissues (yolk and serosa) after bacterial challenge, but not in embryos (PubMed:14728663). By bacterial infection. Belongs to the moricin family. +Component of the elongator complex, a multiprotein complex which is required for multiple tRNA modifications, including mcm5U (5-methoxycarbonylmethyl uridine), mcm5s2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-carbamoylmethyl uridine) (PubMed:22768388). The elongator complex catalyzes formation of carboxymethyluridine in the wobble base at position 34 in tRNAs (PubMed:29332244). tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis. Component of the elongator complex. Belongs to the ELP4 family. The elongator complex was originally thought to play a role in transcription elongation. However, it is no longer thought to play a direct role in this process and its primary function is thought to be in tRNA modification. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Promotes the exchange of GDP for GTP in EF-1-alpha/GDP, thus allowing the regeneration of EF-1-alpha/GTP that could then be used to form the ternary complex EF-1-alpha/GTP/AAtRNA. Belongs to the EF-1-beta/EF-1-delta family. +Belongs to the PPR family. P subfamily. +Forms an icosahedral capsid with a T=7 symmetry and a 50 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. Binds to heparan sulfate proteoglycans on cell surface of basal layer keratinocytes to provide initial virion attachment. This binding mediates a conformational change in the virus capsid that facilitates efficient infection. The virion enters the host cell via endocytosis. During virus trafficking, L1 protein dissociates from the viral DNA and the genomic DNA is released to the host nucleus. The virion assembly takes place within the cell nucleus. Encapsulates the genomic DNA together with protein L2. Self-assembles into homopentamers. The capsid has an icosahedral symmetry and consists of 72 capsomers, with each capsomer being a pentamer of L1. Interacts with the minor capsid protein L2; this interaction is necessary for viral genome encapsidation. Interacts with protein E2; this interaction enhances E2-dependent replication and transcription activation. Belongs to the papillomaviridae L1 protein family. +Binds cholesterol. Colocalizes with PROM1 (By similarity). Associates with membrane in a cholesterol-dependent manner. Localizes to the apical and basolateral membranes of epithelial cells. Expressed in kidney and testis. Present in urine within small membrane particles (at protein level). In the submandibular gland, expressed in seromucous acini. In the parotid gland, expressed in the serous acini and in all segments of the duct system. In the sublingual gland, expressed in large excretory ducts, but absent in intercalated ducts. In the extraorbital lacrimal gland, expressed in the serous acini. In the eyelid, expressed in the acini of the meibomian gland. Glycosylated. Belongs to the prominin family. +Belongs to the UPF0114 family. +H(+) + orotidine 5'-phosphate = CO2 + UMP Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. Belongs to the OMP decarboxylase family. Type 2 subfamily. +Serves as the first electron transfer protein in all the mitochondrial P450 systems. Acts as an electron transfer protein. Essential for viability. H(+) + NADP(+) + 2 reduced [adrenodoxin] = NADPH + 2 oxidized [adrenodoxin] Belongs to the ferredoxin--NADP reductase type 1 family. +Calcium-dependent cell adhesion protein; preferentially mediates homotypic cell-cell adhesion by dimerization with a CDH2 chain from another cell. Cadherins may thus contribute to the sorting of heterogeneous cell types. Acts as a regulator of neural stem cells quiescence by mediating anchorage of neural stem cells to ependymocytes in the adult subependymal zone: upon cleavage by MMP24, CDH2-mediated anchorage is affected, leading to modulate neural stem cell quiescence. Plays a role in cell-to-cell junction formation between pancreatic beta cells and neural crest stem (NCS) cells, promoting the formation of processes by NCS cells (By similarity). CDH2 may be involved in neuronal recognition mechanism. In hippocampal neurons, may regulate dendritic spine density. Homodimer (via extracellular region). Can also form heterodimers with other cadherins (via extracellular region). Dimerization occurs in trans, i.e. with a cadherin chain from another cell (By similarity). Interacts with CDCP1 (PubMed:16007225). Interacts with PCDH8; this complex may also include TAOK2 (By similarity). The interaction with PCDH8 may lead to internalization through TAOK2/p38 MAPK pathway (By similarity). Identified in a complex containing FGFR4, NCAM1, CDH2, PLCG1, FRS2, SRC, SHC1, GAP43 and CTTN. May interact with OBSCN (via protein kinase domain 2) (By similarity). Colocalizes with TMEM65 at the intercalated disk in cardiomyocytes. Colocalizes with OBSCN at the intercalated disk and at sarcolemma in cardiomyocytes. Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain. Calcium-binding sites are occupied sequentially in the order of site 3, then site 2 and site 1. Cleaved by MMP24. Ectodomain cleavage leads to the generation of a soluble 90 kDa N-terminal soluble fragment and a 45 kDa membrane-bound C-terminal fragment 1 (CTF1), which is further cleaved by gamma-secretase into a 35 kDa (By similarity). Cleavage in neural stem cells by MMP24 affects CDH2-mediated anchorage of neural stem cells to ependymocytes in the adult subependymal zone, leading to modulate neural stem cell quiescence (By similarity). May be phosphorylated by OBSCN. The disease may be caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. +Belongs to the UPF0725 (EMB2204) family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +Heme-dependent dioxygenase that catalyzes the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring and converts L-tryptophan to N-formyl-L-kynurenine. Catalyzes the oxidative cleavage of the indole moiety. L-tryptophan + O2 = N-formyl-L-kynurenine Binds 1 heme group per subunit. Amino-acid degradation; L-tryptophan degradation via kynurenine pathway; L-kynurenine from L-tryptophan: step 1/2. Pigment biosynthesis; ommochrome biosynthesis. Homotetramer. Dimer of dimers. Belongs to the tryptophan 2,3-dioxygenase family. +Plays a role in viral particle release. Presumably acts by facilitating the fission of the virion bud at the cell surface. May prevent the antiviral activity of murine APOBEC3. Glycosylated by host. Cleaved by host near the middle of the molecule, releasing the c-terminal half containing capsid and nucleoprotein domains op GAG. +Modulates RecA activity. Belongs to the RecX family. +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX. coproporphyrinogen III + 2 H(+) + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; protoporphyrinogen-IX from coproporphyrinogen-III (O2 route): step 1/1. Homodimer. Belongs to the aerobic coproporphyrinogen-III oxidase family. +Guanine nucleotide exchange factor (GEF) which may activate RAB9A and RAB9B. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. +Cell wall formation. Synthesis of cross-linked peptidoglycan from the lipid intermediates. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (cross-linking of the peptide subunits). [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H(+) Preferential cleavage: (Ac)2-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine. Cell wall biogenesis; peptidoglycan biosynthesis. In the N-terminal section; belongs to the glycosyltransferase 51 family. In the C-terminal section; belongs to the transpeptidase family. +Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn-glycerol 3-phosphate. ATP + glycerol = ADP + H(+) + sn-glycerol 3-phosphate Activity of this regulatory enzyme is affected by several metabolites. Allosterically and non-competitively inhibited by fructose 1,6-bisphosphate (FBP) and unphosphorylated phosphocarrier protein EIIA-Glc (III-Glc), an integral component of the bacterial phosphotransferase (PTS) system. Polyol metabolism; glycerol degradation via glycerol kinase pathway; sn-glycerol 3-phosphate from glycerol: step 1/1. Homotetramer and homodimer (in equilibrium). Heterodimer with EIIA-Glc. Binds 1 zinc ion per glycerol kinase EIIA-Glc dimer. The zinc ion is important for dimerization. Belongs to the FGGY kinase family. +Part of the ABC transporter complex PhnCDE involved in phosphonates import. Responsible for energy coupling to the transport system. ATP + H2O + phosphonate(out) = ADP + H(+) + phosphate + phosphonate(in) The complex is composed of two ATP-binding proteins (PhnC), two transmembrane proteins (PhnE) and a solute-binding protein (PhnD). Belongs to the ABC transporter superfamily. Phosphonates importer (TC 3.A.1.9.1) family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity (By similarity). Belongs to the universal ribosomal protein uS4 family. +The surface protein (SU) attaches the virus to the host cell by binding to its receptor. This interaction triggers the refolding of the transmembrane protein (TM) and is thought to activate its fusogenic potential by unmasking its fusion peptide. Fusion occurs at the host cell plasma membrane (By similarity). The transmembrane protein (TM) acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Membranes fusion leads to delivery of the nucleocapsid into the cytoplasm (By similarity). The mature envelope protein (Env) consists of a trimer of SU-TM heterodimers attached by a labile interchain disulfide bond. It is probably concentrated at the site of budding and incorporated into the virions possibly by contacts between the cytoplasmic tail of Env and the N-terminus of Gag. The surface protein is not anchored to the viral envelope, but associates with the extravirion surface through its binding to TM. It is probably concentrated at the site of budding and incorporated into the virions possibly by contacts between the cytoplasmic tail of Env and the N-terminus of Gag (By similarity). The 17 amino acids long immunosuppressive region is present in many retroviral envelope proteins. Synthetic peptides derived from this relatively conserved sequence inhibit immune function in vitro and in vivo (By similarity). Specific enzymatic cleavages in vivo yield mature proteins. Envelope glycoproteins are synthesized as an inactive precursor that is N-glycosylated and processed likely by host cell furin or by a furin-like protease in the Golgi to yield the mature SU and TM proteins. The cleavage site between SU and TM requires the minimal sequence [KR]-X-[KR]-R (By similarity). The CXXC motif is highly conserved across a broad range of retroviral envelope proteins. It is thought to participate in the formation of a labile disulfide bond possibly with the CX6CC motif present in the transmembrane protein. Isomerization of the intersubunit disulfide bond to an SU intrachain disulfide bond is thought to occur upon receptor recognition in order to allow membrane fusion (By similarity). The transmembrane protein is palmitoylated. +May be involved in maintaining Golgi structure and in intra-Golgi transport. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across the thylakoid membrane. Involved in delta pH-dependent protein transport required for chloroplast development, especially thylakoid membrane formation. TATC and TATB mediate precursor recognition, whereas TATA facilitates translocation. In thylakoid membranes, TATC and TATB form a large receptor complex, containing about eight TATC-TATB pairs, which binds the precursor protein. Twin arginine signal peptide promotes pH-triggered docking of TATA oligomers to TATC-TATB receptor complex, inducing a conformational switch of TATA that results in activation of the translocase. TATA dissociates from TATC-TATB upon completion of translocation (By similarity). The C-terminus is located in the stroma. Seedling lethality after the development of three to four leaves. Non-photosynthetic mutants possess near normal pigment levels but lack one or more elements of the electron transport activity in chloroplasts. Defects in protein targeting across chloroplast thylakoid membrane (PubMed:7664731). Belongs to the TatA/E family. +Catalyzes the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH 5,10-methenyltetrahydrofolate + H2O = (6S)-10-formyltetrahydrofolate + H(+) One-carbon metabolism; tetrahydrofolate interconversion. Homodimer. Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family. +Catalyzes the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. S-(hydroxymethyl)glutathione = formaldehyde + glutathione Binds 2 Zn(2+) ions per subunit. One-carbon metabolism; formaldehyde degradation; formate from formaldehyde (glutathione route): step 1/3. Belongs to the Gfa family. +Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis. The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance. As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia. The TRiC complex plays a role in the folding of actin and tubulin. Component of the chaperonin-containing T-complex (TRiC), a heterooligomeric complex of about 850 to 900 kDa that forms two stacked rings, 12 to 16 nm in diameter. Interacts with PACRG. Interacts with GBA (By similarity). Interacts with DLEC1 (By similarity). Belongs to the TCP-1 chaperonin family. +Lipase which is essential for lysis of subvacuolar cytoplasm to vacuole targeted bodies and intravacuolar autophagic bodies. Involved in the lysis of intravacuolar multivesicular body (MVB) vesicles. The intravacuolar membrane disintegration by atg15 is critical to life span extension (By similarity). a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H(+) Binds to both phosphatidylinositol (PI) and phosphatidylinositol 3,5-bisphosphate (PIP2). From ER, targeted to vacuolar lumen at the MVB vesicles via the Golgi and the prevacuolar compartment (PVC). Belongs to the AB hydrolase superfamily. Lipase family. +Component of the type IV secretion system VirB/VirD4 which could be a major virulence determinant for subversion of human endothelial cell (HEC) function. Belongs to the TrbL/VirB6 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase gamma chain family. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +Negatively regulates the expression of the glaH-lhgD-gabDTP operon in a temporal manner during entry into stationary phase or during the first few hours of carbon starvation (PubMed:14731280, PubMed:30498244). Thereby is involved in the regulation of a L-lysine degradation pathway that proceeds via cadaverine, glutarate and L-2-hydroxyglutarate (PubMed:30498244). Binds to two primary and two secondary sites in the promoter region of the glaH operon with the consensus sequences TTGTN5TTTT and ATGTN5TTTT of the primary sites, each separated by six nucleotides (PubMed:30498244). The repressive effect at the glaH promoter site is specifically relieved upon glutarate binding. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides. Release of any N-terminal amino acid, including proline, that is linked to proline, even from a dipeptide or tripeptide. Binds 2 manganese ions per subunit. Belongs to the peptidase M24B family. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Homodimer. Belongs to the GrpE family. +Meiotic recombination factor component of recombination bridges involved in meiotic double-strand break repair. Modulates the localization of recombinases DMC1:RAD51 to meiotic double-strand break (DSB) sites through the interaction with BRCA2 and its recruitment during meiotic recombination. Indispensable for the DSB repair, homologous synapsis, and crossover formation that are needed for progression past metaphase I, is essential for spermatogenesis and male fertility (PubMed:31242413, PubMed:32345962, PubMed:32463460, PubMed:30760716). Required for proper recombinase recruitment in female meiosis (PubMed:30760716, PubMed:32845237). Inhibits BNC1 transcriptional activity during spermatogenesis, probably by sequestering it in the cytoplasm (PubMed:23707421). May be involved in modulating HSF2 activation in testis (By similarity). Interacts (via C-terminus) with BNC1 (PubMed:23707421). Associates with HSF2. The interaction seems to occur between the trimerization domain of HSF2 and the N-terminal hydrophilic region of HSF2BP (By similarity). Interacts (via N-terminus) with BRME1 (PubMed:32463460, PubMed:32460033, PubMed:32345962). Interacts with BRCA2 and BRME1; the interactions are direct and allow the formation of a ternary complex (PubMed:32345962, PubMed:32460033, PubMed:32463460, PubMed:31242413, PubMed:30760716, PubMed:32845237). The complex BRME1:HSF2BP:BRCA2 interacts with SPATA22, MEIOB and RAD51 (PubMed:32345962, PubMed:30760716). Localizes on double-strand breaks (DSBs) in mitotic and meiotic chromosomes. Expressed in testis and, to a lesser extent, in lung and muscle. Detected at low levels from birth to 3 days post partum, thereafter the expression level increases from 5 days post partum to adult. In spermatocytes, shows punctate localization along chromosome axes specifically in early meiotic prophase I cells. Foci start to appear from the leptotene stage, reach their greatest number in the zygotene stage, persist until the early pachytene stage, and finally disappear in the late pachytene stage (PubMed:30760716). Sumoylated by UBE2I in response to MEKK1-mediated stimuli. Male mutants are infertile (PubMed:31242413, PubMed:30760716). They have smaller-than-normal testes with no sperm (PubMed:31242413, PubMed:30760716). Female mutants exhibit a fertility with 40% reduction in litter size compared to wild-type females. They show reduced follicle formation (PubMed:30760716, PubMed:32845237). Mutant oocytes show a delay in prophase I progression with the majority of cells at zygotene stage in 17.5 days post-coitum (dpc) females (PubMed:32845237). +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 30 kDa subunit family. +hydrogen sulfide + O-acetyl-L-serine = acetate + L-cysteine Amino-acid biosynthesis; L-cysteine biosynthesis; L-cysteine from L-serine: step 2/2. Homodimer. Belongs to the cysteine synthase/cystathionine beta-synthase family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Belongs to the BPG-independent phosphoglycerate mutase family. A-PGAM subfamily. +Belongs to the baculoviridae p33 family. +Functions as an intestinal M-cell transcytotic receptor specific of type-I-piliated bacteria that participates in the mucosal immune response toward these bacteria. At the apical membrane of M-cells it binds fimH, a protein of the bacteria type I pilus tip. Internalizes bound bacteria, like E.coli and S.typhimurium, from the lumen of the intestine and delivers them, through M-cells, to the underlying organized lymphoid follicles where they are captured by antigen-presenting dendritic cells to elicit a mucosal immune response. Interacts with SYCN. Secreted, after cleavage, in the pancreatic juice. Expressed in pancreas (at protein level) (PubMed:8666297, PubMed:10760606). Specifically expressed by M (microfold) cells which are atypical epithelial cells of the intestine (at protein level) (PubMed:19907495). N-glycosylated. It is uncertain whether Met-1 or Met-8 is the initiator. +Endoplasmic reticulum transmembrane protein involved in vesicle-mediated transport, which is required for neutrophil function. Belongs to the jagunal family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Binds 2 manganese ions per subunit. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Belongs to the BPG-independent phosphoglycerate mutase family. +Molecular chaperone that interacts specifically with outer membrane proteins, thus maintaining the solubility of early folding intermediates during passage through the periplasm. Homotrimer. Belongs to the Skp family. +Component of the anaphase-promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin-protein ligase complex that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C is thought to confer substrate specificity and, in the presence of ubiquitin-conjugating E2 enzymes, it catalyzes the formation of protein-ubiquitin conjugates that are subsequently degraded by the 26S proteasome. May play a pivotal role in the control of anaphase. The APC/C is composed of at least 13 subunits: apc1, apc2, nuc2, apc4, apc5, cut9, apc8, apc10, apc11, hcn1, apc13, apc14 and apc15. Homodimer. Interacts directly with nuc2 and hcn1. TPR repeats 1-7 mediate homodimerization while TPR repeats 8 and 10-13 bind to hcn1, burying its N-terminal acetyl-methionine. Phosphorylated. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +A cytochrome P450 monooxygenase involved in sterol biosynthesis. Catalyzes 14-alpha demethylation of lanosterol and 24,25-dihydrolanosterol likely through sequential oxidative conversion of 14-alpha methyl group to hydroxymethyl, then to carboxylaldehyde, followed by the formation of the delta 14,15 double bond in the sterol core and concomitant release of formic acid (PubMed:7665087, PubMed:10544287, PubMed:11328599). Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (CPR; NADPH-ferrihemoprotein reductase) (PubMed:7665087, PubMed:10544287, PubMed:11328599). a 14alpha-methyl steroid + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = a Delta(14) steroid + formate + 4 H(+) + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase] lanosterol + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = 4,4-dimethyl-5alpha-cholesta-8,14,24-trien-3beta-ol + formate + 4 H(+) + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase] 24,25-dihydrolanosterol + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = 4,4-dimethyl-8,14-cholestadien-3beta-ol + formate + 4 H(+) + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase] Inhibited by azalanstat (PubMed:7665087). Inhibited by azole antifungal agents ketoconazole, itraconazole and fluconazole (PubMed:10544287). Steroid biosynthesis; zymosterol biosynthesis; zymosterol from lanosterol: step 1/6. Belongs to the cytochrome P450 family. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain. acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine Binds 1 Mg(2+) ion per subunit. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; N-acetyl-alpha-D-glucosamine 1-phosphate from alpha-D-glucosamine 6-phosphate (route II): step 2/2. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; UDP-N-acetyl-alpha-D-glucosamine from N-acetyl-alpha-D-glucosamine 1-phosphate: step 1/1. Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. In the N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family. In the C-terminal section; belongs to the transferase hexapeptide repeat family. +Catalyzes the NADPH-dependent reduction of glyoxylate and hydroxypyruvate into glycolate and glycerate, respectively. glycolate + NADP(+) = glyoxylate + H(+) + NADPH (R)-glycerate + NAD(+) = 3-hydroxypyruvate + H(+) + NADH (R)-glycerate + NADP(+) = 3-hydroxypyruvate + H(+) + NADPH Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. GhrA subfamily. +Proton-coupled antiporter flippase that catalyzes the translocation, from the inner to the outer leaflet of the cell membrane, of the lipid-linked disaccharide (anchor-LLD) that anchors lipoteichoic acids (LTA) to the cell membrane (PubMed:32367070, PubMed:17209021). Displays high selectivity towards the headgroup of its substrate (PubMed:32367070). Plays an important role during infection (PubMed:17209021). Contributes to S.aureus survival under physiological acidic conditions (PubMed:32367070). Flipping activity is inhibited by increasing concentrations of gentiobiose, a disaccharide with the same chemical composition and conformation as the anchor-LLD headgroup. Not inhibited by other disaccharides such as lactose, sucrose and trehalose at a similar concentration. Cell wall biogenesis; lipoteichoic acid biosynthesis. Interacts with YpfP/UgtP, LtaS, and with numerous cell division and peptidoglycan synthesis proteins. Distributed all around the membrane. The N-terminal hydrophilic pocket is crucial for flipping activity. The central cavity of LtaA shows a unique amphiphilic architecture. Deletion mutant does not show a growth defect at high pH, but it shows very strong growth retardation at low pH (PubMed:32367070). At low pH, mutant displays aberrant cell morphologies, including enlarged cells, defects in the formation and localization of the division septum and abnormal cell-wall shape (PubMed:32367070). Inactivation of the gene causes structural changes in staphylococcal LTA but does not affect glycolipid synthesis (PubMed:17209021). Mutants lacking this gene display a virulence defect in a murine abscess model (PubMed:17209021). Belongs to the major facilitator superfamily. LtaA family. +May be involved in the trafficking and dendritic transport of signaling proteins, such as the receptor-type guanylate cyclases gcy-12 and daf-11, to the cilia. In ciliated sensory neurons, required for the calcium flux to the cytoplasm in response to onset and removal of a nitric oxide (NO) stimulus and is thereby required for the behavioral avoidance response to NO-producing organisms like P.aeruginosa (PubMed:30014846). Expressed in many ciliated sensory neurons. Fails to localize guanylate cyclase gcy-12 to sensory cilia. +Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain. Dimer of alpha and beta chains. A typical microtubule is a hollow water-filled tube with an outer diameter of 25 nm and an inner diameter of 15 nM. Alpha-beta heterodimers associate head-to-tail to form protofilaments running lengthwise along the microtubule wall with the beta-tubulin subunit facing the microtubule plus end conferring a structural polarity. Microtubules usually have 13 protofilaments but different protofilament numbers can be found in some organisms and specialized cells. Belongs to the tubulin family. +Possible taste receptor. Tongue specific. Belongs to the G-protein coupled receptor 1 family. +Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine. 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the FPG family. +Homodimer. Belongs to the UPF0210 family. +Thioesterase that has relatively broad substrate specificity, hydrolyzing primarily medium- and long-chain acyl-CoA substrates to free fatty acids and CoA (PubMed:1645722, PubMed:24271180, PubMed:20547355). Functions in the thioesterase-dependent pathway of beta-oxidation of oleate and conjugated linoleate ((9Z,11E)-octadecadienoate or CLA), which provides all energy and carbon precursors required for the growth of E.coli. Thus, supports growth on oleate or conjugated linoleate as the sole source of carbon by hydrolyzing 3,5-tetradecadienoyl-CoA, the terminal metabolite of oleate beta-oxidation via the alternative thioesterase-dependent pathway, and 3,5-dodecadienoyl-CoA, the end product of CLA beta-oxidation, respectively (PubMed:18702504, PubMed:14707139). Seems to be involved in 3-hydroxyalkanoate production in E.coli (PubMed:20547355). a fatty acyl-CoA + H2O = a fatty acid + CoA + H(+) H2O + tetradecanoyl-CoA = CoA + H(+) + tetradecanoate (3E,5Z)-tetradecadienoyl-CoA + H2O = (3E,5Z)-tetradecadienoate + CoA + H(+) dodecanoyl-CoA + H2O = CoA + dodecanoate + H(+) (3Z,5E)-dodecadienoyl-CoA + H2O = (3Z,5E)-dodecadienoate + CoA + H(+) decanoyl-CoA + H2O = CoA + decanoate + H(+) H2O + octanoyl-CoA = CoA + H(+) + octanoate H2O + hexanoyl-CoA = CoA + H(+) + hexanoate H2O + pentanoyl-CoA = CoA + H(+) + pentanoate butanoyl-CoA + H2O = butanoate + CoA + H(+) 4-methylpentanoyl-CoA + H2O = 4-methylpentanoate + CoA + H(+) (3R)-3-hydroxypentanoyl-CoA + H2O = (3R)-3-hydroxypentanoate + CoA + H(+) (3S)-3-hydroxypentanoyl-CoA + H2O = (3S)-3-hydroxypentanoate + CoA + H(+) H2O + hexadecanoyl-CoA = CoA + H(+) + hexadecanoate H2O + octadecanoyl-CoA = CoA + H(+) + octadecanoate (9Z)-octadecenoyl-CoA + H2O = (9Z)-octadecenoate + CoA + H(+) (3R)-3-hydroxybutanoyl-CoA + H2O = (R)-3-hydroxybutanoate + CoA + H(+) (3S)-3-hydroxybutanoyl-CoA + H2O = (S)-3-hydroxybutanoate + CoA + H(+) (2E)-dodecenoyl-CoA + H2O = (2E)-dodecenoate + CoA + H(+) 3-oxododecanoyl-CoA + H2O = 3-oxododecanoate + CoA + H(+) 3-hydroxydodecanoyl-CoA + H2O = 3-hydroxydodecanoate + CoA + H(+) Inhibited by iodoacetamide and diethylpyrocarbonate in vitro, but is insensitive to iodoacetate treatment. kcat is 83 sec(-1) with decanoyl-CoA as substrate. Homotetramer. Deletion of this gene decreases the growth rate of cells on conjugated linoleate but not on palmitate (PubMed:18702504). Deletion of this gene also decreases 3-hydroxybutanoate, 3-hydroxyhexanoate, 3-hydroxyoctanoate, and hexanoate in medium after cultivation with oleate as a sole carbon source (PubMed:20547355). Has been used in the engineered enzymatic high-level production of enantiomerically pure (R)- and (S)-3-hydroxybutanoate, used as a building block for the synthesis of optically active fine chemicals, such as vitamins, antibiotics, pheromones, and flavor compounds. Chemical synthesis of chiral 3-hydroxybutanoate (3HB) is not economically feasible. Belongs to the C/M/P thioester hydrolase family. +Belongs to the universal ribosomal protein uL29 family. +Belongs to the UPF0154 family. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs. uridine(13) in tRNA = pseudouridine(13) in tRNA Belongs to the pseudouridine synthase TruD family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Heterotetramer of two delta chains and two alpha chains. Red blood cells. Belongs to the globin family. +Removes 5-oxoproline from various penultimate amino acid residues except L-proline. Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro. Homotetramer. Belongs to the peptidase C15 family. +Participates in electron transfer between P700 and the cytochrome b6-f complex in photosystem I. Loosely bound to the inner thylakoid membrane surface in chloroplasts (By similarity). Belongs to the plastocyanin family. +[thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(R)-S-oxide-[protein] Binds 1 zinc ion per subunit. The zinc ion is important for the structural integrity of the protein. Belongs to the MsrB Met sulfoxide reductase family. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. +Decapping enzyme required for the removal of the 5'-end m7GpppN cap tethered to viral and host mRNAs to allow their decay in cells (PubMed:19695654). May therefore accelerate viral and cellular mRNA turnover to eliminate competing host mRNAs and allow stage-specific synthesis of viral proteins. Acceleration of the turnover of cellular transcripts may even promote the shutoff of host protein synthesis (PubMed:29021398). In addition to the mRNA cap, g5R also efficiently hydrolyzes diphosphoinositol polyphosphates. Down-regulation of the level of PP-InsP5 (diphosphoinositol pentakisphosphate) may play a role in viral manipulation of the cellular secretory pathway, a step necessary for the formation of virions (PubMed:11773415). Binds viral and cellular poly(A) mRNAs, thereby decreasing both types of mRNAs (PubMed:19695654, PubMed:29021398). diphospho-myo-inositol polyphosphate + H2O = myo-inositol polyphosphate + phosphate. Optimum pH is 9.5. Interacts with host RPL23A. Accumulates at the periphery of the viral factories. Expressed early and up to late in the infection cycle. Belongs to the Nudix hydrolase family. DIPP subfamily. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+). Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis. By novobiocin and repressed by sucrose. There are two genes for gyrB in this organism. One which is novobiocin-sensitive (gyrBS) and one which is resistant (gyrBR). Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes. Belongs to the type II topoisomerase GyrB family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 13 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 2 family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Component of the methyl-coenzyme M reductase (MCR) I that catalyzes the reductive cleavage of methyl-coenzyme M (CoM-S-CH3 or 2-(methylthio)ethanesulfonate) using coenzyme B (CoB or 7-mercaptoheptanoylthreonine phosphate) as reductant which results in the production of methane and the mixed heterodisulfide of CoB and CoM (CoM-S-S-CoB). This is the final step in methanogenesis. coenzyme B + methyl-coenzyme M = coenzyme M-coenzyme B heterodisulfide + methane Binds 2 coenzyme F430 non-covalently per MCR complex. Coenzyme F430 is a yellow nickel porphinoid. Methyl-coenzyme-M reductase is activated when the enzyme-bound coenzyme F430 is reduced to the Ni(I) oxidation state. One-carbon metabolism; methyl-coenzyme M reduction; methane from methyl-coenzyme M: step 1/1. MCR is a hexamer of two alpha, two beta, and two gamma chains, forming a dimer of heterotrimers. Belongs to the methyl-coenzyme M reductase gamma subunit family. +Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 19 (CSTX) family. 01 subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 49 kDa subunit family. +Belongs to the universal ribosomal protein uS2 family. +D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5. Homotetramer. Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. +Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance. Localizes at the nuclear basket and at or near the nuclear entry to the gated channel of the pore. Expressed throughout early development, with embryonic expression primarily in anterior neural tissues. Belongs to the nucleoporin interacting component (NIC) family. +Light-emitting reaction in luminous bacteria. The specific role of the beta subunit is unknown, but it is absolutely required for bioluminescence activity. a long-chain fatty aldehyde + FMNH2 + O2 = a long-chain fatty acid + FMN + 2 H(+) + H2O + hnu Heterodimer of an alpha and a beta chain. Belongs to the bacterial luciferase oxidoreductase family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 1 subfamily. +This protein may be involved in virus assembly. Essential for virus function. +Not yet known. To PsiA protein of plasmid R6-5. +Transcriptional coregulator (By similarity). Involved in control of the cell cycle (PubMed:10629049, PubMed:10779346, PubMed:15190068, PubMed:16624878, PubMed:23629655). Also antagonizes transactivation by ZBTB17 and GABP2; represses ZBTB17 activation of the p15(INK4b) promoter and inhibits its ability to recruit p300 (PubMed:10675337, PubMed:12244100). Coactivator for EGR2 and GABP2 (PubMed:12244100, PubMed:14532282). Tethers the chromatin modifying Set1/Ash2 histone H3 'Lys-4' methyltransferase (H3K4me) and Sin3 histone deacetylase (HDAC) complexes (involved in the activation and repression of transcription, respectively) together (PubMed:12670868). Component of a THAP1/THAP3-HCFC1-OGT complex that is required for the regulation of the transcriptional activity of RRM1 (PubMed:20200153). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues (PubMed:20018852). Recruits KMT2E/MLL5 to E2F1 responsive promoters promoting transcriptional activation and thereby facilitates G1 to S phase transition (PubMed:23629655). Modulates expression of homeobox protein PDX1, perhaps acting in concert with transcription factor E2F1, thereby regulating pancreatic beta-cell growth and glucose-stimulated insulin secretion (By similarity). May negatively modulate transcriptional activity of FOXO3 (By similarity). (Microbial infection) In case of human herpes simplex virus (HSV) infection, HCFC1 forms a multiprotein-DNA complex with the viral transactivator protein VP16 and POU2F1 thereby enabling the transcription of the viral immediate early genes. Composed predominantly of six polypeptides ranging from 110 to 150 kDa and a minor 300 kDa polypeptide (PubMed:10920196). The majority of N- and C-terminal cleavage products remain tightly, albeit non-covalently, associated (PubMed:10920196). Interacts with POU2F1, CREB3, ZBTB17, EGR2, E2F4, CREBZF, SP1, GABP2, Sin3 HDAC complex (SIN3A, HDAC1, HDAC2, SUDS3), SAP30, SIN3B and FHL2 (PubMed:9271389, PubMed:9389645, PubMed:10675337, PubMed:10976766, PubMed:10629049, PubMed:10871379, PubMed:10984507, PubMed:12244100, PubMed:14532282, PubMed:12670868, PubMed:15705566, PubMed:16624878). Component of a MLL1 complex, composed of at least the core components KMT2A/MLL1, ASH2L, HCFC1, WDR5 and RBBP5, as well as the facultative components BAP18, CHD8, DPY30, E2F6, HCFC2, HSP70, INO80C, KANSL1, LAS1L, MAX, MCRS1, MEN1, MGA, KAT8, PELP1, PHF20, PRP31, RING2, RUVBL1, RUVBL2, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9 and TEX10 (PubMed:15199122, PubMed:15960975). Component of a THAP1/THAP3-HCFC1-OGT complex that is required for the regulation of the transcriptional activity of RRM1 (PubMed:20200153). Interacts directly with THAP3 (via its HBM) (PubMed:20200153). Interacts (via the Kelch-repeat domain) with THAP1 (via the HBM); the interaction recruits HCHC1 to the RRM1 (PubMed:20200153). Interacts directly with OGT; the interaction, which requires the HCFC1 cleavage site domain, glycosylates and promotes the proteolytic processing of HCFC1, retains OGT in the nucleus and impacts the expression of herpes simplex virus immediate early viral genes (PubMed:12670868, PubMed:21285374, PubMed:23353889). Component of the SET1 complex, at least composed of the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L, CXXC1, HCFC1 and DPY30 (PubMed:17998332, PubMed:18838538). Component of the NSL complex at least composed of MOF/KAT8, KANSL1, KANSL2, KANSL3, MCRS1, PHF20, OGT1/OGT, WDR5 and HCFC1 (PubMed:20018852). Component of a complex at least composed of ZNF335, HCFC1, CCAR2, EMSY, MKI67, RBBP5, ASH2L and WDR5; the complex is formed as a result of interactions between components of a nuclear receptor-mediated transcription complex and a histone methylation complex (PubMed:19131338). Within the complex interacts with ZNF335 (PubMed:19131338). Interacts with TET2 and TET3 (PubMed:23353889). Interacts with HCFC1R1 (PubMed:12235138). Interacts with THAP11 (By similarity). Interacts (via Kelch domain) with KMT2E/MLL5 isoform 3 (via HBM motif) (PubMed:23629655). Interacts with E2F1 (PubMed:23629655). (Microbial infection) Associates with the VP16-induced complex; binding to HCFC1 activates the viral transcriptional activator VP16 for association with POU2F1, to form a multiprotein-DNA complex responsible for activating transcription of the viral immediate early genes (PubMed:10629049). Interacts with the viral transactivator protein VP16 (PubMed:9271389, PubMed:9389645, PubMed:10629049). HCFC1R1 modulates its subcellular localization and overexpression of HCFC1R1 leads to accumulation of HCFC1 in the cytoplasm (PubMed:12235138). Non-processed HCFC1 associates with chromatin. Colocalizes with CREB3 and CANX in the ER. Highly expressed in fetal tissues and the adult kidney. Present in all tissues tested. The HCF repeat is a highly specific proteolytic cleavage signal. The kelch repeats fold into a 6-bladed kelch beta-propeller called the beta-propeller domain which mediates interaction with HCFC1R1. Proteolytically cleaved at one or several PPCE--THET sites within the HCF repeats (PubMed:7590226, PubMed:10920196, PubMed:21285374). Further cleavage of the primary N- and C-terminal chains results in a 'trimming' and accumulation of the smaller chains. Cleavage is promoted by O-glycosylation (PubMed:21285374, PubMed:28302723, PubMed:28584052). O-glycosylated. GlcNAcylation by OGT promotes proteolytic processing. Ubiquitinated. Lys-1807 and Lys-1808 are ubiquitinated both via 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. BAP1 mediated deubiquitination of 'Lys-48'-linked polyubiquitin chains; deubiquitination by BAP1 does not seem to stabilize the protein. The disease is caused by variants affecting the gene represented in this entry. The N- and the C-terminal fragments fail to associate. Was originally thought to be part of the MLL5-L complex, at least composed of KMT2E, STK38, PPP1CA, PPP1CB, PPP1CC, HCFC1, ACTB and OGT (PubMed:19377461). However, the corresponding article has been retracted (PubMed:24336203). Truncated N-terminus. +Globally modulates RNA abundance by binding to RNase E (Rne) and regulating its endonucleolytic activity. Can modulate Rne action in a substrate-dependent manner by altering the composition of the degradosome. Modulates RNA-binding and helicase activities of the degradosome. Homotrimer. Binds to both RNA-binding sites in the C-terminal region of Rne and to RhlB. Belongs to the RraA family. +Vascular tissues, specifically in phloem companion cell-sieve element complexes. +This protein negatively controls the transcription initiation of genes such as deoCABD, udp, and cdd encoding catabolizing enzymes and nupC, nupG, and tsx encoding transporting and pore-forming proteins. Binds cytidine and adenosine as effectors (By similarity). +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +The glycine cleavage system catalyzes the degradation of glycine. (6S)-5,6,7,8-tetrahydrofolate + (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[protein] = (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + NH4(+) The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvT family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Plays a role in viral genome replication by driving entry of quiescent cells into the cell cycle. Stimulation of progression from G1 to S phase allows the virus to efficiently use the cellular DNA replicating machinery to achieve viral genome replication. E7 protein has both transforming and trans-activating activities. Induces the disassembly of the E2F1 transcription factor from RB1, with subsequent transcriptional activation of E2F1-regulated S-phase genes. Interferes with host histone deacetylation mediated by HDAC1 and HDAC2, leading to transcription activation. Also plays a role in the inhibition of both antiviral and antiproliferative functions of host interferon alpha. Interaction with host TMEM173/STING impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta). Homodimer. Homooligomer. Interacts with host RB1; this interaction induces dissociation of RB1-E2F1 complex thereby disrupting RB1 activity. Interacts with host EP300; this interaction represses EP300 transcriptional activity. Interacts with protein E2; this interaction inhibits E7 oncogenic activity. Interacts with host TMEM173/STING; this interaction impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta). Predominantly found in the host nucleus. The E7 terminal domain is an intrinsically disordered domain, whose flexibility and conformational transitions confer target adaptability to the oncoprotein. It allows adaptation to a variety of protein targets and exposes the PEST degradation sequence that regulates its turnover in the cell. Highly phosphorylated. Belongs to the papillomaviridae E7 protein family. +Snake venom zinc metalloprotease that induces apoptosis in vascular endothelial cells (VEC), without degrading the extracellular matrix (it cannot cleave collagen) or inhibiting adhesion of VEC. Has also fibrinogenolytic and hemorrhagic activities (By similarity). Binds 1 zinc ion per subunit. Homodimer; disulfide-linked. Expressed by the venom gland. Belongs to the venom metalloproteinase (M12B) family. P-III subfamily. P-IIIc sub-subfamily. +Hydroperoxy fatty acid reductase essential for the removal of lipid hydroperoxides under normal and stress conditions, leading to the protection of membrane integrity. a hydroperoxy polyunsaturated fatty acid + H(+) + NADPH = a hydroxy polyunsaturated fatty acid + H2O + NADP(+) Mercaptosuccinate, pCMB, and nethylmaleimide act as inhibitors of the catalytic activity. Optimum pH is 8.2. Optimum temperature is 37 degrees Celsius. Monomer. High light, methylviologen, and salt stress conditions increase the expression level. Belongs to the glutathione peroxidase family. +Belongs to the UPF0319 family. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +Binds 2 calcium ions per subunit. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 1 subfamily. +Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. 2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2 The D1/D2 heterodimer binds P680, chlorophylls that are the primary electron donor of PSII, and subsequent electron acceptors. It shares a non-heme iron and each subunit binds pheophytin, quinone, additional chlorophylls, carotenoids and lipids. D1 provides most of the ligands for the Mn4-Ca-O5 cluster of the oxygen-evolving complex (OEC). There is also a Cl(-1) ion associated with D1 and D2, which is required for oxygen evolution. The PSII complex binds additional chlorophylls, carotenoids and specific lipids. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Tyr-161 forms a radical intermediate that is referred to as redox-active TyrZ, YZ or Y-Z. C-terminally processed by CTPA; processing is essential to allow assembly of the oxygen-evolving complex and thus photosynthetic growth. 2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water. Herbicides such as atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer. Belongs to the reaction center PufL/M/PsbA/D family. +Regulator of peptidoglycan synthesis that is essential for the function of penicillin-binding protein 1A (PBP1a). Interacts with PBP1a. Belongs to the LpoA family. Extended N-terminus. +Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-terminal L-methionyl-[peptide] Binds 1 Fe(2+) ion. Belongs to the polypeptide deformylase family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +May play a role in apoptosis. May act as a tumor suppressor (By similarity). Belongs to the small GTPase superfamily. Arf family. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +Transcription factor that negatively regulates jasmonate (JA) signaling (PubMed:30610166). Negatively regulates JA-dependent response to wounding, JA-induced expression of defense genes, JA-dependent responses against herbivorous insects, and JA-dependent resistance against Botrytis cinerea infection (PubMed:30610166). Plays a positive role in resistance against the bacterial pathogen Pseudomonas syringae pv tomato DC3000 (PubMed:30610166). Interacts with MYC2 (via N-terminus) (PubMed:30610166). MTB1 competes with MED25 for binding to MYC2 (PubMed:30610166). Interacts (via N-terminus) with JAZ7 (PubMed:30610166). Induced by wounding, feeding with herbivorous insects, infection with the fungal pathogen Botrytis cinerea and infection with the bacterial pathogen Pseudomonas syringae pv tomato DC3000. Contains a degenerate basic motif not likely to bind DNA. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue. Belongs to the radical SAM superfamily. RlmN family. +Catalyzes the hydrolysis of 6-phosphogluconolactone to 6-phosphogluconate. 6-phospho-D-glucono-1,5-lactone + H2O = 6-phospho-D-gluconate + H(+) Carbohydrate degradation; pentose phosphate pathway; D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 2/3. Belongs to the cycloisomerase 2 family. +Catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)]. [thioredoxin]-dithiol + arsenate + H(+) = [thioredoxin]-disulfide + arsenite + H2O Belongs to the low molecular weight phosphotyrosine protein phosphatase family. Thioredoxin-coupled ArsC subfamily. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Catalyzes the sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine. H2O + L-histidinol + 2 NAD(+) = 3 H(+) + L-histidine + 2 NADH Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 9/9. Belongs to the histidinol dehydrogenase family. +Catalyzes the facilitated diffusion of 2-acyl-glycero-3-phosphoethanolamine (2-acyl-GPE) into the cell. Belongs to the major facilitator superfamily. LplT (TC 2.A.1.42) family. +(6S)-5-formyl-5,6,7,8-tetrahydrofolate + ATP = 5,10-methenyltetrahydrofolate + ADP + phosphate Belongs to the 5-formyltetrahydrofolate cyclo-ligase family. +Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. [protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family. +Involved in cell fusion during mating by stabilizing the plasma membrane fusion event. Localizes at sites of cell fusion during mating. By pheromones during mating, through the regulation by the STE12 transcription factor. Also induced in respiratory-deficient cells. Belongs to the PRM1 family. +Binds mRNA and regulates the stability of target mRNA. Homodimer. Interacts with STYX (By similarity). Detected at cytoplasmic stress granules and P-bodies. Detected at exosome granules where mRNA is degraded (By similarity). Widely expressed. Can be phosphorylated by DYRK2 (in vitro) (By similarity). Dephosphorylated by calcineurin in a Ca(2+) dependent manner, and probably by PP2A or PP4 serine phosphatases in cAMP- and PKC-mediated pathways. +Catalyzes the formation of flavonols from dihydroflavonols. It can act on dihydrokaempferol to produce kaempferol, on dihydroquercetin to produce quercitin and on dihydromyricetin to produce myricetin. 2-oxoglutarate + a (2R,3R)-dihydroflavonol + O2 = a flavonol + CO2 + H2O + succinate 2-oxoglutarate + a (2S)-flavan-4-one + O2 = a (2R,3R)-dihydroflavonol + CO2 + succinate Binds 1 Fe cation per subunit. Binds 1 ascorbate molecule per subunit. Secondary metabolite biosynthesis; flavonoid biosynthesis. Temporally expressed during flower development. Belongs to the iron/ascorbate-dependent oxidoreductase family. +Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline. carbamoyl phosphate + L-ornithine = H(+) + L-citrulline + phosphate Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 1/3. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. OTCase family. +Ligand for the receptor complex composed of ilcr-1 and ilcr-2. Binding to the ilcr-1/2 receptor complex triggers a signaling cascade, activating the downsteam signaling components actl-1, pik-1 and nfki-1, and results in increased neuronal activity in RMG interneurons in response to input from oxygen-sensing neurons. This leads to increased animal movement and promotes aggregation behavior. Plays a role in the responsiveness of RMG interneurons to ascaroside pheromones. Homodimer; disulfide-linked. Interacts with the receptor complex composed of ilcr-1 and ilcr-2 with the interaction being mediated by ilcr-2. Expressed in RMG and AUA interneurons and ASE sensory neurons. Belongs to the IL-17 family. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +A non-essential component of RNA polymerase (RNAP). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) RNAP is composed of a core of 2 alpha, a beta and a beta' subunit. The core is associated with a delta subunit, and at least one of epsilon or omega. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit epsilon family. +Involved in initiation control of chromosome replication. Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. Belongs to the YabA family. +Acts as a component of the essential kinetochore-associated NDC80 complex, which is required for chromosome segregation and spindle checkpoint activity to ensure proper cell division. Component of the NDC80 complex, which consists of NDC80, NUF2, SPC24 and SPC25. Embryonic lethality due to division arrest before the globular stage. Belongs to the NUF2 family. The predicted gene has been split into 2 genes: At1g60995 and At1g61000. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Plays a role in the establishment of the epidermal barrier on plantar skin (By similarity). Involved in the maintenance of cell layer development and keratin filament bundles in suprabasal cells of the epithelium (By similarity). (Microbial infection) Acts as a mediator of S.aureus adherence to desquamated nasal epithelial cells via clfB, and hence may play a role in nasal colonization. (Microbial infection) Binds S.pneumoniae PsrP, mediating adherence of the bacteria to lung cell lines. Reduction of levels of KRT10 keratin decrease adherence, overexpression increases adherence. Neither protein has to be glycosylated for the interaction to occur. Heterotetramer of two type I and two type II keratins. Heterodimer with KRT1 (PubMed:24940650, PubMed:27595935). Two heterodimers of KRT1 and KRT10 form a heterotetramer (PubMed:27595935). The KRT10 subunit in the heterotetramer is probably disulfide-linked (PubMed:27595935). Interacts with PLEC isoform 1C, when in a heterodimer with KRT1 (PubMed:24940650). (Microbial infection) Interacts (via C-terminal tail domain) with the S.aureus clumping factor, clfB; this interaction probably mediates S.aureus attachment to the keratinized squamous epithelial cells from the nasal cavity. (Microbial infection) Interacts (via the C-terminal tail domain) with S.pneumoniae serine-rich repeat protein PsrP; this interaction probably mediates S.pneumoniae adherence to lung tissue and subsequent pathogenesis. Neither protein has to be glycosylated for the interaction to occur. Seen in all suprabasal cell layers including stratum corneum. Expressed on the surface of lung cell lines (PubMed:19627498). Localized on the surface of desquamated nasal epithelial cells (at protein level) (PubMed:12427098). Repressed in keratinocytes by all-trans retinoic acid (ATRA), via reduction of mRNA stability. A number of alleles are known that mainly differ in the Gly-rich region (positions 490-560). The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. There are two types of cytoskeletal and microfibrillar keratin: I (acidic; 40-55 kDa) and II (neutral to basic; 56-70 kDa). Belongs to the intermediate filament family. Truncated N-terminus. Keratin-10 entry +Completely overlaps SRB8. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Seems to play a role in the dimerization of PSII. Belongs to the PsbT family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Belongs to the complex I subunit 2 family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +Involved in cytoplasm to vacuole transport (Cvt) and autophagic vesicle formation. Autophagy is essential for maintenance of amino acid levels and protein synthesis under nitrogen starvation. Required for selective autophagic degradation of the nucleus (nucleophagy). Also required for mitophagy, which eliminates defective or superfluous mitochondria in order to fulfill cellular energy requirements and prevent excess ROS production. Conjugation with atg12, through a ubiquitin-like conjugating system involving atg7 as an E1-like activating enzyme and atg10 as an E2-like conjugating enzyme, is essential for its function. The atg12-atg5 conjugate acts as an E3-like enzyme which is required for lipidation of atg8 and atg8 association to the vesicle membranes (By similarity). Has a role in meiosis and sporulation. Conjugated with atg12. Interacts with atg16 and atg18. Conjugated to atg12; which is essential for autophagy. Impairs atg8-processing. Belongs to the ATG5 family. +Transforms N(2)-succinylglutamate into succinate and glutamate. H2O + N-succinyl-L-glutamate = L-glutamate + succinate Binds 1 zinc ion per subunit. Amino-acid degradation; L-arginine degradation via AST pathway; L-glutamate and succinate from L-arginine: step 5/5. Belongs to the AspA/AstE family. Succinylglutamate desuccinylase subfamily. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Binds 1 zinc ion per subunit. Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily. +With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS5 family. +Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Mating type proteins are sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. Silenced copy of mat-Mi at mat3-M. There are three genetic loci for mating type genes in S.pombe, mat1, mat2-P and mat3-M. Cell type is determined by the alternate allele present in mat1, either P (plus) in a h+ or M (minus) in a h- cell. Mat2-P and mat3-M serve as donor of information that is transposed to mat1 during a switch of mating type. +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Binds 1 zinc ion per subunit. Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily. +N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 3/5. Belongs to the TrpF family. +Potential calcium-dependent cell-adhesion protein. +Belongs to the bacterial ribosomal protein bL36 family. +Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) with (2E,6E)-farnesyl diphosphate (E,E-FPP) to yield (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-undecaprenyl diphosphate (di-trans,octa-cis-UPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide. (2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = di-trans,octa-cis-undecaprenyl diphosphate + 8 diphosphate Binds 2 magnesium ions per subunit. Homodimer. Belongs to the UPP synthase family. +3-isopropylmalate dehydratase large subunit; part of the gene cluster that mediates the biosynthesis of pneumocandins, lipohexapeptides of the echinocandin family that prevent fungal cell wall formation by non-competitive inhibition of beta-1,3-glucan synthase (PubMed:23688303, PubMed:25270390). Possibly secretes antifungal pneumocandins, thus avoiding of intracellular accumulation and ameliorating the toxicity to the producing cells (PubMed:23688303). Belongs to the ABC transporter superfamily. ABCC family. Conjugate transporter (TC 3.A.1.208) subfamily. +Catalyzes the reduction of free flavins (FMN, FAD and riboflavin) by NADH. Subsequently, the reduced flavins diffuse to the large HpaB component or to other electron acceptors such as cytochrome c and Fe(3+) ion (By similarity). a reduced flavin + NAD(+) = an oxidized flavin + 2 H(+) + NADH Aromatic compound metabolism; 4-hydroxyphenylacetate degradation; pyruvate and succinate semialdehyde from 4-hydroxyphenylacetate: step 1/7. Homodimer (Probable). 4-HPA 3-monooxygenase consists of a reductase component HpaC and an oxygenase component HpaB (By similarity). Belongs to the non-flavoprotein flavin reductase family. HpaC subfamily. +Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP), the rate-limiting step in the metabolic pathway that produces glucose from lactate and other precursors derived from the citric acid cycle. Facilitates the recycling of lactate carbon in the liver. GTP + oxaloacetate = CO2 + GDP + phosphoenolpyruvate Binds 1 Mn(2+) ion per subunit. Carbohydrate biosynthesis; gluconeogenesis. Monomer. Present in liver and kidney. Appears to be constitutively expressed. In eukaryotes there are two isozymes: a cytoplasmic one and a mitochondrial one. In birds, PEPCK-M is the sole form of hepatic PEPCK, but it constitutes 60% of the enzyme in the kidney. Belongs to the phosphoenolpyruvate carboxykinase [GTP] family. +Belongs to the nucleosome assembly protein (NAP) family. +Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Belongs to the Nudix hydrolase family. RppH subfamily. +Redox regulated molecular chaperone. Protects both thermally unfolding and oxidatively damaged proteins from irreversible aggregation. Plays an important role in the bacterial defense system toward oxidative stress. Under oxidizing conditions two disulfide bonds are formed involving the reactive cysteines. Under reducing conditions zinc is bound to the reactive cysteines and the protein is inactive. Belongs to the HSP33 family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +mRNA-binding protein involved in proper cytoplasmic distribution of mitochondria. May associate with the eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the CLU family. +a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + ATP = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + ADP + H(+) Belongs to the PI3/PI4-kinase family. +Has antibacterial activity against the Gram-negative bacteria E.coli and P.aeruginosa, and the Gram-positive bacteria S.aureus and M.luteus. Has antiprotozoal activity against L.amazonensis. No hemolytic activity. Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Dermaseptin subfamily. +Involved in protein export. The function of the beta subunit is unknown, but it may be involved in stabilization of the trimeric complex. Component of the protein translocase complex. Heterotrimer consisting of alpha (SecY), beta (SecG) and gamma (SecE) subunits. Can form oligomers of the heterotrimer. Belongs to the SEC61-beta family. +Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + UDP-N-acetyl-alpha-D-glucosamine = a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + holo-[ACP] Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 1/6. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxA subfamily. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. +ATP + D-tagatofuranose 6-phosphate = ADP + D-tagatofuranose 1,6-bisphosphate + H(+) Carbohydrate metabolism; D-tagatose 6-phosphate degradation; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-tagatose 6-phosphate: step 1/2. Belongs to the carbohydrate kinase PfkB family. LacC subfamily. +Serine protease that displays ATP-independent proteolytic activity towards peptides and unfolded proteins and ATP-dependent activity for the cleavage of folded proteins. Mg(2+). Exhibits no peptide cleavage activity without Mg(2+), regardless of the presence or the absence of ATP. Can also use other divalent cations such as Ni(2+), Ca(2+), Mn(2+) and Co(2+). ADP inhibits the peptide cleavage activity of LonTk, but the enzyme retains 57% activity in comparison to the condition with the addition of ATP. Optimum pH is 9 for the ATP-independent peptide cleavage activity and for ATPase activity. Optimum temperature is 70 degrees Celsius for the ATP-independent peptide cleavage activity, and 95 degrees Celsius for ATPase activity. Homohexamer. Organized in a ring with a central cavity (By similarity). Possesses a two-domain structure consisting of an N-terminal ATPase domain belonging to the AAA(+) superfamily and a C-terminal protease domain. The ATPase domain likely acts as a molecular chaperone functioning in the unfolding of protein structures, along with ATP hydrolysis. Belongs to the peptidase S16 family. Archaeal LonB subfamily. +Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. 2 D-sedoheptulose 7-phosphate = D-glycero-alpha-D-manno-heptose 7-phosphate + D-glycero-beta-D-manno-heptose 7-phosphate Binds 1 zinc ion per subunit. Carbohydrate biosynthesis; D-glycero-D-manno-heptose 7-phosphate biosynthesis; D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate from sedoheptulose 7-phosphate: step 1/1. Homotetramer. The reaction produces a racemic mixture of D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate. Belongs to the SIS family. GmhA subfamily. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Belongs to the UPF0301 (AlgH) family. +Catalyzes the hydrolysis of UDP-3-O-myristoyl-N-acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate, the committed step in lipid A biosynthesis. a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 2/6. Belongs to the LpxC family. +Palmitoyltransferase that catalyzes the addition of palmitate onto various protein substrates such as CTNND2, CD36, STAT3 and S1PR1 thus plays a role in various biological processes including cell adhesion, fatty acid uptake, bacterial sensing or cardiac functions. Plays an important role in the regulation of synapse efficacy by mediating palmitoylation of delta-catenin/CTNND2, thereby increasing synaptic delivery and surface stabilization of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs). Under basal conditions, remains at the synaptic membrane through FYN-mediated phosphorylation that prevents association with endocytic proteins. Neuronal activity enhances the internalization and trafficking of DHHC5 from spines to dendritic shafts where it palmitoylates delta-catenin/CTNND2. Regulates cell adhesion at the plasma membrane by palmitoylating GOLGA7B and DSG2. Plays a role in innate immune response by mediating the palmitoylation of NOD1 and NOD2 and their proper recruitment to the bacterial entry site and phagosomes. Participates also in fatty acid uptake by palmitoylating CD36 and thereby targeting it to the plasma membrane. Upon binding of fatty acids to CD36, gets phosphorylated by LYN leading to inactivation and subsequent CD36 caveolar endocytosis. hexadecanoyl-CoA + L-cysteinyl-[protein] = CoA + S-hexadecanoyl-L-cysteinyl-[protein] The DHHC domain is required for palmitoyltransferase activity. Phosphorylation regulates association with endocytic proteins and its subcellular localization. Phosphorylation by LYN during fatty acid uptake leads to inactivation of the activity. Autopalmitoylated (By similarity). Palmitoylation of the C-terminal tail regulates stimulation-dependent plasma membrane motility (By similarity). Belongs to the DHHC palmitoyltransferase family. ERF2/ZDHHC9 subfamily. +Transport of potassium into the cell. Belongs to the HAK/KUP transporter (TC 2.A.72) family. +Regulator of type 1 phosphatases which maintains protein phosphatase activity under strict control. Belongs to the YPI1 family. +Probably part of an ABC transporter complex. Responsible for energy coupling to the transport system (By similarity). Belongs to the ABC transporter superfamily. +Cell division protein that is part of the divisome complex and is recruited early to the Z-ring. Probably stimulates Z-ring formation, perhaps through the cross-linking of FtsZ protofilaments. Its function overlaps with FtsA. Homodimer. Interacts with FtsZ. Localizes to the division site, in a FtsZ-dependent manner. Belongs to the SepF family. +Orphan nuclear receptor. May act concomitantly with NURR1 in regulating the expression of delayed-early genes during liver regeneration. Binds the NGFI-B response element (NBRE) 5'-AAAAGGTCA-3'. May inhibit NF-kappa-B transactivation of IL2. Participates in energy homeostasis by sequestrating the kinase STK11 in the nucleus, thereby attenuating cytoplasmic AMPK activation (By similarity). Interacts with GADD45GIP1. Interacts with STK11. Binds DNA as a monomer (By similarity). Heterodimer (via DNA-binding domain) with RXRA (via C-terminus); DNA-binding of the heterodimer is enhanced by 9-cis retinoic acid (By similarity). Competes for the RXRA interaction with EP300 and thereby attenuates EP300 mediated acetylation of RXRA (By similarity). Translocation to the mitochondrion upon interaction with RXRA and upon the presence of 9-cis retinoic acid. Phosphorylated at Ser-351 by RPS6KA1 and RPS6KA3 in response to mitogenic or stress stimuli. Acetylated by p300/CBP, acetylation increases stability. Deacetylated by HDAC1 (By similarity). Belongs to the nuclear hormone receptor family. NR4 subfamily. +Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses fumarate or nitrate as electron acceptor. a quinone + sn-glycerol 3-phosphate = a quinol + dihydroxyacetone phosphate Polyol metabolism; glycerol degradation via glycerol kinase pathway; glycerone phosphate from sn-glycerol 3-phosphate (anaerobic route): step 1/1. Composed of a catalytic GlpA/B dimer and of membrane bound GlpC. Belongs to the anaerobic G-3-P dehydrogenase subunit B family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Belongs to the imidazoleglycerol-phosphate dehydratase family. +Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2+), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is required for the activation of the lactate racemase LarA. May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes. Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide = Ni(2+) + pyridinium-3,5-bisthiocarboxylate mononucleotide Induced by L-lactate and repressed by D-lactate. Is thus regulated by the L-lactate/D-lactate ratio. Makes part of the lar operon (larABCDE). Deletion of this gene leads to a loss of lactate racemase activity. Expression of the full-length LarC protein requires a -1 ribosomal frameshift to allow contiguous translation of larC1 and larC2 ORFs, leading to the functional form of the protein. The exact position of the frameshift cannot be determined but likely occurs in the stretch of 10 consecutive adenines present at the end of larC1. Produced from conventional translation of the larC1 ORF. Expression of LarC1 alone does not show lactate racemase activity. Belongs to the LarC family. The exact position of the ribosomal frameshift cannot be determined but likely occurs in the 10 consecutive adenines present at the end of larC1. +Catalyzes the phosphorylation of N-acetylmannosamine (ManNAc) to ManNAc-6-P. an N-acyl-D-mannosamine + ATP = ADP + an N-acyl-D-mannosamine 6-phosphate + H(+) Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 2/5. Homodimer. Belongs to the ROK (NagC/XylR) family. NanK subfamily. Extended N-terminus. Extended N-terminus. +The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. Belongs to the RecF family. +Transcription activator that binds DNA in a sequence-specific manner, likely 5'-GAAATTTTGG-3', to promote the expression of target genes. Interacts with calmodulin (CaM). Belongs to the plant ACBP60 protein family. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL30 family. +Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA, also called 7,8-diammoniononanoate) to form a ureido ring. (7R,8S)-7,8-diammoniononanoate + ATP + CO2 = (4R,5S)-dethiobiotin + ADP + 3 H(+) + phosphate Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 1/2. Homodimer. Belongs to the dethiobiotin synthetase family. +Catalyzes the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH 5,10-methenyltetrahydrofolate + H2O = (6S)-10-formyltetrahydrofolate + H(+) One-carbon metabolism; tetrahydrofolate interconversion. Homodimer. Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family. +Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit. S-adenosyl-L-methionine + uridine(2552) in 23S rRNA = 2'-O-methyluridine(2552) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase RlmE family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +May be implicated in biomineralization processes. Has a function in binding of osteoblasts via the alpha(V)beta(3)-integrin (By similarity). Binds the alpha(V)beta(3)-integrin. Bone specific. Binds keratan sulfate chains. Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Belongs to the eukaryotic ribosomal protein eL15 family. +Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella. Important for motility and virulence. Heteromer of FlaA and FlaB. FlaB is located proximal to the hook while the remainder of the filament is composed of the predominant FlaA. Belongs to the bacterial flagellin family. +Channel that opens in response to stretch forces in the membrane lipid bilayer. Forms a nonselective ion channel with a conductance of about 4 nanosiemens. May participate in the regulation of osmotic pressure changes within the cell. Homopentamer. Belongs to the MscL family. +Belongs to the YejK family. +Belongs to the UPF0597 family. +Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit binds the periplasmic potassium ions and delivers the ions to the membrane domain of KdpB through an intramembrane tunnel. The system is composed of three essential subunits: KdpA, KdpB and KdpC. Belongs to the KdpA family. +Possible formation of a ternary complex RavA-ViaA-CadA. Belongs to the ViaA family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +Lipase that, together with lipl-1, plays a role in the response to nutrient deprivation by controlling lipid metabolism (PubMed:23604316). Specifically, involved in the breakdown of lipids during lipophagy, a process during which lipids contained in lipid droplets that have been delivered to lysosomes by autophagy are degraded (PubMed:23604316). Optimum pH is acidic. Secreted into the intestinal lumen. Up-regulated in the intestine by fasting (PubMed:23604316). Down-regulated in response to a high-glucose diet (PubMed:29113111). Belongs to the AB hydrolase superfamily. Lipase family. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +G-protein coupled receptor for CRH (corticotropin-releasing factor), UCN (urocortin), UCN2 and UCN3. Has high affinity for UCN. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and down-stream effectors, such as adenylate cyclase. Promotes the activation of adenylate cyclase, leading to increased intracellular cAMP levels (By similarity). The transmembrane domain is composed of seven transmembrane helices that are arranged in V-shape. Transmembrane helix 7 assumes a sharply kinked structure (By similarity). The uncleaved pseudo signal peptide prevents receptor's oligomerization and coupling to G(i) subunits. It is also responsible for the rather low receptor localization at the plasma membrane (By similarity). A N-glycosylation site within the signal peptide impedes its proper cleavage and function. Belongs to the G-protein coupled receptor 2 family. +Specifically methylates the guanosine in position 1516 of 16S rRNA. guanosine(1516) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(2)-methylguanosine(1516) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmJ family. +Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P). S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate Belongs to the eIF-2B alpha/beta/delta subunits family. MtnA subfamily. +To H.pylori HP0495/JHP0447. +Involved in pyrimidine catabolism. May facilitate the hydrolysis of carbamate, a reaction that can also occur spontaneously. carbamate + 2 H(+) = CO2 + NH4(+) Belongs to the AB hydrolase superfamily. Hydrolase RutD family. +Troponin I is the inhibitory subunit of troponin, the thin filament regulatory complex which confers calcium-sensitivity to striated muscle actomyosin ATPase activity. Interacts with TRIM63 (By similarity). Binds to actin and tropomyosin. Interacts with STK4/MST1 (By similarity). Phosphorylated at Ser-23 and Ser-24 by PRKD1; phosphorylation reduces myofilament calcium sensitivity. Phosphorylated preferentially at Thr-32. Phosphorylation by STK4/MST1 alters its binding affinity to TNNC1 (cardiac Tn-C) and TNNT2 (cardiac Tn-T) (By similarity). Phosphorylated at Ser-43 and Ser-45 by PRKCE; phosphorylation increases myocardium contractile dysfunction. Belongs to the troponin I family. +Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6-phosphate and D-lactate. H2O + N-acetyl-D-muramate 6-phosphate = (R)-lactate + N-acetyl-D-glucosamine 6-phosphate Amino-sugar metabolism; N-acetylmuramate degradation. Homodimer. A lyase-type mechanism (elimination/hydration) is suggested for the cleavage of the lactyl ether bond of MurNAc 6-phosphate, with the formation of an alpha,beta-unsaturated aldehyde intermediate with (E)-stereochemistry, followed by the syn addition of water to give product. Belongs to the GCKR-like family. MurNAc-6-P etherase subfamily. +Bacteriostatic action for Gram-positive bacteria. Expressed by the dorsal and submental skin glands. +Covalent carrier of the coenzyme of citrate lyase. Oligomer with a subunit composition of (alpha,beta,gamma)6. Belongs to the CitD family. +Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. ATP + NAD(+) = ADP + H(+) + NADP(+) Belongs to the NAD kinase family. +An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. Monomer. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family. +Participates in the formation of a gel matrix (sperm coagulum) entrapping the accessory gland secretions and ejaculated spermatozoa. Interacts with SERPINA5. Belongs to the semenogelin family. +Component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins. Component of the mitochondrial ribosome small subunit (28S) which comprises a 12S rRNA and about 30 distinct proteins. Belongs to the mitochondrion-specific ribosomal protein mL42 family. Has been found in the mitochondrial ribosome large and small subunits. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Exports L-alanine. Belongs to the AlaE exporter family. +Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate. 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = H(+) + 2 H2O + phosphate + pyridoxine 5'-phosphate Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. Homooctamer; tetramer of dimers. Belongs to the PNP synthase family. +Cleaves tripeptides from the N-termini of proteins. Does not cleave mono- or dipeptides, or N-terminally blocked peptides. Belongs to the peptidase S33 family. +Part of the bacABCDEF operon responsible for the biosynthesis of the nonribosomally synthesized dipeptide antibiotic bacilysin, composed of L-alanine and L-anticapsin. Bacilysin is an irreversible inactivator of the glutaminase domain of glucosamine synthetase. BacB catalyzes the allylic isomerization of the endocyclic-delta(4),delta(8)-7R-dihydro-hydroxyphenylpyruvate (en-H2HPP) to generate a mixture of 3E,7R- and 3Z, 7R-olefins of the exocyclic-delta(3),delta(5)-dihydro-hydroxyphenylpyruvate (ex-H2HPP). 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate = 3-[(1E,4R)-4-hydroxycyclohex-2-en-1-ylidene]pyruvate Binds 2 Fe(2+) or Co(2+) ions per subunit. Antibiotic biosynthesis; bacilysin biosynthesis. Monomer. +Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu). ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. +ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl-tRNA(Gln) Belongs to the class-I aminoacyl-tRNA synthetase family. +Belongs to the GAGE family. +Plays an important role in growth control. Its major role in stimulating body growth is to stimulate the liver and other tissues to secrete IGF-1. It stimulates both the differentiation and proliferation of myoblasts. It also stimulates amino acid uptake and protein synthesis in muscle and other tissues. Belongs to the somatotropin/prolactin family. +Mediates the conversion of chorismate to prephenate. chorismate = prephenate No allosteric regulation. Metabolic intermediate biosynthesis; prephenate biosynthesis; prephenate from chorismate: step 1/1. Homodimer. Expressed in root, stem, stigma, anther, leaf, petal tube, petal limb and sepal tissues with highest levels in petal tubes and stems. Expressed at similar levels throughout all flowering stages but accumulates in senescing flowers. +Permease for high affinity iron uptake (PubMed:17138696). Expression regulated by iron through the urbs1 transcription factor (PubMed:17138696). During pathogenic development, expression is confined to the phase of hyphal proliferation inside the plant (PubMed:17138696). Strongly reduces virulence (PubMed:17138696). Belongs to the oxidase-dependent Fe transporter (OFeT) (TC 9.A.10.1) family. +May determine the nasotemporal axis of the retina, and consequently specify the topographical projection of the retinal ganglion-cell axons to the tectum by controlling expression of their target genes. Retina. Can be detected in regions including primordial retina and neuroepithelium by embryonic day 2 (E2). At E3, expressed in the temporal retina and associated pigment epithelium as well as in part of the diencephalon, and at E7 is expressed in retinal ganglion cells. Levels begin to decline from E4 and almost disappear by E10. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. Required to maintain the reduced state of SoxR. The complex is composed of six subunits: RsxA, RsxB, RsxC, RsxD, RsxE and RsxG. Belongs to the NqrDE/RnfAE family. +Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P). S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 1/6. Belongs to the eIF-2B alpha/beta/delta subunits family. MtnA subfamily. +Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA. Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule. Binds 2 Zn(2+) ions. Homodimer. Mainly cytosolic. Widely expressed. Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Belongs to the RNase Z family. +Pectinolytic enzymes consist of four classes of enzymes: pectin lyase, polygalacturonase, pectin methylesterase and rhamnogalacturonase. Among pectinolytic enzymes, pectin lyase is the most important in depolymerization of pectin, since it cleaves internal glycosidic bonds of highly methylated pectins (By similarity). Eliminative cleavage of (1->4)-alpha-D-galacturonan methyl ester to give oligosaccharides with 4-deoxy-6-O-methyl-alpha-D-galact-4-enuronosyl groups at their non-reducing ends. Belongs to the polysaccharide lyase 1 family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +Removes maltotriose and maltotetraose chains that are attached by 1,6-alpha-linkage to the limit dextrin main chain, generating a debranched limit dextrin. Hydrolysis of (1->6)-alpha-D-glucosidic linkages to branches with degrees of polymerization of three or four glucose residues in limit dextrin. Glycan degradation; glycogen degradation. Belongs to the glycosyl hydrolase 13 family. +Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil. Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family. +May play an important role in cardiac development and function. May regulate cardiac conduction and the function of the gap junction protein GJA1. May contribute to the stability and proper localization of GJA1 to cardiac intercalated disk thereby regulating gap junction communication (By similarity). Regulates mitochondrial respiration and mitochondrial DNA copy number maintenance (By similarity). Monomer. Homodimer. Interacts with GJA1. Interacts weakly with DSP. Localizes at the intercalated disk in ventricular tissue and cardiomyocytes. +May assist in the assembly of the 50S subunit. Disruption of the gene does not affect growth of the cell. Enhanced expression can restore both growth and sporulation of a temperature-sensitive mutation in rplB, designated rplB142. +Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetE route): step 1/1. By superoxide. In response to oxidative stress, Cys-719 can react with bacillithiol (BSH) to form mixed disulfides. S-bacillithiolation leads to loss of catalytic activity and methionine auxotrophy. Belongs to the vitamin-B12 independent methionine synthase family. +Completely overlaps HIR3. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Belongs to the LysR transcriptional regulatory family. +Component of the mitochondrial ribosome. May have a function in the assembly/stability of nascent mitochondrial polypeptides exiting the ribosome. Component of the mitochondrial large ribosomal subunit (mt-LSU). Belongs to the ribonuclease III family. Mitochondrion-specific ribosomal protein mL44 subfamily. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'-nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Magnesium is required for nucleotidyltransferase activity. Nickel for phosphatase activity. Monomer. Can also form homodimers and oligomers. Comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain associated with both phosphodiesterase and phosphatase activities. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 1 subfamily. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +As part of the exocyst, may play a role in regulated exocytosis of insulin granules. Interacts with EXOC2, EXOC4 and EXOC5; may be part of the exocyst. Colocalizes with insulin granules. Ubiquitously expressed. Belongs to the SEC6 family. +Lipid metabolism; bile acid degradation. Belongs to the major facilitator superfamily. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Belongs to the UPF0060 family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Matrix protein p15 targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex. Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization (By similarity). Capsid protein p30 is a homohexamer, that further associates as homomultimer. The virus core is composed of a lattice formed from hexagonal rings, each containing six capsid monomers (By similarity). Late-budding domains (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. Gag-p12 contains one L domain: a PPXY motif which potentially interacts with the WW domain 3 of NEDD4 E3 ubiquitin ligase (Potential). Specific enzymatic cleavages by the viral protease yield mature proteins. The protease is released by autocatalytic cleavage. The polyprotein is cleaved during and after budding, this process is termed maturation (By similarity). +Catalyzes an oxidative deamination of predominantly hydrophobic and aromatic L-amino acids, thus producing hydrogen peroxide that may contribute to the diverse toxic effects of this enzyme (PubMed:15142548). Is highly active on L-Phe > L-Tyr > L-Met > L-Leu, and is weakly or not active on other amino acids (PubMed:15142548). Exhibits diverse biological activities, such as slight hemorrhage, induction of platelet aggregation, edema in the mouse paw and bactericidal activity against both Gram-positive (S.aureus) and Gram-negative (E.coli) bacteria (PubMed:15142548). May also induce hemolysis, apoptosis of vascular endothelial cells or tumor cell lines, and may have antiparasitic activities (By similarity). Effects of snake L-amino oxidases on platelets are controversial, since they either induce aggregation or inhibit agonist-induced aggregation. These different effects are probably due to different experimental conditions. an L-alpha-amino acid + H2O + O2 = a 2-oxocarboxylate + H2O2 + NH4(+) H2O + L-leucine + O2 = 4-methyl-2-oxopentanoate + H2O2 + NH4(+) H2O + L-phenylalanine + O2 = 3-phenylpyruvate + H2O2 + NH4(+) H2O + L-methionine + O2 = 4-methylsulfanyl-2-oxobutanoate + H2O2 + NH4(+) H2O + L-tyrosine + O2 = 3-(4-hydroxyphenyl)pyruvate + H2O2 + NH4(+) Homodimer; non-covalently linked. Expressed by the venom gland. Contains 2 disulfide bonds. N-glycosylated. The enzymatic activity is not affected by deglycosylation. Belongs to the flavin monoamine oxidase family. FIG1 subfamily. The existence of several isoforms has been reported that may be due to either different composition or different glycosylation or by the synthesis from different genes. +Important for breakdown of endosperm starch during germination. Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units. Binds 3 Ca(2+) ions per subunit. Monomer. More abundant in germinating seeds, than in callus, young roots and leaves. Expressed at a high level during germination in the aleurones cells under the control of the plant hormone gibberellic acid and in the developing grains at a low level. Only cereal amylase known to be glycosylated. Binds starch not only at the active site, but also via accessory binding sites on the protein surface that are important for efficient binding to starch granules and thereby increase enzyme activity. Belongs to the glycosyl hydrolase 13 family. +Belongs to the alphaherpesvirinae HHV-1 UL55 family. +IFN-induced antiviral protein which acts as an inhibitor of cellular as well as viral processes, cell migration, proliferation, signaling, and viral replication. Enhances MAVS-mediated host antiviral responses by serving as an adapter bridging TBK1 to MAVS which leads to the activation of TBK1 and phosphorylation of IRF3 and phosphorylated IRF3 translocates into nucleus to promote antiviral gene transcription. Exhibits an antiproliferative activity via the up-regulation of cell cycle negative regulators CDKN1A/p21 and CDKN1B/p27. Normally, CDKN1B/p27 turnover is regulated by COPS5, which binds CDKN1B/p27 in the nucleus and exports it to the cytoplasm for ubiquitin-dependent degradation. IFIT3 sequesters COPS5 in the cytoplasm, thereby increasing nuclear CDKN1B/p27 protein levels. Up-regulates CDKN1A/p21 by down-regulating MYC, a repressor of CDKN1A/p21. Can negatively regulate the apoptotic effects of IFIT2 (By similarity). Component of an interferon-dependent multiprotein complex, at least composed of IFIT1, IFIT2 and IFIT3 (By similarity). Interacts with IFIT1 and IFIT2 (By similarity). Interacts (via N-terminus) with MAVS, TBK1, TRAF6 and DDX58 (By similarity). Interacts with COPS5 (By similarity). Induced by T.gondii infection in the testes and uterus. Belongs to the IFIT family. +Bifunctional enzyme with a methyltransferase domain that catalyzes the ring contraction and methylation of C-17 in cobalt-factor III to form cobalt-factor IV, and an isomerase domain that catalyzes the conversion of cobalt-precorrin-8 to cobyrinate. Co(II)-factor III + H(+) + S-adenosyl-L-methionine = Co(II)-factor IV + S-adenosyl-L-homocysteine Co-precorrin-8X = cob(II)yrinate Cofactor biosynthesis; adenosylcobalamin biosynthesis; cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route): step 3/10. Cofactor biosynthesis; adenosylcobalamin biosynthesis; cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route): step 9/10. In the N-terminal section; belongs to the precorrin methyltransferase family. In the C-terminal section; belongs to the CobH family. +Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. The branch chain-length distribution of the reaction products shows degree of polymerization (DP) of 5 to 30, with two local maxima at DP 6 and DP 11. Exhibits an alpha-retaining catalytic mechanism. Does not display alpha-galactosidase or pullulanase activity, since melibiose and pullulan are not substrates. Is not able to catalyze the hydrolysis or transglycosylation of maltoheptaose, suggesting that the TK1436 protein contains neither alpha-amylase nor 4-alpha-glucanotransferase activity. Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain. Optimum pH is 7.0. Optimum temperature is 70 degrees Celsius. Is thermostable up to 90 degrees Celsius. Monomer. Up-regulated by maltodextrin. The C-terminus contains two copies of a helix-hairpin-helix (HhH) motif that are dispensable for activity and thermal stability. Belongs to the glycosyl hydrolase 57 family. +Regulatory protein, which plays a central role in chromosome stability, in the p53/TP53 pathway, and DNA repair. Probably acts by blocking the action of key proteins. During the mitosis, it blocks Separase/ESPL1 function, preventing the proteolysis of the cohesin complex and the subsequent segregation of the chromosomes. At the onset of anaphase, it is ubiquitinated, conducting to its destruction and to the liberation of ESPL1. Its function is however not limited to a blocking activity, since it is required to activate ESPL1. Negatively regulates the transcriptional activity and related apoptosis activity of p53/TP53. The negative regulation of p53/TP53 may explain the strong transforming capability of the protein when it is overexpressed. May also play a role in DNA repair via its interaction with Ku, possibly by connecting DNA damage-response pathways with sister chromatid separation (By similarity). Interacts with the caspase-like ESPL1, and prevents its protease activity probably by covering its active site. Interacts with p53/TP53 and blocks its activity probably by blocking its binding to DNA. Interacts with the Ku 70 kDa subunit of ds-DNA kinase. Interacts with PTTG1IP. Interacts with RPS10 and DNAJA1 (By similarity). The N-terminal destruction box (D-box) acts as a recognition signal for degradation via the ubiquitin-proteasome pathway. The TEK-boxes are required for 'Lys-11'-linked ubiquitination and facilitate the transfer of the first ubiquitin and ubiquitin chain nucleation. TEK-boxes may direct a catalytically competent orientation of the UBE2C/UBCH10-ubiquitin thioester with the acceptor lysine residue (By similarity). Phosphorylated by CDK1 during mitosis. Phosphorylated in vitro by ds-DNA kinase. Ubiquitinated through 'Lys-11' linkage of ubiquitin moieties by the anaphase promoting complex (APC) at the onset of anaphase, conducting to its degradation. 'Lys-11'-linked ubiquitination is mediated by the E2 ligase UBE2C/UBCH10 (By similarity). Belongs to the securin family. +Involved in the oxidation of myo-inositol (MI) to 2-keto-myo-inositol (2KMI or 2-inosose). myo-inositol + NAD(+) = H(+) + NADH + scyllo-inosose Homotetramer. Belongs to the Gfo/Idh/MocA family. +Belongs to the MHC class II family. +Usually encoded in the trnK tRNA gene intron. Probably assists in splicing its own and other chloroplast group II introns. Belongs to the intron maturase 2 family. MatK subfamily. +Mitochondrial GTP/GDP transporter required for GTP uptake and GDP exit from mitochondria. Involved in mitochondrial iron transport and essential for mitochondrial genome maintenance. Belongs to the mitochondrial carrier (TC 2.A.29) family. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +This b-type cytochrome is tightly associated with the reaction center of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. With its partner (PsbE) binds heme. PSII binds additional chlorophylls, carotenoids and specific lipids. Heterodimer of an alpha subunit and a beta subunit. Cyanobacterial PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins PsbO, PsbU, PsbV and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbE/PsbF family. +Modulates exocytosis of dense-core granules and secretion of hormones in the pancreas and the pituitary. Interacts with vesicles containing negatively charged phospholipids in a Ca(2+)-independent manner (By similarity). Part of a ternary complex containing STX1A and RAB27A. Can bind both dominant negative and dominant active mutants of RAB27A. Binds STXBP1, RAB3A, RAB8A and RAB27B. Interacts with MYO5A (By similarity). Detected close to the plasma membrane and on secretory granules. In pancreas, interacts with insulin-containing vesicles (By similarity). May be due to an intron retention. +Protein N-lysine methyltransferase. Trimethylates KIN at Lys-135 (in vitro). L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine Interacts with members of the heat shock protein 90 and 70 families; these proteins probably are methylation substrates. Belongs to the methyltransferase superfamily. METTL22 family. +Adhesin necessary for successful cytadherence and virulence. Integral and surface exposed membrane protein that localizes to the membrane at the attachment organelle. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Probably acts as an electrical shunt for an outwardly-directed proton pump that is linked to amino acid decarboxylation, as part of the extreme acid resistance (XAR) response. Belongs to the chloride channel (TC 2.A.49) family. ClcB subfamily. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds 2 heme A groups non-covalently per subunit. Binds a copper B center. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of a catalytic core of 3 subunits and several supernumerary subunits. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII). Belongs to the heme-copper respiratory oxidase family. +(6S)-10-formyltetrahydrofolate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide = (6S)-5,6,7,8-tetrahydrofolate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide H2O + IMP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide Purine metabolism; IMP biosynthesis via de novo pathway; 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide (10-formyl THF route): step 1/1. Purine metabolism; IMP biosynthesis via de novo pathway; IMP from 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide: step 1/1. The IMP cyclohydrolase activity resides in the N-terminal region. Belongs to the PurH family. +Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding a ubiquitin-E1 thioester and free AMP. ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine. Protein modification; protein ubiquitination. Monomer. Expressed in leaves, flowers, roots and stems. Detected in germinating seeds, cotyledons, hypocotyls, vascular tissues, anthers, filaments, pollen, style, stigma, sepals, petals, ovary, developing ovules, funiculi and silique walls. Expressed over the entire range of development. No visible phenotype and no changes in disease susceptibility. Both UBA1 and UBA2 are able to activate ubiquitin and transfer it to the E2s with equal efficiency. Belongs to the ubiquitin-activating E1 family. +Involved in cell division. Belongs to the CrgA family. +Catalyzes the oxidation of erythronate-4-phosphate to 3-hydroxy-2-oxo-4-phosphonooxybutanoate. 4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + H(+) + NADH Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 2/5. Homodimer. Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine Purine metabolism; AMP biosynthesis via salvage pathway; AMP from adenine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. +Possible formation of a ternary complex RavA-ViaA-CadA. Belongs to the ViaA family. +Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate. 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = H(+) + 2 H2O + phosphate + pyridoxine 5'-phosphate Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. Homooctamer; tetramer of dimers. Belongs to the PNP synthase family. +DNA-binding protein that preferentially recognizes a curved DNA sequence. It is probably a functional analog of DnaJ; displays overlapping activities with DnaJ, but functions under different conditions, probably acting as a molecular chaperone in an adaptive response to environmental stresses other than heat shock. Lacks autonomous chaperone activity; binds native substrates and targets them for recognition by DnaK. Its activity is inhibited by the binding of CbpM. +Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. Binds 3 Zn(2+) ions. Belongs to the AP endonuclease 2 family. +Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Heterotetramer composed of ParC and ParE. Belongs to the type II topoisomerase GyrA/ParC subunit family. ParC type 1 subfamily. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +Redox regulated molecular chaperone. Protects both thermally unfolding and oxidatively damaged proteins from irreversible aggregation. Plays an important role in the bacterial defense system toward oxidative stress. Under oxidizing conditions two disulfide bonds are formed involving the reactive cysteines. Under reducing conditions zinc is bound to the reactive cysteines and the protein is inactive. Belongs to the HSP33 family. +Makes mgtA transcription sensitive to intracellular proline levels. Under low levels of proline this protein cannot be fully translated, and a stem loop forms which permits transcription of the downstream mgtA gene (By similarity). Belongs to the MgtL family. Extended N-terminus. +Plus end-directed microtubule-dependent motor protein involved in endosome transport and receptor recycling and degradation. Regulates the plus end motility of early endosomes and the balance between recycling and degradation of receptors such as EGF receptor (EGFR) and FGF receptor (FGFR). Regulates the Golgi to endosome transport of FGFR-containing vesicles during early development, a key process for developing basement membrane and epiblast and primitive endoderm lineages during early postimplantation development. Interacts with PTPN21 (By similarity). Interacts with RAB14. It is unclear whether association with endosomes is mediated via phosphatidylinositol 3-phosphate (PtdIns(3)P)-binding or via its interaction with RAB14. The PX domain mediates binding to phosphatidylinositol 3-phosphate (PtdIns(3)P), phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2), phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) and phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). Does not bind phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) (By similarity). Embryonic death. Embryos are arrested at the blastocyst stage: the primitive endoderm and epiblast cannot be distinguished and appear as cell clumps resembling the inner cell mass (ICM) of the blastocyst. Embryos do not develop an epiblast epithelium and the uterine reaction appears to be incomplete. Development of the primitive endoderm and a basement membrane derived from it are severely affected in embryos at 4.5 dpc. Belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Kinesin family. Partially unspliced pre-RNA. +Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. Binds 1 [2Fe-2S] cluster. Belongs to the 2Fe2S plant-type ferredoxin family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex (By similarity). Belongs to the universal ribosomal protein uL10 family. +Plays a major role in the integrity and stability of the capsule. Secreted via the ESX-5 / type VII secretion system (T7SS). Mutants have impaired capsule integrity as well as reduced surface hydrophobicity. Mutants have reduced amounts of surface localized proteins and glycolipids, and morphological differences in the capsular layer. Disruption of the gene is associated with reduced ubiquitin association in cell infection and attenuated virulence in the early stages of infection. Belongs to the mycobacterial PPE family. +Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. [protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family. +Envelope glycoprotein that forms spikes at the surface of virion envelope. Essential for the initial attachment to heparan sulfate moieties of the host cell surface proteoglycans. Involved in fusion of viral and cellular membranes leading to virus entry into the host cell. Following initial binding to its host receptors, membrane fusion is mediated by the fusion machinery composed at least of gB and the heterodimer gH/gL. May be involved in the fusion between the virion envelope and the outer nuclear membrane during virion egress. Homotrimer; disulfide-linked. Binds to heparan sulfate proteoglycans. Interacts with gH/gL heterodimer. During virion morphogenesis, this protein probably accumulates in the endosomes and trans-Golgi where secondary envelopment occurs. It is probably transported to the cell surface from where it is endocytosed and directed to the trans-Golgi network (TGN). A proteolytic cleavage by host furin generates two subunits that remain linked by disulfide bonds. Belongs to the herpesviridae glycoprotein B family. +Together with LptE, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Component of the lipopolysaccharide transport and assembly complex. Interacts with LptE and LptA. Belongs to the LptD family. +Involved in the transfer of galactofuranose (Galf) onto an alpha-D-gluco-configured acceptor substrate to form a beta-1,6-linkage. It uses n-octyl alpha-D-glucopyranoside as an acceptor substrate for the addition of galactofuranose from the donor substrate UDP-galactofuranose. It is not able to use beta-D-glucopyranoside isomers. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. +Expressed in liver, kidney, pancreas, prostate and weakly detected in testis and ovary. Belongs to the DMRT family. +Catalyzes the conversion of biologically active 11beta-hydroxyglucocorticoids (11beta-hydroxysteroid) such as corticosterone, to inactive 11-ketoglucocorticoids (11-oxosteroid) such as 11-dehydrocorticosterone, in the presence of NAD(+) (PubMed:7649078). Functions as a dehydrogenase (oxidase), thereby decreasing the concentration of active glucocorticoids, thus protecting the nonselective mineralocorticoid receptor from occupation by glucocorticoids (PubMed:7649078, PubMed:34028587). Plays an important role in maintaining glucocorticoids balance during preimplantation and protects the fetus from excessive maternal corticosterone exposure (PubMed:34028587). Catalyzes the oxidation of 11beta-hydroxytestosterone (11beta,17beta-dihydroxyandrost-4-ene-3-one) to 11-ketotestosterone (17beta-hydroxyandrost-4-ene-3,11-dione), a major bioactive androgen (By similarity). Catalyzes the conversion of 11beta-hydroxyandrostenedione (11beta-hydroxyandrost-4-ene-3,17-dione) to 11-ketoandrostenedione (androst-4-ene-3,11,17-trione), which can be further metabolized to 11-ketotestosterone (By similarity). Converts 7-beta-25-dihydroxycholesterol to 7-oxo-25-hydroxycholesterol in vitro (By similarity). 7-beta-25-dihydroxycholesterol (not 7-oxo-25-hydroxycholesterol) acts as ligand for the G-protein-coupled receptor (GPCR) Epstein-Barr virus-induced gene 2 (EBI2) and may thereby regulate immune cell migration (By similarity). an 11beta-hydroxysteroid + NAD(+) = an 11-oxosteroid + H(+) + NADH corticosterone + NAD(+) = 11-dehydrocorticosterone + H(+) + NADH 11beta,17beta-dihydroxyandrost-4-ene-3-one + NAD(+) = 17beta-hydroxyandrost-4-ene-3,11-dione + H(+) + NADH 11beta-hydroxyandrost-4-ene-3,17-dione + NAD(+) = androst-4-ene-3,11,17-trione + H(+) + NADH Inhibited by glycyrrhetinic acid (By similarity). Induced by progesterone, through the Ihh signaling pathway (By similarity). Steroid metabolism. Interacts with ligand-free cytoplasmic NR3C2. Highly expressed in kidney, adrenal gland and distal colon, and at much lower levels in lung, hypothalamus, hippocampus, and midbrain. Homozygous knockout pups have reduced Na(+) and water content in the skin at birth, but retain higher levels of Na(+) and water in the skin throughout development and into adulthood at the expense of K(+), manifesting hypokalaemia by 15 days of age and contributing to salt sensitive hypertension. Belongs to the short-chain dehydrogenases/reductases (SDR) family. Rats and mice do not produce appreciable cortisol, because they do not express the 17-alpha hydroxylase (Cyp17a1) enzyme in the adrenals. +Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the insertion of ferrous iron into coproporphyrin III to form Fe-coproporphyrin III. Fe-coproporphyrin III + 2 H(+) = coproporphyrin III + Fe(2+) Porphyrin-containing compound metabolism; protoheme biosynthesis. Belongs to the ferrochelatase family. +Lanthionine-containing peptide antibiotic (lantibiotic) active on certain Gram-positive bacteria. The bactericidal activity of lantibiotics is based on depolarization of energized bacterial cytoplasmic membranes, initiated by the formation of aqueous transmembrane pores. Induces its own expression in at least strain M25. Maturation of lantibiotics involves the enzymatic conversion of Thr, and Ser into dehydrated AA and the formation of thioether bonds with cysteine. This is followed by membrane translocation and cleavage of the modified precursor (By similarity). A longer form (streptin 2, with three more amino acids at the N-terminus) is probably due to incomplete processing. Other forms also exist, some of which are due to differing levels of dehydration. Belongs to the type A lantibiotic family. +Catalyzes the NAD(+)-dependent oxidation of L-threonine to 2-amino-3-ketobutyrate. L-threonine + NAD(+) = (2S)-2-amino-3-oxobutanoate + H(+) + NADH Binds 2 Zn(2+) ions per subunit. Amino-acid degradation; L-threonine degradation via oxydo-reductase pathway; glycine from L-threonine: step 1/2. Homotetramer. Belongs to the zinc-containing alcohol dehydrogenase family. +Binds to the G-box-like motif (5'-ACGTGGC-3') of the chalcone synthase (CHS) gene promoter. G-box and G-box-like motifs are defined in promoters of certain plant genes which are regulated by such diverse stimuli as light-induction or hormone control. Binds DNA as a dimer. Belongs to the bZIP family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Homodimer. Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily. +Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. Homotetramer; dimer of dimers. Belongs to the DapA family. Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB. +Usually encoded in the trnK tRNA gene intron. Probably assists in splicing its own and other chloroplast group II introns. Belongs to the intron maturase 2 family. MatK subfamily. +Stabilizes the head shell following the rearrangement of the gp7 subunits of the head shell lattice that accompanies expansion of the head. Belongs to the lambda phage gpD family. +This protein catalyzes the committed step to the synthesis of the acidic phospholipids. a CDP-1,2-diacyl-sn-glycerol + sn-glycerol 3-phosphate = 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycero-3'-phosphate) + CMP + H(+) Optimum pH is 8.5. Phospholipid metabolism; phosphatidylglycerol biosynthesis; phosphatidylglycerol from CDP-diacylglycerol: step 1/2. Belongs to the CDP-alcohol phosphatidyltransferase class-I family. +Mitogen-activated protein kinase involved in a signal transduction pathway that is activated by changes in the osmolarity of the extracellular environment. Controls osmotic regulation of transcription of target genes (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by tyrosine and threonine phosphorylation. The TXY motif contains the threonine and tyrosine residues whose phosphorylation activates the MAP kinases. Dually phosphorylated on Thr-171 and Tyr-173, which activates the enzyme. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. MAP kinase subfamily. HOG1 sub-subfamily. +Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate. 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = H(+) + 2 H2O + phosphate + pyridoxine 5'-phosphate Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. Homooctamer; tetramer of dimers. Belongs to the PNP synthase family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate. (R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA + diphosphate Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 4/5. Homohexamer. Belongs to the bacterial CoaD family. +This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL13 family. +Catalyzes the phosphorylation of D-glucose to D-glucose 6-phosphate using ADP as the phosphate donor. GDP and CDP can replace ADP, but with reduced efficiency (By similarity). ADP + D-glucose = AMP + D-glucose 6-phosphate + H(+) Binds 1 Mg(2+) ion per subunit. Carbohydrate degradation; glycolysis. Monomer. Belongs to the ADP-dependent glucokinase family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. GTPBP1 subfamily. +Catalyzes the dehydration of D-mannonate. D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O Carbohydrate metabolism; pentose and glucuronate interconversion. Belongs to the mannonate dehydratase family. +Has a role in meiotic nuclear oscillation and recombination. Required to remodel astral microtubules into the 'horsetail' astral array maintaining the 'horsetail' nuclear movement. Promotes homologous paring of chromosomes during this movement. Interacts with alp4, kms1 and mbo1. Localizes to the spindle pole body until the onset of meiosis I. +Subunit of the V0 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (By similarity). V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells, thus providing most of the energy required for transport processes in the vacuolar system (By similarity). May play a role in coupling of proton transport and ATP hydrolysis (By similarity). V-ATPase is a heteromultimeric enzyme made up of two complexes: the ATP-hydrolytic V1 complex and the proton translocation V0 complex (By similarity). The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H (By similarity). The proton translocation complex V0 consists of the proton transport subunit a, a ring of proteolipid subunits c9c'', rotary subunit d, subunits e and f, and the accessory subunits VhaAC45 and ATP6AP2 (By similarity). Belongs to the V-ATPase V0D/AC39 subunit family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Transcription factor involved the regulation of plant development. Together with TCP15, modulates plant stature by promoting cell division in young internodes. Represses cell proliferation in leaf and floral tissues (PubMed:21668538). Together with TCP15, acts downstream of gibberellin (GA), and the stratification pathways that promote seed germination. Involved in the control of cell proliferation at the root apical meristem (RAM) by regulating the activity of CYCB1-1 (PubMed:25655823). Involved in the regulation of seed germination. May regulate the activation of embryonic growth potential during seed germination (PubMed:17953649, PubMed:22155632). Acts together with SPY to promote cytokinin responses that affect leaf shape and trichome development in flowers (PubMed:22267487). Transcription factor involved in the regulation of endoreduplication. Represses endoreduplication by activating the gene expression of the key cell-cycle regulators RBR1 and CYCA2-3 (PubMed:25757472). Regulates the expression of the defense gene pathogenesis-related protein 2 (PR2) in antagonism to SRFR1, a negative regulator of effector-triggered immunity (PubMed:24689742). Involved in positive regulation of plant defense. Represses jasmonate (JA) response to promote disease resistance. Regulates the plant immune system by transcriptionally repressing a subset of JA-responsive genes (PubMed:28132837). Interacts with DOF3.2 (PubMed:22155632). Interacts with SPY (PubMed:22267487). Interacts with SRFR1 (PubMed:24689742). Interacts with GAI and RGL2 (PubMed:25655823). Interacts with DA1, DAR1 and DAR2 (PubMed:25757472). Interacts with the Pseudomonas syringae type III effector HopBB1 (PubMed:28132837). Interacts with SCE1 (PubMed:29250092). Interacts with MOS1 (PubMed:29086441). Localizes in sub-nuclear foci. Expressed in the vascular tissues of the embryo (PubMed:17953649). Expressed in young proliferating tissues (PubMed:21668538). Induced during seed imbibition (PubMed:17953649). Circadian-regulation with the lowest expression in the middle of the dark period (PubMed:17953649). Ubiquitinated (Probable). Targeted for degradation by the SCF(COI1) E3 ubiquitin ligase-proteasome pathway during jasmonate signaling in response to Pseudomonas syringae infection and the secreted type III effector HopBB1 (PubMed:28132837). Delayed germination (PubMed:17953649). No visible phenotype under normal growth conditions, but the double mutant plants tcp14 and tcp15 exhibit reduction in inflorescence height and pedicel length (PubMed:21668538). Plants overexpressing TCP14 exhibit altered plant development and occasionally are lethal (PubMed:22267487). Plants overexpressing TCP14 are modestly reduced in size and exhibit enhanced resistance to the bacterial pathogen Pseudomonas syringae pv tomato strain DC3000, and the oomycete Hyaloperonospora arabidopsidis (PubMed:28132837). Truncated N-terminus. +Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. 2-oxoglutarate + O-phospho-L-serine = 3-phosphooxypyruvate + L-glutamate 2-oxoglutarate + 4-(phosphooxy)-L-threonine = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate Binds 1 pyridoxal phosphate per subunit. Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 2/3. Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 3/5. Homodimer. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. SerC subfamily. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX. Accelerates cholesterol efflux from endothelial cells to high-density lipoprotein (HDL) and thereby regulates angiogenesis (By similarity). (6R)-NADHX = (6S)-NADHX (6R)-NADPHX = (6S)-NADPHX Binds 1 potassium ion per subunit. Homodimer (By similarity). Interacts with APOA1 and APOA2 (By similarity). In sperm, secretion gradually increases during capacitation. Undergoes physiological phosphorylation during sperm capacitation, downstream to PKA activation. Belongs to the NnrE/AIBP family. +Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. AH2 + H2O2 = A + 2 H2O 2 H2O2 = 2 H2O + O2 Binds 1 heme b (iron(II)-protoporphyrin IX) group per dimer. Homodimer or homotetramer. Formation of the three residue Trp-Tyr-Met cross-link is important for the catalase, but not the peroxidase activity of the enzyme. Belongs to the peroxidase family. Peroxidase/catalase subfamily. +Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Binds 2 divalent ions per subunit. Binds 1 potassium ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Homotetramer; dimer of dimers. Belongs to the AdoMet synthase family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Cytochrome P450 monooxygenase that is able to use dehydroabietic acid as a substrate for oxidation. Secondary metabolite biosynthesis. Belongs to the cytochrome P450 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Belongs to the RNR ribonuclease family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA (By similarity). acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterotetramer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits of ACCase subunit beta/alpha. In the N-terminal section; belongs to the AccD/PCCB family. In the C-terminal section; belongs to the AccA family. +This protein is one of the chains of the nonenzymatic membrane component (F0) of mitochondrial ATPase. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase C chain family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +Catalyzes the sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine. H2O + L-histidinol + 2 NAD(+) = 3 H(+) + L-histidine + 2 NADH Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 9/9. Homodimer. Belongs to the histidinol dehydrogenase family. +Catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde, which spontaneously cyclizes to quinolinate. 3-hydroxyanthranilate + O2 = (2Z,4Z)-2-amino-3-carboxymuconate 6-semialdehyde Cofactor biosynthesis; NAD(+) biosynthesis; quinolinate from L-kynurenine: step 3/3. Belongs to the 3-HAO family. +N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 3/5. Belongs to the TrpF family. +Catalyzes the transfer of pyrophosphate from adenosine triphosphate (ATP) to 6-hydroxymethyl-7,8-dihydropterin, an enzymatic step in folate biosynthesis pathway. 6-hydroxymethyl-7,8-dihydropterin + ATP = (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H(+) Cofactor biosynthesis; tetrahydrofolate biosynthesis; 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate from 7,8-dihydroneopterin triphosphate: step 4/4. Belongs to the HPPK family. +Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)). 7-carboxy-7-deazaguanine + ATP + NH4(+) = 7-cyano-7-deazaguanine + ADP + H(+) + H2O + phosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. Belongs to the QueC family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 2 subfamily. +Belongs to the universal ribosomal protein uS9 family. +Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP. an acyl phosphate + sn-glycerol 3-phosphate = a 1-acyl-sn-glycero-3-phosphate + phosphate Lipid metabolism; phospholipid metabolism. Probably interacts with PlsX. Belongs to the PlsY family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Use of phenylalanine and phenylacetate as a carbon source. 4-fumarylacetoacetate + H2O = acetoacetate + fumarate + H(+) Amino-acid degradation; L-phenylalanine degradation; acetoacetate and fumarate from L-phenylalanine: step 6/6. By phenylacetate (PhoAc), 2OH-PhoAc, 3OH-PhoAc, 4OH-PhoAc, phenylalanine, and tyrosine. Not induced by acetate or glutamate. Expression is partially repressed by glucose. Disruption of the fahA gene results in phenylalanine toxicity, secretion of succinylacetone and the absence of growth. This is analogous to the genetic disease, type I hereditary tyrosinemia in humans. Belongs to the FAH family. +May function as an integrase. Belongs to the 'phage' integrase family. +Provides the (R)-glutamate required for cell wall biosynthesis. L-glutamate = D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the aspartate/glutamate racemases family. +Responsible for synthesis of pseudouridine from uracil-2457 in 23S ribosomal RNA. uridine(2457) in 23S rRNA = pseudouridine(2457) in 23S rRNA Belongs to the pseudouridine synthase RsuA family. +D-serine = NH4(+) + pyruvate Monomer. Belongs to the serine/threonine dehydratase family. DsdA subfamily. +With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Part of the 30S ribosomal subunit. Contacts proteins S4 and S8. The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS5 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Allosterically activated by GTP. Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Cell wall formation. NADP(+) + UDP-N-acetyl-alpha-D-muramate = H(+) + NADPH + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurB family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA. Binds to the 5S rRNA independently of L5 and L18. Belongs to the bacterial ribosomal protein bL25 family. +General factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Binds specifically to the TATA box promoter element which lies close to the position of transcription initiation (By similarity). Belongs to the TBP family. +ATP + L-aspartate + NH4(+) = AMP + diphosphate + H(+) + L-asparagine Amino-acid biosynthesis; L-asparagine biosynthesis; L-asparagine from L-aspartate (ammonia route): step 1/1. Belongs to the class-II aminoacyl-tRNA synthetase family. AsnA subfamily. +(6S)-5,6,7,8-tetrahydrofolate + ATP + formate = (6S)-10-formyltetrahydrofolate + ADP + phosphate One-carbon metabolism; tetrahydrofolate interconversion. Belongs to the formate--tetrahydrofolate ligase family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL11 family. +beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Binds 2 magnesium ions per subunit. Carbohydrate biosynthesis; gluconeogenesis. Homotetramer. Belongs to the FBPase class 1 family. +IF-3 binds to the 28S ribosomal subunit and shifts the equilibrum between 55S ribosomes and their 39S and 28S subunits in favor of the free subunits, thus enhancing the availability of 28S subunits on which protein synthesis initiation begins. Belongs to the IF-3 family. +Belongs to the universal ribosomal protein uL29 family. +Component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of the MRP ribonuclease complex, which cleaves pre-rRNA sequences. Component of nuclear RNase P and RNase MRP ribonucleoproteins. RNase P consists of a catalytic RNA moiety and about 10 protein subunits; POP1, POP4, POP5, POP7, RPP14, RPP21, RPP25, RPP30, RPP38 and RPP40. Within the RNase P complex, POP1, POP7 and RPP25 form the 'finger' subcomplex, POP5, RPP14, RPP40 and homodimeric RPP30 form the 'palm' subcomplex, and RPP21, POP4 and RPP38 form the 'wrist' subcomplex. All subunits of the RNase P complex interact with the catalytic RNA. Several subunits of RNase P are also part of the RNase MRP complex. RNase MRP consists of a catalytic RNA moiety and about 8 protein subunits; POP1, POP7, RPP25, RPP30, RPP38, RPP40 and possibly also POP4 and POP5. +Belongs to the CinA family. +Promotes mitochondrial protein synthesis. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Binds to mitochondrial ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway (By similarity). Preferentially binds double-stranded DNA (dsDNA) (By similarity). Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits. RPC3/POLR3C, RPC6/POLR3F and RPC7/POLR3G form a Pol III subcomplex (By similarity). Directly interacts with POLR3C (By similarity). Interacts with TBP and TFIIIB90 and GTF3C4 (By similarity). Interacts with MAF1 (By similarity). Belongs to the eukaryotic RPC34/RPC39 RNA polymerase subunit family. +Catalyzes the conversion of allantoin (5-ureidohydantoin) to allantoic acid by hydrolytic cleavage of the five-member hydantoin ring. (S)-allantoin + H2O = allantoate + H(+) Binds 2 Zn(2+) ions per subunit. Nitrogen metabolism; (S)-allantoin degradation; allantoate from (S)-allantoin: step 1/1. Homotetramer. Carboxylation allows a single lysine to coordinate two zinc ions. Belongs to the metallo-dependent hydrolases superfamily. Allantoinase family. +Belongs to the major facilitator superfamily. MFSD6 family. +Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP. an acyl phosphate + sn-glycerol 3-phosphate = a 1-acyl-sn-glycero-3-phosphate + phosphate Lipid metabolism; phospholipid metabolism. Probably interacts with PlsX. Belongs to the PlsY family. +Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'-nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases. a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate Magnesium is required for nucleotidyltransferase activity. Nickel for phosphatase activity. Monomer. Can also form homodimers and oligomers. Comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain associated with both phosphodiesterase and phosphatase activities. A single active site specifically recognizes both ATP and CTP and is responsible for their addition. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Bacterial CCA-adding enzyme type 1 subfamily. +Produced by macrophages, IFN-alpha have antiviral activities. Interferon stimulates the production of two enzymes: a protein kinase and an oligoadenylate synthetase. Belongs to the alpha/beta interferon family. +Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Binds 1 potassium ion per subunit. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. +Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate. AH2 + GTP + S-adenosyl-L-methionine = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + A + H(+) + L-methionine Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate. Cofactor biosynthesis; molybdopterin biosynthesis. Monomer and homodimer. Belongs to the radical SAM superfamily. MoaA family. +Not known. Binds calcium ions. Extensively O-glycosylated and also N-glycosylated. About four tyrosines are sulfated. In the N-terminal section; belongs to the type-B carboxylesterase/lipase family. +Shows cytolytic activity on many different cells by forming pore in lipid membranes. In vivo, increases heart rate or kills the animal by cardiac arrest. In addition, it binds to heparin with high affinity, interacts with Kv channel-interacting protein 1 (KCNIP1) in a calcium-independent manner, and binds to integrin alpha-V/beta-3 (ITGAV/ITGB3) with moderate affinity. Monomer in solution; Homodimer and oligomer in the presence of negatively charged lipids forming a pore with a size ranging between 20 and 30 Angstroms. Expressed by the venom gland. Is classified as a P-type cytotoxin, since a proline residue stands at position 51 (Pro-31 in standard classification). Belongs to the snake three-finger toxin family. Short-chain subfamily. Type IA cytotoxin sub-subfamily. +Catalyzes the formation of a hydroxyacyl-CoA by addition of water on enoyl-CoA. Also exhibits 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities. a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O a 4-saturated-(3S)-3-hydroxyacyl-CoA = a (3E)-enoyl-CoA + H2O a (3S)-3-hydroxyacyl-CoA + NAD(+) = a 3-oxoacyl-CoA + H(+) + NADH (3S)-3-hydroxybutanoyl-CoA = (3R)-3-hydroxybutanoyl-CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadJ) and two beta chains (FadI). In the N-terminal section; belongs to the enoyl-CoA hydratase/isomerase family. In the central section; belongs to the 3-hydroxyacyl-CoA dehydrogenase family. +Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit binds the periplasmic potassium ions and delivers the ions to the membrane domain of KdpB through an intramembrane tunnel. The system is composed of three essential subunits: KdpA, KdpB and KdpC. Belongs to the KdpA family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Allosterically activated by GTP. Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Required for the proteolytic cleavage of the transcription factor RIM101 in response to alkaline ambient pH. Belongs to the arrestin family. PalF/RIM8 subfamily. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Catalyzes the ATP dependent decarboxylation of (R)-5-diphosphomevalonate to form isopentenyl diphosphate (IPP). Functions in the mevalonate (MVA) pathway leading to isopentenyl diphosphate (IPP), a key precursor for the biosynthesis of isoprenoids and sterol synthesis. (R)-5-diphosphomevalonate + ATP = ADP + CO2 + isopentenyl diphosphate + phosphate Steroid biosynthesis; cholesterol biosynthesis. Homodimer. Belongs to the diphosphomevalonate decarboxylase family. Was originally thought to be located in the peroxisome. However, was later shown to be cytosolic. +Cytokine that plays important roles in allergic inflammation and immune response to parasite infection. Synergizes with IL2 in regulating interferon-gamma synthesis. Stimulates B-cell proliferation, and activation of eosinophils, basophils, and mast cells (By similarity). Plays an important role in controlling IL33 activity by modulating the production of transmembrane and soluble forms of interleukin-1 receptor-like 1/IL1RL1 (By similarity). Displays the capacity to antagonize Th1-driven proinflammatory immune response and downregulates synthesis of many proinflammatory cytokines including IL1, IL6, IL10, IL12 and TNF-alpha through a mechanism that partially involves suppression of NF-kappa-B (By similarity). Functions also on nonhematopoietic cells, including endothelial cells where it induces vascular cell adhesion protein 1/VCAM1, which is important in the recruitment of eosinophils. Exerts its biological effects through its receptors which comprises the IL4R chain and the IL13RA1 chain, to activate JAK1 and TYK2, leading to the activation of STAT6. Aside from IL13RA1, another receptor IL13RA2 acts as a high affinity decoy for IL13 and mediates internalization and depletion of extracellular IL13 (By similarity). Interacts with IL13RA2. Belongs to the IL-4/IL-13 family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Histatins are salivary proteins that are considered to be major precursors of the protective proteinaceous structure on tooth surfaces (enamel pellicle). In addition, histatins exhibit antibacterial and antifungal activities. His3-(20-43)-peptide (histatin-5) is especially effective against C.albicans and C.neoformans, and inhibits Lys-gingipain and Arg-gingipain (rgpB) from P.gingivalis. In addition, His3-(20-43)-peptide is a potent inhibitor of metalloproteinases MMP2 and MMP9. His3-(20-43)-peptide is a homodimer. Histatin-3 and His3-(20-43)-peptide interact with yeast SSA1 and SSA2 proteins. Secreted by serous acinar and demilune cells. 24 proteolytic products are found in saliva. There are two alleles of HTN3, HIS2(1) (shown here) and HIS2(2) that codes for the variant histatin-3-2 found primarily and in high frequencies in black populations. The recommended nomenclature of salivary peptides follows published guidelines (PubMed:20973643). In agreement with the authors, it has been decided to indicate the boundaries of the peptides according to the positions within the precursor, and not in the mature protein, as has formerly been proposed. Belongs to the histatin/statherin family. +Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + H(+) + holo-[ACP] Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxD subfamily. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +Snake venom phospholipase A2 (PLA2) that displays edema-inducing activities (activity that is inhibited by EDTA and dexamethasone), inhibits phospholipid-dependent collagen/ADP-induced platelet aggregation, possess hypotensive as well as anticoagulant activities. In addition, this enzyme shows bactericidal activity against E.coli and S.aureus. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) Binds 1 Ca(2+) ion per subunit. Inhibited by EDTA and bromophenacyl bromide (BPB). Homodimer; non-covalently linked. Expressed by the venom gland. LD(50) is 25 mg/kg by intraperitoneal injection into mice. LD(50) is 7.5 mg/kg by intravenous injection into mice. LD(50) is 0.5 mg/kg by intracerebroventricular injection. This enzyme has been found to be not myotoxic, not cytotoxic, not hemorrhagic and not lethal. Belongs to the phospholipase A2 family. Group II subfamily. D49 sub-subfamily. +One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. +The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein. 16 ATP + 16 H2O + N2 + 8 reduced [2Fe-2S]-[ferredoxin] = 16 ADP + 6 H(+) + H2 + 2 NH4(+) + 8 oxidized [2Fe-2S]-[ferredoxin] + 16 phosphate Hexamer of two alpha, two beta, and two delta chains. +beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Binds 2 magnesium ions per subunit. Carbohydrate biosynthesis; gluconeogenesis. Homotetramer. Belongs to the FBPase class 1 family. +Component of the large ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Component of the large ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Belongs to the bacterial ribosomal protein bL32 family. +Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). Homodimer. Dimerization may be necessary for its function in neuronal dendritic development. Interacts (via C-terminus) with CREBBP (via N-terminus), EP300 and SMARCA4/BRG1. Interacts with the nBAF complex. Association with CREBBP facilitates transcription while the association with SMARCA4/BRG1 suppresses CREST-mediated transcription in resting neurons (By similarity). Localizes to nuclear bodies. Colocalizes with SGO1 at kinetochore (By similarity). Ubiquitous; with lowest levels in spleen. The MFD (multi-functional domain) domain is involved in transcription transactivation, nuclear body targeting and dimerization. Belongs to the SS18 family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. RnhC subfamily. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +Catalyzes the oxidation of L-fucose to L-fuconolactone in the presence of NADP(+). Also active against L-galactose and, to a much lesser degree, D-arabinose. Uses NADP(+) as a hydrogen acceptor much more efficiently than NAD(+). a D-threo-aldose + NAD(+) = a D-threo-aldono-1,5-lactone + H(+) + NADH Inhibited strongly by Hg(2+), Cd(2+) and para-chloromercuribenzoic acid (PCMB) and weakly by Zn(2+) and iodoacetamide. Also inhibited strongly by L-xylose but not D-glucose. Exhibits a shoulder at 289 nm, but the characteristic absorption spectrum caused by prosthetic group is not observed. Optimum pH is 9-10.5. Optimum temperature is 37-40 degrees Celsius. Activity decreases at 50 degrees Celsius. Belongs to the aldo/keto reductase family. +Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. an organic molecule + O2 + reduced [NADPH--hemoprotein reductase] = an alcohol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Expressed in liver. By pregnenolone 16-alpha-carbonitrile (PNCN) and dexamethasone. Belongs to the cytochrome P450 family. +Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine. [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(S)-S-oxide-[protein] [thioredoxin]-disulfide + H2O + L-methionine = [thioredoxin]-dithiol + L-methionine (S)-S-oxide Belongs to the MsrA Met sulfoxide reductase family. +Probable transcription factor that promotes early floral meristem identity in synergy with APETALA1, FRUITFULL and LEAFY. Is required subsequently for the transition of an inflorescence meristem into a floral meristem. Seems to be partially redundant to the function of APETALA1 (By similarity). Homodimer capable of binding to CArG-box sequences. CAULIFLOWER may contribute to the shape of the floral meristem. This trait has likely been selected by early farmers during the domestication of modified inflorescence structures. +Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex. The BCR(KLHL7) complex acts by mediating ubiquitination and subsequent degradation of substrate proteins. Probably mediates 'Lys-48'-linked ubiquitination (By similarity). Protein modification; protein ubiquitination. Homodimer. Component of the BCR(KLHL7) E3 ubiquitin ligase complex (By similarity). +This protein is an anticoagulant protein that acts as an indirect inhibitor of the thromboplastin-specific complex, which is involved in the blood coagulation cascade. A pair of annexin repeats may form one binding site for calcium and phospholipid. Belongs to the annexin family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Has antimicrobial activity. Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Dermaseptin subfamily. +Belongs to the bacterial ribosomal protein bL33 family. +Catalyzes the covalent attachment of the prokaryotic ubiquitin-like protein modifier Pup to the proteasomal substrate proteins, thereby targeting them for proteasomal degradation. This tagging system is termed pupylation. The ligation reaction involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a substrate lysine. ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N(6)-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine. Protein degradation; proteasomal Pup-dependent pathway. Protein modification; protein pupylation. The reaction mechanism probably proceeds via the activation of Pup by phosphorylation of its C-terminal glutamate, which is then subject to nucleophilic attack by the substrate lysine, resulting in an isopeptide bond and the release of phosphate as a good leaving group. Belongs to the Pup ligase/Pup deamidase family. Pup-conjugating enzyme subfamily. +SIII, also known as elongin, is a general transcription elongation factor that increases the RNA polymerase II transcription elongation past template-encoded arresting sites. Subunit A is transcriptionally active and its transcription activity is strongly enhanced by binding to the dimeric complex of the SIII regulatory subunits B and C (elongin BC complex) (By similarity). In embryonic stem cells, the elongin BC complex is recruited by EPOP to Polycomb group (PcG) target genes in order generate genomic region that display both active and repressive chromatin properties, an important feature of pluripotent stem cells (By similarity). Core component of multiple cullin-RING-based ECS (ElonginB/C-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of target proteins. This includes the von Hippel-Lindau ubiquitination complex CBC(VHL). By binding to BC-box motifs it seems to link target recruitment subunits, like VHL and members of the SOCS box family, to Cullin/RBX1 modules that activate E2 ubiquitination enzymes. A number of ECS complexes (containing either KLHDC2, KLHDC3, KLHDC10, APPBP2, FEM1A, FEM1B or FEM1C as substrate-recognition component) are part of the DesCEND (destruction via C-end degrons) pathway, which recognizes a C-degron located at the extreme C terminus of target proteins, leading to their ubiquitination and degradation. Protein modification; protein ubiquitination. Heterotrimer of an A (ELOA, ELOA2 or ELOA3P), ELOB and ELOC subunit (By similarity). The elongin BC complex interacts with EPOP; leading to recruit the elongin BC complex to Polycomb group (PcG) target genes, thereby restricting excessive activity of the PRC2/EED-EZH2 complex (By similarity). Part of E3 ubiquitin ligase complexes with CUL5 or CUL2, RBX1 and a substrate adapter protein that can be either ASB2, KLHDC2, KLHDC3, KLHDC10, APPBP2, FEM1A, FEM1B, FEM1C, SOCS1, SOCS5, ELOA, VHL or WSB1. The elongin BC complex is part of a complex with VHL and hydroxylated HIF1A. Part of an E3 ubiquitin-protein ligase complex including ZYG11B, CUL2 and Elongin BC. Part of an E3 ubiquitin-protein ligase complex including ZER1, CUL2 and Elongin BC. Interacts with VHL. Interacts with TMF1. Interacts with SPSB1. Interacts with SPSB1. Interacts with KLHDC10; which may be an E3 ubiquitin ligase complex substrate recognition component. Interacts with NOS2 in the presence of SPSB1 or SPSB2 or SPSB4 (By similarity). Ubiquitinated by the DCX(AMBRA1) complex, leading to its degradation by the proteasome. Belongs to the SKP1 family. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the eIF-3 subunit J family. +Involved in the cell-cell adhesion. Has both calcium-independent homophilic cell-cell adhesion activity and calcium-independent heterophilic cell-cell adhesion activity with IGSF4, NECTIN1 and NECTIN3. Interaction with EPB41L1 may regulate structure or function of cell-cell junctions. Homodimer. Can form trans-heterodimers with NECTIN3. Interacts with EPB41L1, DLG3, PALS2 and CASK. Mainly expressed in brain, in neuronal cell bodies of cerebellum, cortex, hippocampus, hypothalamus and spinal cord. In spinal cord predominantly expressed in motor neurons. Expressed in axons, presynaptic nerve terminals, glia cell processes. At 14.5 dpc predominantly expressed in the nervous system. The cytoplasmic region mediates interaction with EPB41L1, DLG3, PALS2 and CASK. Belongs to the nectin family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +1-(5-phospho-beta-D-ribosyl)-ATP + H2O = 1-(5-phospho-beta-D-ribosyl)-5'-AMP + diphosphate + H(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 2/9. Belongs to the PRA-PH family. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +Forms an icosahedral capsid with a T=7 symmetry and a 50 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with L2 proteins. Binds to heparan sulfate proteoglycans on cell surface of basal layer keratinocytes to provide initial virion attachment. This binding mediates a conformational change in the virus capsid that facilitates efficient infection. The virion enters the host cell via endocytosis. During virus trafficking, L1 protein dissociates from the viral DNA and the genomic DNA is released to the host nucleus. The virion assembly takes place within the cell nucleus. Encapsulates the genomic DNA together with protein L2. Self-assembles into homopentamers. The capsid has an icosahedral symmetry and consists of 72 capsomers, with each capsomer being a pentamer of L1. Interacts with the minor capsid protein L2; this interaction is necessary for viral genome encapsidation. Interacts with protein E2; this interaction enhances E2-dependent replication and transcription activation. Belongs to the papillomaviridae L1 protein family. +Seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. +Required for preprotein translocation. Part of a complex that contains SEC61, SEC62, SEC63, SEC66 and SEC72. Belongs to the SEC62 family. +Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-methionine = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily. +Has minor fucosyltransferase activity toward biantennary N-glycan acceptors. Does not fucosylate GlcNAc residue within type 2 lactosamine unit. Has fucosyltransferase activity toward biantennary N-glycan acceptors. Does not fucosylate GlcNAc residue within type 2 lactosamine unit. Protein modification; protein glycosylation. Belongs to the glycosyltransferase 10 family. Fucosyltransferase 11 +Belongs to the bacterial ribosomal protein bL32 family. +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Binds 1 zinc ion per subunit. Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Nonribosomal peptide synthetase; part of the gene cluster 14 that mediates the biosynthesis of a ferrichrome A-like siderophore which may contribute to organismal virulence (Probable). The first step of siderophore biosynthesis is performed by the HMG-CoA synthase (HMGS) MYCGRDRAFT_54740 which catalyzes the generation of HMG-CoA and CoA using acetoacetyl-CoA and acetyl-CoA as substrates (By similarity). The enoyl-CoA isomerase/hydratase MYCGRDRAFT_76805 then catalyzes the conversion of HMG-CoA to methylglutaconyl-CoA (By similarity). The acyltransferase MYCGRDRAFT_85486 then fuses methylglutaconyl-CoA with hydroxyornithine to yield methylglutaconyl hydroxyornithine (By similarity). Methylglutaconyl hydroxyornithine is then available for use by the nonribosomal peptide synthetase NRPS2 to generate the ferrichrome A-like siderophore (By similarity). Siderophore biosynthesis. NRP synthetases are composed of discrete domains (adenylation (A), thiolation (T) or peptidyl carrier protein (PCP) and condensation (C) domains) which when grouped together are referred to as a single module. Each module is responsible for the recognition (via the A domain) and incorporation of a single amino acid into the growing peptide product. Thus, an NRP synthetase is generally composed of one or more modules and can terminate in a thioesterase domain (TE) that releases the newly synthesized peptide from the enzyme. Occasionally, epimerase (E) domains (responsible for L- to D- amino acid conversion) are present within the NRP synthetase. NRPS2 has the following architecture: A-T-C-T-C-A-T-C-T-C-T-C (Probable). The lack of corresponding A domains in the 3 modules suggests that A domains have to be used iteratively to incorporate the six amino acids in the siderophore (By similarity). Belongs to the NRP synthetase family. +Member of the two-component regulatory system SrrA/SrrB, which is involved in the global regulation of staphylococcal virulence factors in response to environmental oxygen levels as well as biofilm formation. Also plays an essential role in host-derived nitric oxide resistance by regulating hmp/flavohemoglobin, an enzyme that detoxifies nitric oxide by converting it to nitrate (By similarity). Functions as a transcription regulator by direct binding to promoter regions of target genes (By similarity). Phosphorylated by SrrB. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Required for insertion of 4Fe-4S clusters. Binds 1 iron-sulfur cluster per subunit. Homodimer. Belongs to the HesB/IscA family. +Belongs to the oxygen-dependent FAD-linked oxidoreductase family. +Involved in the binding of tRNA to the ribosomes. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS10 family. +KAHRP might mimick human histidine-rich glycoproteins to anchor host thrombospondin or a parasite analog in a binding complex with the endothelial cell receptor. Cytoplasmic side of the membrane of infected erythrocytes. +Oxygen-binding protein. May be involved in a storage mechanism or for delivery to oxygen-requiring enzymes. The oxygen-binding site contains two iron atoms. Monomer. Belongs to the hemerythrin family. +Synthesizes the galactose-alpha(1,3)-galactose group by catalyzing the transfer of a galactose residue, with an alpha-1,3 linkage, on terminal lactosaminide (Gal-beta-1,4-GlcNAc-R) disaccharide borne by a glycoprotein or a glycolipid. Preferentially glycosylates proteins, can synthesize galactose-alpha(1,3)-galactose on glycoproteins but cannot synthesize the glycolipid called isoglobotrihexosylceramide or isogloboside 3 (iGb3). a beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + UDP-alpha-D-galactose = an alpha-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + H(+) + UDP Binds 1 Mn(2+) ion per subunit. Protein modification; protein glycosylation. Membrane-bound form in trans cisternae of Golgi. The conserved DXD motif is involved in cofactor binding. The manganese ion interacts with the beta-phosphate group of UDP and may also have a role in catalysis. Belongs to the glycosyltransferase 6 family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase. Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Prokaryotic type I sub-subfamily. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Structural protein that makes short spikes at the surface of the virus. Contains receptor binding and receptor-destroying activities. Mediates de-O-acetylation of N-acetyl-4-O-acetylneuraminic acid, which is probably the receptor determinant recognized by the virus on the surface of erythrocytes and susceptible cells. This receptor-destroying activity is important for virus release as it probably helps preventing self-aggregation and ensures the efficient spread of the progeny virus from cell to cell. May serve as a secondary viral attachment protein for initiating infection, the spike protein being the major one. May become a target for both the humoral and the cellular branches of the immune system. H2O + N-acetyl-9-O-acetylneuraminate = acetate + H(+) + N-acetylneuraminate H2O + N-acetyl-4-O-acetylneuraminate = acetate + H(+) + N-acetylneuraminate Homodimer; disulfide-linked. Forms a complex with the M protein in the pre-Golgi. Associates then with S-M complex to form a ternary complex S-M-HE. In infected cells becomes incorporated into the envelope of virions during virus assembly at the endoplasmic reticulum and cis Golgi. However, some may escape incorporation into virions and subsequently migrate to the cell surface. N-glycosylated in the host RER. Belongs to the influenza type C/coronaviruses hemagglutinin-esterase family. +Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the insertion of ferrous iron into coproporphyrin III to form Fe-coproporphyrin III. Fe-coproporphyrin III + 2 H(+) = coproporphyrin III + Fe(2+) Porphyrin-containing compound metabolism; protoheme biosynthesis. Belongs to the ferrochelatase family. +Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion. alpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + NH4(+) Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 5/5. Belongs to the glucosamine/galactosamine-6-phosphate isomerase family. NagB subfamily. +Belongs to the UPF0391 family. +Binds to chromosome ends in a sequence-dependent manner and is required for telomere capping. Interacts (via C-terminus) with Su(var)205 dimer (via hinge and chromoshadow domain) and with moi to form the terminin, telomere-capping, complex. Interacts with HP6, which is also part of the terminin complex (By similarity). Multiple telomeric associations (TAs) in the same metaphase spread often result in multicentric linear chromosomes that resemble little 'trains' of chromosomes, hence the name 'caravaggio', an Italian train. +Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria. 3-deoxy-alpha-D-manno-oct-2-ulosonate + CTP = CMP-3-deoxy-beta-D-manno-octulosonate + diphosphate Nucleotide-sugar biosynthesis; CMP-3-deoxy-D-manno-octulosonate biosynthesis; CMP-3-deoxy-D-manno-octulosonate from 3-deoxy-D-manno-octulosonate and CTP: step 1/1. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsB family. +Probable cell surface metalloreductase. May be involved in iron or copper homeostasis (By similarity). Belongs to the ferric reductase (FRE) family. AIM14 subfamily. +Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6-phosphate and D-lactate. Together with AnmK, is also required for the utilization of anhydro-N-acetylmuramic acid (anhMurNAc) either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling. H2O + N-acetyl-D-muramate 6-phosphate = (R)-lactate + N-acetyl-D-glucosamine 6-phosphate Amino-sugar metabolism; 1,6-anhydro-N-acetylmuramate degradation. Amino-sugar metabolism; N-acetylmuramate degradation. Cell wall biogenesis; peptidoglycan recycling. Homodimer. Induced by MurNAc 6-phosphate that releases the repressor MurR from the DNA. Repressed by MurR in the absence of MurNAc 6-phosphate. A lyase-type mechanism (elimination/hydration) is suggested for the cleavage of the lactyl ether bond of MurNAc 6-phosphate, with the formation of an alpha,beta-unsaturated aldehyde intermediate with (E)-stereochemistry, followed by the syn addition of water to give product. Belongs to the GCKR-like family. MurNAc-6-P etherase subfamily. +Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo-MPT) cofactor (Moco or molybdenum cofactor) to form Mo-molybdopterin guanine dinucleotide (Mo-MGD) cofactor. GTP + H(+) + Mo-molybdopterin = diphosphate + Mo-molybdopterin guanine dinucleotide The N-terminal domain determines nucleotide recognition and specific binding, while the C-terminal domain determines the specific binding to the target protein. Belongs to the MobA family. +Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL. ATP + H2O + L-glutamine + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide = 2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ADP + H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole from N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide: step 1/2. Part of the FGAM synthase complex composed of 1 PurL, 1 PurQ and 2 PurS subunits. +Belongs to the major facilitator superfamily. Organophosphate:Pi antiporter (OPA) (TC 2.A.1.4) family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Linear cationic alpha-helical peptide that acts as antimicrobial peptide by forming pore in membrane. Has antibacterial activities against both Gram-positive and Gram-negative strains. Has more potent activities against the yeast C.albicans. Shows moderate mast cell degranulation and leishmanicidal activities. Has a very low hemolytic activity. Assumes an amphipathic alpha-helical conformation in a lipid environment. Forms a membrane channel in the prey (By similarity). Expressed by the venom gland. Belongs to the MCD family. Mastoparan subfamily. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Belongs to the PLEKHD1 family. +DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. Belongs to the NAD-dependent DNA ligase family. LigA subfamily. +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily. +Specifically methylates the N7 position of a guanine in 16S rRNA. Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-amino acid + H(+) Monomer. Belongs to the PTH family. +May play a role in photosystem I and II biogenesis. Belongs to the PsbN family. Originally thought to be a component of PSII; based on experiments in Synechocystis, N.tabacum and barley, and its absence from PSII in T.elongatus and T.vulcanus, this is probably not true. +Transport of potassium into the cell. Belongs to the HAK/KUP transporter (TC 2.A.72) family. +Exhibits cGTPase activity; binds and hydrolyzes specifically GTP (PubMed:18801746). May participate in ribosome assembly and stability and thus regulates protein synthesis in chloroplasts. The GTPase activity requires MgCl(2)and the presence of either KCl or (NH(4))(2)SO(4). Involved in the post-transcriptional regulation of the methylerythritol phosphate (MEP) pathway. Involved in chlorophyll-a fluorescence regulation. May mediate the production or accumulation of nitric oxide (NO) which is a messenger molecule involved in hormonal signaling and defense responses in plant (PubMed:14526079, PubMed:16272429, PubMed:16690168 and PubMed:17351048). Acts as an antisenescence agent. Plays a crucial role in both extracellular calmodulin (ExtCaM)-triggered and salicylic acid (SA)-mediated H(2)O(2)-dependent stomatal closure. H(+) + 2 L-arginine + 3 NADPH + 4 O2 = 4 H2O + 2 L-citrulline + 3 NADP(+) + 2 nitric oxide Stimulated by calcium/calmodulin. Inhibited by L-NAME. Not activated by tetrahydrobiopterin (BH4), FAD, FMN, or heme. Was initially thought to be mitochondrial (PubMed:16272429). In fact seems to be chloroplastic (PubMed:18469163). Expressed in aleurone layer and the embryo. Constitutively expressed. Induced by abscisic acid (ABA) and lipopolysaccharides. Pale seedlings with a delayed development and greening of true leaves resulting in small plants with a characteristic virescent phenotype of pale young leaves but green mature leaves. Loss of NOS activity in mitochondria. Reduced extracellular calmodulin- (ExtCaM-) triggered and salicylic acid (SA)-mediated increase in NO levels and subsequent H(2)O(2)-dependent stomatal closure. Faster dark-induced senescence in leaves. Higher accumulation of hydrogen peroxide, superoxide anion, oxidized lipid, and oxidized protein. Increased hypersensitivity to salt stress and methyl viologen (MV) treatment. Enhanced accumulation of Na(+) but reduced accumulation of K(+) when exposed to NaCl leading to an enhanced sensitivity to salt. Post-transcriptional up-regulation of the methylerythritol phosphate (MEP) pathway. Enhanced resistance to fosmidomycin (FSM). Disturbed chlorophyll-a fluorescence induction in response to temperature variation, accompanied with altered polyamines accumulation. Belongs to the TRAFAC class YlqF/YawG GTPase family. NOA1 subfamily. Nitric oxide synthase (NOS) activity is dubious. +Component of the cap-binding complex (CBC), which binds co-transcriptionally to the 5' cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing, translation regulation, nonsense-mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBC complex is involved in mRNA export from the nucleus via its interaction with ALYREF/THOC4/ALY, leading to the recruitment of the mRNA export machinery to the 5' end of mRNA and to mRNA export in a 5' to 3' direction through the nuclear pore. The CBC complex is also involved in mediating U snRNA and intronless mRNAs export from the nucleus. The CBC complex is essential for a pioneer round of mRNA translation, before steady state translation when the CBC complex is replaced by cytoplasmic cap-binding protein eIF4E. The pioneer round of mRNA translation mediated by the CBC complex plays a central role in nonsense-mediated mRNA decay (NMD), NMD only taking place in mRNAs bound to the CBC complex, but not on eIF4E-bound mRNAs. The CBC complex enhances NMD in mRNAs containing at least one exon-junction complex (EJC) via its interaction with UPF1, promoting the interaction between UPF1 and UPF2. The CBC complex is also involved in 'failsafe' NMD, which is independent of the EJC complex, while it does not participate in Staufen-mediated mRNA decay (SMD). During cell proliferation, the CBC complex is also involved in microRNAs (miRNAs) biogenesis via its interaction with SRRT/ARS2, thereby being required for miRNA-mediated RNA interference. The CBC complex also acts as a negative regulator of PARN, thereby acting as an inhibitor of mRNA deadenylation. In the CBC complex, NCBP2/CBP20 recognizes and binds capped RNAs (m7GpppG-capped RNA) but requires NCBP1/CBP80 to stabilize the movement of its N-terminal loop and lock the CBC into a high affinity cap-binding state with the cap structure. The conventional cap-binding complex with NCBP2 binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus (By similarity). Component of the nuclear cap-binding complex (CBC), a heterodimer composed of NCBP1/CBP80 and NCBP2/CBP20 that interacts with m7GpppG-capped RNA. Found in a U snRNA export complex with PHAX/RNUXA, NCBP1/CBP80, NCBP2/CBP20, RAN, XPO1 and m7G-capped RNA. Interacts with PHAX/RNUXA, EIF4G1, HNRNPF, HNRNPH1 and ALYREF/THOC4/ALY. Interacts with SRRT/ARS2 and KPNA3 (By similarity). Belongs to the RRM NCBP2 family. +Part of the gene cluster that mediates the biosynthesis of sordarin and hypoxysordarin, glycoside antibiotics with a unique tetracyclic diterpene aglycone structure (PubMed:27072286). First, the geranylgeranyl diphosphate synthase sdnC constructs GGDP from farnesyl diphosphate and isopentenyl diphosphate (PubMed:27072286). The diterpene cyclase sdnA then catalyzes the cyclization of GGDP to afford cycloaraneosene (PubMed:27072286). Cycloaraneosene is then hydroxylated four times by the putative cytochrome P450 monooxygenases sdnB, sdnE, sdnF and sdnH to give a hydroxylated cycloaraneosene derivative such as cycloaraneosene-8,9,13,19-tetraol (PubMed:27072286). Although the order of the hydroxylations is unclear, at least C8, C9 and C13 of the cycloaraneosene skeleton are hydroxylated before the sordaricin formation (PubMed:27072286). Dehydration of the 13-hydroxy group of the hydroxylated cycloaraneosene derivative might be catalyzed by an unassigned hypothetical protein such as sdnG and sdnP to construct the cyclopentadiene moiety (PubMed:27072286). The FAD-dependent oxidoreductase sdnN is proposed to catalyze the oxidation at C9 of the hydroxylated cycloaraneosene derivative and also catalyze the Baeyer-Villiger oxidation to give the lactone intermediate (PubMed:27072286). The presumed lactone intermediate would be hydrolyzed to give an acrolein moiety and a carboxylate moiety (PubMed:27072286). Then, [4+2]cycloaddition would occur between the acrolein moiety and the cyclopentadiene moiety to give sordaricin (PubMed:27072286). SdnN might also be involved in the [4+2]cycloaddition after the hypothesized oxidation to accommodate the oxidized product and prompt the [4+2]cycloaddition (PubMed:27072286). GDP-6-deoxy-D-altrose may be biosynthesized from GDP-D-mannose by the putative GDP-mannose-4,6-dehydratase sdnI and the short-chain dehydrogenase sdnK (PubMed:27072286). The glycosyltransferase sdnJ catalyzes the attachment of 6-deoxy-D-altrose onto the 19-hydroxy group of sordaricin to give 4'-O-demethylsordarin (PubMed:27072286). The methyltransferase sdnD would complete the biosynthesis of sordarin (PubMed:27072286). Sordarin can be further modified into hypoxysordarin (PubMed:27072286). The unique acyl chain at the 3'-hydroxy group of hypoxysordarin would be constructed by an iterative type I PKS sdnO and the trans-acting polyketide methyltransferase sdnL. SdnL would be responsible for the introduction of an alpha-methyl group of the polyketide chain (PubMed:27072286). Alternatively, the beta-lactamase-like protein sdnR might be responsible for the cleavage and transfer of the polyketide chain from the PKS sdnO to sordarin (PubMed:27072286). Two putative cytochrome P450 monooxygenases, sdnQ and sdnT, might catalyze the epoxidations of the polyketide chain to complete the biosynthesis of hypoxysordarin (PubMed:27072286). Transcriptional regulators sdnM and sdnS are presumably encoded for the transcriptional regulation of the expression of the sdn gene cluster (PubMed:27072286). Antibiotic biosynthesis. +Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. Homohexamer. The homohexamer assembles into an open ring structure. Belongs to the Rho family. +Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions. As a reducing substrate of peroxiredoxin 1, thioredoxin 2 is preferred over thioredoxin 1 (By similarity). Belongs to the thioredoxin family. +Voltage-dependent rectifying anion channel that facilitates the translocation between chloroplast and cytoplasm of phosphorylated carbohydrates such as triosephosphate, 3-phosphoglycerate and inorganic phosphate (Pi) depending of ATP to triosephosphate ratio in the plastidial intermembrane space; in high triosephosphate/ATP conditions (e.g. photosynthesis), export of triosphosphate from chloroplast (outward rectifying channels), but in high ATP/triosephosphate conditions (e.g. dark phase), import of phosphosolutes (inward rectifying channels) (By similarity). Present in non-green root plastids. Belongs to the plastid outer envelope porin OEP21 (TC 1.B.29) family. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Aggregation substance allows donor and recipient strains to form tight aggregates which allow the non-motile bacteria to maintain physical contact over a period of time sufficient to permit conjugative transfer of the sex pheromone plasmid from donor to recipient strains. Belongs to the antigen I/II family. +glucuronate acceptor + UDP-alpha-D-glucuronate = acceptor beta-D-glucuronoside + H(+) + UDP Interacts with cmd-1 in the presence of Ca(2+). Belongs to the UDP-glycosyltransferase family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Homodimer and monomer. In vivo most of the ribosomes are in complex with monomeric TF. Uncomplexed TF, however, is in a monomer-dimer equilibrium with approximately two thirds of TF existing in a dimeric state. About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing. ATP + H2O = ADP + H(+) + phosphate Associates with polysomes. The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis. Belongs to the DEAD box helicase family. DDX5/DBP2 subfamily. +Involved in the final steps of cytoplasmic maturation of the 40S ribosomal subunit (By similarity). In vitro, has strong ATPase activity and only low protein kinase activity (PubMed:24948609). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Autophosphorylated. Belongs to the protein kinase superfamily. RIO-type Ser/Thr kinase family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA. Homotetramer, a dimer of dimers. One homotetramer interacts with 1 SecA dimer. Belongs to the SecB family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +PPIases accelerate the folding of proteins. Substrate specificity carried out with 'Suc-Ala-Xaa-Pro-Phe-4-nitroanilide', where Xaa is the amino acid tested, was found to be Phe > Leu >> Ile > Lys = Ala > Trp > His >> Gln (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the FKBP-type PPIase family. +Functions as a transcriptional regulator of the adaptive response to hypoxia. Binds to core DNA sequence 5'-[AG]CGTG-3' within the hypoxia response element (HRE) of target gene promoters. Efficient DNA binding requires dimerization with another bHLH protein. Interacts with Vhl. Cytoplasmic in normoxia, nuclear translocation in response to hypoxia. Ubiquitously expressed in the embryo. By hypoxia. The oxygen-dependent degradation (ODD) domain is required for cytoplasmic localization in normoxia. +acetyl-CoA + L-glutamate = CoA + H(+) + N-acetyl-L-glutamate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 1/4. Homohexamer. Belongs to the acetyltransferase family. ArgA subfamily. +Probable member of the two-component regulatory system SERP2405/SERP2406. May activate SERP2406 by phosphorylation (By similarity). ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. Autophosphorylated. +Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner. ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) Monomer. ValRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated threonine is translocated from the active site to the editing site. The C-terminal coiled-coil domain is crucial for aminoacylation activity. Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily. +Catalyzes the dephosphorylation of the nucleoside 5'-monophosphates deoxyadenosine monophosphate (dAMP), deoxycytidine monophosphate (dCMP), deoxyguanosine monophosphate (dGMP) and deoxythymidine monophosphate (dTMP). a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-deoxyribonucleoside + phosphate Binds 2 divalent metal cations (By similarity). Shows activity with Mn(2+), Co(2+) and Mg(2+) but shows no activity with Zn(2+) (By similarity). Homodimer. Belongs to the HDDC2 family. +Thiolesterase that catalyzes the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid. an S-(2-hydroxyacyl)glutathione + H2O = a 2-hydroxy carboxylate + glutathione + H(+) Binds 2 Zn(2+) ions per subunit. Secondary metabolite metabolism; methylglyoxal degradation; (R)-lactate from methylglyoxal: step 2/2. Monomer. Belongs to the metallo-beta-lactamase superfamily. Glyoxalase II family. +Involved in telomere length regulation. Belongs to the mitochondrion-specific ribosomal protein mS41 family. +Belongs to the calmodulin family. +ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl-tRNA(Gln) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP. Allosterically activated by GTP. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uracil: step 1/1. Belongs to the UPRTase family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Belongs to the nitrobindin family. Lacks the conserved His residue that binds heme iron in the nitrobindin family. +Functions redudantly with AGC1-5 as signaling component in the pollen tube. Required for polarized growth of pollen tubes. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by PDPK1/PDK1. Interacts with PDPK1/PDK1. Specifically expressed in pollen grains. Autophosphorylated and phosphorylated by PDPK1/PDK1. No visible phenotype under normal growth conditions, but pollen of the double mutants agc1.5 and agc1.7 is impaired in polarized growth of pollen tube. Belongs to the protein kinase superfamily. AGC Ser/Thr protein kinase family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Belongs to the UPF0386 family. +The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex (PubMed:22158466). Acts redundantly with RPT2A in the regulation of gametogenesis (PubMed:21784786, PubMed:22158466). With RPT2A plays a critical role in 26S proteasome assembly (PubMed:22158466). Component of the 19S regulatory particle (RP/PA700) base subcomplex of the 26S proteasome. The 26S proteasome is composed of a core protease (CP), known as the 20S proteasome, capped at one or both ends by the 19S regulatory particle (RP/PA700). The RP/PA700 complex is composed of at least 17 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and distal to the 20S proteolytic core, respectively. Preferentially expressed in the root and shoot apical meristem. No visible phenotype under normal growth conditions (PubMed:22158466). The double mutants rpt2a and rpt2b are blocked in both male and female gametogenesis (PubMed:22158466, PubMed:21784786). Belongs to the AAA ATPase family. +Catalyzes the reversible hydration of cis-homoaconitate to (2R,3S)-homoisocitrate, a step in the alpha-aminoadipate pathway for lysine biosynthesis. (2R,3S)-homoisocitrate = cis-homoaconitate + H2O Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-lysine biosynthesis via AAA pathway; L-alpha-aminoadipate from 2-oxoglutarate: step 3/5. Belongs to the aconitase/IPM isomerase family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Belongs to the class-II aminoacyl-tRNA synthetase family. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +Binds to the 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL15 family. +Involved in the biosynthesis of 6-O-methylglucose lipopolysaccarides (MGLPs). Catalyzes the transfer of the glucose moiety from a nuleotide sugar such as UDP-alpha-D-glucose to the position 2 of 3-phospho-D-glycerate (3-PGA) to form glucosyl-3-phosphoglycerate (GPG). It can use UDP-glucose, ADP-glucose and GDP-glucose as sugar donor substrates with decreasing affinity and with 3-PGA as an acceptor. D-glycerate can only be an acceptor with ADP-glucose and at a very low rate. (2R)-3-phosphoglycerate + an NDP-alpha-D-glucose = (2R)-2-O-(alpha-D-glucopyranosyl)-3-phospho-glycerate + a ribonucleoside 5'-diphosphate + H(+) (2R)-3-phosphoglycerate + UDP-alpha-D-glucose = (2R)-2-O-(alpha-D-glucopyranosyl)-3-phospho-glycerate + H(+) + UDP (2R)-3-phosphoglycerate + ADP-alpha-D-glucose = (2R)-2-O-(alpha-D-glucopyranosyl)-3-phospho-glycerate + ADP + H(+) (2R)-3-phosphoglycerate + GDP-D-glucose = (2R)-2-O-(alpha-D-glucopyranosyl)-3-phospho-glycerate + GDP + H(+) Requires divalent cations for activity. The maximum activity is observed between 20 and 75 mM of MgCl(2). Optimum pH is 8. Optimum temperature is 45 degrees Celsius. The activity is undetectable below 20 and above 55 degrees Celsius. Homotrimer. Belongs to the glycosyltransferase 2 family. +Belongs to the bacterial ribosomal protein bL28 family. +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6-phosphate and D-lactate. H2O + N-acetyl-D-muramate 6-phosphate = (R)-lactate + N-acetyl-D-glucosamine 6-phosphate Amino-sugar metabolism; N-acetylmuramate degradation. Homodimer. A lyase-type mechanism (elimination/hydration) is suggested for the cleavage of the lactyl ether bond of MurNAc 6-phosphate, with the formation of an alpha,beta-unsaturated aldehyde intermediate with (E)-stereochemistry, followed by the syn addition of water to give product. Belongs to the GCKR-like family. MurNAc-6-P etherase subfamily. +Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA). S-adenosyl-L-methionine + uridine(54) in tRNA = 5-methyluridine(54) in tRNA + H(+) + S-adenosyl-L-homocysteine S-adenosyl-L-methionine + uridine(341) in tmRNA = 5-methyluridine(341) in tmRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. TrmA subfamily. +Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP). isopentenyl diphosphate = dimethylallyl diphosphate Binds 1 Mg(2+) ion per subunit. The magnesium ion binds only when substrate is bound. Binds 1 Mn(2+) ion per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1. Homodimer. Belongs to the IPP isomerase type 1 family. +Attaches the virus to host cellular receptor, inducing endocytosis of the virion. In the endosome, the acidic pH induces conformational changes in the glycoprotein trimer, which trigger fusion between virus and cell membrane. There is convincing in vitro evidence that the muscular form of the nicotinic acetylcholine receptor (nAChR), the neuronal cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR) bind glycoprotein and thereby facilitate rabies virus entry into cells (By similarity). Homotrimer. Interacts with matrix protein (By similarity). Glycosylated and palmitoylated by host. Glycosylation is crucial for glycoprotein export at the cell surface (By similarity). Primary surface antigen capable of inducing and reacting with virus-neutralizing antibodies. Almost all human and veterinary vaccines are based on the functional aspects of the G protein. Arg-352 is highly involved in rabies virus pathogenicity. Its mutation dramatically attenuates the virus (By similarity). Belongs to the lyssavirus glycoprotein family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. Belongs to the YqgF nuclease family. +Positively regulates the transcription of the maltose regulon whose gene products are responsible for uptake and catabolism of malto-oligosaccharides. Specifically binds to the promoter region of its target genes, recognizing a short DNA motif called the MalT box. Activated by ATP and maltotriose, which are both required for DNA binding. Monomer in solution. Oligomerizes to an active state in the presence of the positive effectors ATP and maltotriose. Belongs to the MalT family. +Required for the formation of cilia. Plays an indirect role in sonic hedgehog signaling, cilia being required for all activity of the hedgehog pathway. Has pro-apoptotic function via its interaction with HIP1, leading to recruit caspase-8 (CASP8) and trigger apoptosis. Has the ability to bind DNA sequence motif 5'-AAAGACATG-3' present in the promoter of caspase genes such as CASP1, CASP8 and CASP10, suggesting that it may act as a transcription regulator; however the relevance of such function remains unclear. Component of the IFT complex B, at least composed of IFT20, IFT22, HSPB11/IFT25, IFT27, IFT46, IFT52, TRAF3IP1/IFT54, IFT57, IFT74, IFT80, IFT81, and IFT88 (PubMed:19253336, PubMed:23810713). Interacts with IFT20 (PubMed:12821668). Interacts with IFT88 (PubMed:11062270, PubMed:19253336, PubMed:23810713). Interacts with IFT80, IFT-81, IFT74, IFT172, TTC30B and KIF17 (PubMed:23810713). Interacts with BLOC1S2 (PubMed:18188704). Interacts with RYBP (PubMed:17874297). Interacts with HOMER1; the interaction possibly prevents the pro-apoptotic effects of IFT57 (PubMed:17107665). Interacts with HIP1 (By similarity). In normal conditions, it poorly interacts with HIP1, HIP1 being strongly associated with HTT (By similarity). However, in mutant HTT proteins with a long poly-Gln region, interaction between HTT and HIP1 is inhibited, promoting the interaction between HIP1 and IFT57, leading to apoptosis (By similarity). Interacts with BFAR (By similarity). Interacts with TTC25 (PubMed:25860617). Interacts with USH1G (By similarity). Concentrates within the inner segment of cilia. Present in retina and testis. In brain, it is present in the cortex, striatum, globus pallidus, hypothalamus and cerebellum. Present at high level in neurons and neuropil throughout the brain (at protein level). Expressed in hippocampal neurons, where it colocalizes with HOMER1 at postsynaptic regions. Ubiquitous through the epiblast. Expression is detected in mesoderm and most strongly in ectoderm, but not in endoderm. Highly expressed in the region of the node, a depression at the surface of the embryo proposed to have a role in left-right axis patterning. At 8.5 dpc, it is widely expressed except in the heart. Stronger expression is observed in the anterior midline, the forebrain and the somites. Strong expression remains in the forebrain at 9.5 dpc and 10.5 dpc and extends to all regions of the neural tube. At those stages, high expression is also found in the branchial arches and in the limb buds. Embryo section at 9.5 dpc also shows expression throughout the neural tube and the mesoderm, but not in the surface ectoderm. The strongest expression is observed on the luminal edge of the neural tube and in the ventral foregut. The pseudo DED region (pDED) mediates the interaction with HIP1. Mice show randomization of the embryo turning process and heart looping, which are hallmarks of defective left-right (LR) axis patterning. Motile monocilia normally present at the surface of the embryonic node, and proposed to initiate the break in LR symmetry, are absent. Furthermore, defects in central nervous system development are observed. The Sonic hedgehog (Shh) pathway is down-regulated in the neural tube, resulting in failure to establish ventral neural cell fate. Belongs to the IFT57 family. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate. adenosylcob(III)inamide-GDP + alpha-ribazole = adenosylcob(III)alamin + GMP + H(+) adenosylcob(III)inamide-GDP + alpha-ribazole 5'-phosphate = adenosylcob(III)alamin 5'-phosphate + GMP + H(+) Cofactor biosynthesis; adenosylcobalamin biosynthesis; adenosylcobalamin from cob(II)yrinate a,c-diamide: step 7/7. Belongs to the CobS family. +Functions as a master transcriptional regulator of the adaptive response to hypoxia. Under hypoxic conditions, activates the transcription of over 40 genes, including erythropoietin, glucose transporters, glycolytic enzymes, vascular endothelial growth factor, HILPDA, and other genes whose protein products increase oxygen delivery or facilitate metabolic adaptation to hypoxia. Plays an essential role in embryonic vascularization, tumor angiogenesis and pathophysiology of ischemic disease. Induced by reactive oxygen species (ROS). Efficient DNA binding requires heterodimerization of an alpha and a beta/ARNT subunit. Cytoplasmic in normoxia, nuclear translocation in response to hypoxia. Contains two independent C-terminal transactivation domains, NTAD and CTAD, which function synergistically. Their transcriptional activity is repressed by an intervening inhibitory domain (ID) (By similarity). In normoxia, is hydroxylated on Pro-402 and Pro-562. The hydroxylated prolines promote interaction with VHL, initiating rapid ubiquitination and subsequent proteasomal degradation. Under hypoxia, proline hydroxylation is impaired and ubiquitination is attenuated, resulting in stabilization (By similarity). In normoxia, is hydroxylated on Asn-788, thus abrogating interaction with CREBBP and EP300 and preventing transcriptional activation. The iron and 2-oxoglutarate dependent 3-hydroxylation of asparagine is (S) stereospecific within HIF CTAD domains. +Required for the normal migration of longitudinal and peripheral glial cells. During larval development, required for the migration of the subretinal glia into the eye disk. During embryonic development, also controls the migration of muscle cells toward their attachment sites. Required in the mesoderm for the correct morphogenesis of embryonic gonad and for tracheal branch fusion during tracheal development. Shg may be cooperating with foi to mediate a common mechanism for gonad and tracheal morphogenesis. Acts as a zinc transporter in both yeast and mammalian cells. Maternal foi has almost completely disappeared by embryonic stage 3 except in the pole cells. In stage 6 embryos, expression is enriched in the invaginating mesoderm. In stage 9 embryos, high levels in the anterior and posterior midgut primordia. In stage 14 embryos, broad expression with low levels in the epidermis. Expressed both maternally and zygotically. Glycosylated. Belongs to the ZIP transporter (TC 2.A.5) family. +May play a role in photosystem I and II biogenesis. Belongs to the PsbN family. Originally thought to be a component of PSII; based on experiments in Synechocystis, N.tabacum and barley, and its absence from PSII in T.elongatus and T.vulcanus, this is probably not true. +Absolutely required for transposition of IS1. Belongs to the transposase 27 family. +Homologous to nicotianamine synthase, but without enzymatic activity. Belongs to the nicotianamine synthase (NAS)-like family. Two forms of this protein have been cloned (NAS5-1 and NAS5-2) which seem to be identical with the exception of a 15 amino acids deletion. +May function as an inhibitor of Wnt/beta-catenin signaling by indirectly interacting with LRP6 and blocking Wnt3a-dependent LRP6 internalization. The C-terminus of LRR N-terminal cap (LRRNT) and LRR 1 are essential for the inhibition of the Wnt signaling pathway. Highly glycosylated. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Homodimer. Belongs to the GrpE family. +Catalyzes the hydrolysis of the adenine ring of phosphoribosyl-AMP. 1-(5-phospho-beta-D-ribosyl)-5'-AMP + H2O = 1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide Binds 1 Mg(2+) ion per subunit. Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 3/9. Homodimer. Belongs to the PRA-CH family. +A protein kinase that phosphorylates Ser and Thr residues. Probably acts to suppress the effects of stress linked to accumulation of reactive oxygen species. Probably involved in the extracytoplasmic stress response. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Monomer. Belongs to the SrkA/RdoA protein kinase family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) Binds 1 [4Fe-4S] cluster. NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 20 kDa subunit family. +Component of the MRN complex, which plays a central role in double-strand break (DSB) repair, DNA recombination, maintenance of telomere integrity and meiosis. The complex possesses single-strand endonuclease activity and double-strand-specific 3'-5' exonuclease activity, which are provided by MRE11. RAD50 may be required to bind DNA ends and hold them in close proximity. This could facilitate searches for short or long regions of sequence homology in the recombining DNA templates, and may also stimulate the activity of DNA ligases and/or restrict the nuclease activity of MRE11 to prevent nucleolytic degradation past a given point. The complex may also be required for DNA damage signaling via activation of the ATM kinase. In telomeres the MRN complex may modulate t-loop formation. Interaction with SAMHD1 stimulates the double-strand-specific 3'-5' exonuclease activity. Component of the MRN complex composed of two heterodimers RAD50/MRE11 associated with a single NBN. As part of the MRN complex, interacts with MCM9; the interaction recruits the complex to DNA repair sites. Component of the BASC complex, at least composed of BRCA1, MSH2, MSH6, MLH1, ATM, BLM, RAD50, MRE11 and NBN. Found in a complex with TERF2. Interacts with DCLRE1C/Artemis and DCLRE1B/Apollo. Interacts with ATF2. Interacts with EXD2. Interacts with MRNIP. Interacts with SAMHD1; leading to stimulate 3'-5' exonuclease activity. Interacts (when ubiquitinated) with UBQLN4 (via its UBA domain) (By similarity). Interacts with CYREN (via XLF motif) (By similarity). Localizes to discrete nuclear foci after treatment with genotoxic agents. Ubiquitinated following DNA damage. Ubiquitination triggers interaction with UBQLN4, leading to MRE11 removal from chromatin and degradation by the proteasome. Belongs to the MRE11/RAD32 family. +Transcription factor that promotes photomorphogenesis in the light by participating in the transmission of phytochrome A (phyA) signals to downstream responses (PubMed:11581165, PubMed:19482971). Probably acts by activating expression of light-induced genes. In darkness, its degradation prevents the activation of light-induced genes (PubMed:11581165). Binds to FHY1 and FHL (PubMed:19482971). Interacts with COP1. Expressed at very low level. Expressed in cauline leaves. By hormones or elicitors treatment. By exposure to abiotic stress. Ubiquitinated by COP1. Ubiquitination takes place in darkness and leads to its subsequent degradation, thereby preventing to activate photomorphogenesis signals. Ubiquitination is stimulated by SPA1. Partially blind to far-red (FR). Impaired inhibition of hypocotyl elongation and cotyledons expansion under continuous FR light conditions. +This protein specifically catalyzes the removal of signal peptides from prolipoproteins. Release of signal peptides from bacterial membrane prolipoproteins. Hydrolyzes -Xaa-Yaa-Zaa-|-(S,diacylglyceryl)Cys-, in which Xaa is hydrophobic (preferably Leu), and Yaa (Ala or Ser) and Zaa (Gly or Ala) have small, neutral side chains. Protein modification; lipoprotein biosynthesis (signal peptide cleavage). Belongs to the peptidase A8 family. +MEKK1, MKK1/MKK2 and MPK4/MPK6 function in a signaling pathway that modulates the expression of genes responding to biotic and abiotic stresses and also plays an important role in pathogen defense by negatively regulating innate immunity. Activates by phosphorylation the downstream MPK4. Acts redundantly with MKK2. MKK1-MPK6 module mediates abscisic acid (ABA)-dependent CAT1 expression with H(2)O(2) production and response to drought and salt stress. MKK1-MPK6 module is also involved in sugar signaling during the process of seed germination. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein] Activated through serine and threonine phosphorylation in response to wounding, cold, drought, salt stresses, abscisic acid (ABA), hydrogen peroxide, bacterial flagellin and laminarin beta-glucan. Interacts with MEKK1 and MPK4. May form a ternary complex composed of MEKK1 and MKK1/MKK2 and MPK4. Interacts with P.syringae type III effector HopF2. Interacts with MPK11. Expressed in roots, stem, flowers and siliques. By wounding. Phosphorylation at Thr-218 and Ser-224 by MAP kinase kinase kinases positively regulates kinase activity. No obvious developmental defects under normal growth conditions. Compromised in resistance to both virulent and avirulent Pseudomonas syringae strains. Reduced sensitivity to abscisic acid (ABA) during germination and reduced drought tolerance of seedlings. Simultaneous knockdown of MKK1 and MKK2 results in dwarf and small plants exhibiting a seedling-lethality phenotype. May be due to an intron retention. Belongs to the protein kinase superfamily. STE Ser/Thr protein kinase family. MAP kinase kinase subfamily. +Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates and thus, functions to process newly synthesized Ubiquitin, to recycle ubiquitin molecules or to edit polyubiquitin chains and prevents proteasomal degradation of substrates. Hydrolyzes both 'Lys-48'- and 'Lys-63'-linked tetraubiquitin chains (By similarity). The muscle-specific isoform (USP25m) may have a role in the regulation of muscular differentiation and function. Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Homodimer or oligomer (By similarity). Interacts with ACTA1 (via its C-terminus); the interaction occurs for all isoforms but is strongest for isoform USP25m in muscle differentiating cells. Interacts (isoform USP25m only) with MYBPC1; the interaction prevents proteasomal degradation of MYBPC1. Interacts (isoform USP25m only) with FLNC (via filament repeats 17-18, 20-21 and 24). Interacts with GAPDH. Interacts with SUMO3; the interaction sumoylates efficiently USP25. Interacts with SUMO2; the interaction sumoylates efficiently USP25. Interacts with SUMO1; the interaction only weakly sumoylates USP25. Interacts with SYK; phosphorylates USP25 and regulates USP25 intracellular levels (By similarity). The longer muscle-specific isoform (USP25m) Some transient punctuate nuclear location in myotubes during myocyte development. A longer muscle-specific isoform, USP25m, also exists. Highly expressed in testis especially in primary and secondary spematocytes and in immature spermatids. Also found in brain, skeletal muscle, liver and heart. At 13.5 dpc and 16.5 dpc, expression in the brain correlates with the proliferate ventricular zone and post-mitotic neurons of the intermediate zone, particularly in the forebrain. More marked expression at 16.5 dpc in the telencephalic septum and in the pallium. In myocytes, expressed throughout differentiation of myotubes. Induced by type I interferons (IFNA and IFNB1) produced in response to lipopolysaccharide (LPS) and viral infection (HIV-1 and SeV viruses) (at protein level). Acetylated. Sumoylation impairs binding to and hydrolysis of ubiquitin chains. Sumoylated preferentially with SUMO2 or SUMO3. Desumoylated by SENP1. Regulated by ubiquitination on the same residue (By similarity). Preferentially monoubiquitinated but can also be polyubiquitinated. Autodeubiquitinated. Ubiquitination activates the enzymatic activity either by preventing sumoylation or by allowing novel interactions (By similarity). Phosphorylation in the C-terminal by SYK regulates USP25 cellular levels. Belongs to the peptidase C19 family. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Transcriptional repressor; binds to the DNA sequence 5'-CCGGAAGT-3'. Plays a role in hematopoiesis and malignant transformation. Can form homodimers or heterodimers with TEL2 or FLI1. Interacts with L3MBTL1 and HDAC9 (By similarity). Belongs to the ETS family. +One of the components of the core complex of photosystem II (PSII), required for its stability and/or assembly. PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, numerous small proteins, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbH family. +Transports viral genome to neighboring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier. Increases plasmodesma size exclusion limit. Acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs (By similarity). Homodimer and homooligomer. Interacts with capsid protein. Interacts with host AGO1; this interaction targets the host protein for degradation, thereby suppressing the antiviral RNA silencing (By similarity). TGBp1, TGBp2 and TGBp3 seem to act together for cell-to-cell propagation. TGBp1 is the main movement protein that physically cross the plasmodesma with the viral genome. TGBp2 and TGBp3 would facilitate TGBp1 function. Belongs to the Tymovirales TGBp1 protein family. +With LigD forms a non-homologous end joining (NHEJ) DNA repair enzyme, which repairs dsDNA breaks with reduced fidelity. Binds linear dsDNA with 5'- and 3'- overhangs but not closed circular dsDNA nor ssDNA. Recruits and stimulates the ligase activity of LigD. Homodimer. Interacts with LigD. Belongs to the prokaryotic Ku family. Extended N-terminus. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. Also binds riboflavin with an unexpected high affinity. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Competitively inhibited by riboflavin (Ki of 17 uM). Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Homopentamer. Belongs to the DMRL synthase family. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + UDP-N-acetyl-alpha-D-glucosamine = beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +Catalyzes the final step of fatty acid oxidation in which acetyl-CoA is released and the CoA ester of a fatty acid two carbons shorter is formed. acetyl-CoA + an acyl-CoA = a 3-oxoacyl-CoA + CoA Lipid metabolism; fatty acid beta-oxidation. Heterotetramer of two alpha chains (FadB) and two beta chains (FadA). Belongs to the thiolase-like superfamily. Thiolase family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 1 subfamily. +This protein is produced by a bicistronic gene which also produces the major prion protein/PRNP from an overlapping reading frame. The alternative prion protein and PRNP (AC P23907) have no apparent direct functional relation since a mutation that removes the start codon of the AltPrP has no apparent effect on the biology of PRNP (By similarity). In mouse and hamster, the alternative initiation AUG codon is absent and is replaced by a GUG codon. +Positive regulator of multiple nitrogen catabolic genes. Present with 1180 molecules/cell in log phase SD medium. +Prevents the establishment of the cellular antiviral state by inhibiting TRIM25-mediated DDX58 ubiquitination, which normally triggers the antiviral transduction signal that leads to the activation of type I IFN genes by transcription factors IRF3 and IRF7. Prevents human EIF2AK2/PKR activation, either by binding double-strand RNA, or by interacting directly with EIF2AK2/PKR. This function may be important at the very beginning of the infection, when NS1 is mainly present in the cytoplasm. Also binds poly(A) and U6 snRNA. Inhibits post-transcriptional processing of cellular pre-mRNA, by binding and inhibiting two cellular proteins that are required for the 3'-end processing of cellular pre-mRNAs: the 30 kDa cleavage and polyadenylation specificity factor/CPSF4 and the poly(A)-binding protein 2/PABPN1. In turn, unprocessed 3' end pre-mRNAs accumulate in the host nucleus and are no longer exported to the cytoplasm. Cellular protein synthesis is thereby shut off very early after virus infection. Viral protein synthesis is not affected by the inhibition of the cellular 3' end processing machinery because the poly(A) tails of viral mRNAs are produced by the viral polymerase through a stuttering mechanism. Homodimer. Interacts with host TRIM25 (via coiled coil); this interaction specifically inhibits TRIM25 multimerization and TRIM25-mediated DDX58 CARD ubiquitination. Interacts with human EIF2AK2/PKR, CPSF4, IVNS1ABP and PABPN1. In uninfected, transfected cells, NS1 is localized in the nucleus. Only in virus infected cells, the nuclear export signal is unveiled, presumably by a viral protein, and a fraction of NS1 is exported in the cytoplasm. The dsRNA-binding region is required for suppression of RNA silencing. Upon interferon induction, ISGylated via host HERC5; this results in the impairment of NS1 interaction with RNA targets due to its inability to form homodimers and to interact with host EIF2AK2/PKR. Belongs to the influenza A viruses NS1 family. +Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Complex I is composed of 45 different subunits. Belongs to the complex I NDUFC1 subunit family. +Required during biogenesis of c-type cytochromes (cytochrome c6 and cytochrome f) at the step of heme attachment. May interact with ccs1. Belongs to the CcmF/CycK/Ccl1/NrfE/CcsA family. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Product of a dubious gene prediction. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Involved in membrane organization and might act as a sensor of sphingolipids that regulates plasma membrane function. Involved in a novel pathway of export of proteins that lack a cleavable signal sequence. Belongs to the NCE102 family. +Bifunctional enzyme which can phosphorylate or dephosphorylate isocitrate dehydrogenase (IDH) on a specific serine residue. This is a regulatory mechanism which enables bacteria to bypass the Krebs cycle via the glyoxylate shunt in response to the source of carbon. When bacteria are grown on glucose, IDH is fully active and unphosphorylated, but when grown on acetate or ethanol, the activity of IDH declines drastically concomitant with its phosphorylation. ATP + L-seryl-[isocitrate dehydrogenase] = ADP + H(+) + O-phospho-L-seryl-[isocitrate dehydrogenase] Belongs to the AceK family. +May interact with a ClpP-like protease involved in degradation of denatured proteins in the chloroplast. Belongs to the ClpA/ClpB family. ClpC subfamily. +Belongs to the bacterial ribosomal protein bL34 family. +Belongs to the UPF0761 family. +Belongs to the bacterial ribosomal protein bL28 family. +Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway. ATP + D-ribose = ADP + D-ribose 5-phosphate + H(+) Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate. Activated by a monovalent cation that binds near, but not in, the active site. The most likely occupant of the site in vivo is potassium. Ion binding induces a conformational change that may alter substrate affinity. Carbohydrate metabolism; D-ribose degradation; D-ribose 5-phosphate from beta-D-ribopyranose: step 2/2. Homodimer. Belongs to the carbohydrate kinase PfkB family. Ribokinase subfamily. +Involved in the assembly of lipopolysaccharide (LPS). Required for the translocation of LPS from the inner membrane to the outer membrane. Facilitates the transfer of LPS from the inner membrane to the periplasmic protein LptA. Could be a docking site for LptA. Component of the lipopolysaccharide transport and assembly complex. Interacts with LptA and the LptBFG transporter complex. Belongs to the LptC family. +Serine protease inhibitor. Homodimer. Belongs to the serpin family. +Regulatory subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Forms a heterodimer with SLX1. Phosphorylated in response to DNA damage. Belongs to the SLX4 family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase delta chain family. +Is involved in NO detoxification in an aerobic process, termed nitric oxide dioxygenase (NOD) reaction that utilizes O(2) and NAD(P)H to convert NO to nitrate, which protects the bacterium from various noxious nitrogen compounds. Therefore, plays a central role in the inducible response to nitrosative stress. NADPH + 2 nitric oxide + 2 O2 = H(+) + NADP(+) + 2 nitrate NADH + 2 nitric oxide + 2 O2 = H(+) + NAD(+) + 2 nitrate Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit. Binds 1 FAD per subunit. Consists of two distinct domains; an N-terminal heme-containing oxygen-binding domain and a C-terminal reductase domain with binding sites for FAD and NAD(P)H. Belongs to the globin family. Two-domain flavohemoproteins subfamily. In the C-terminal section; belongs to the flavoprotein pyridine nucleotide cytochrome reductase family. +Plays a role in viral genome replication by driving entry of quiescent cells into the cell cycle. Stimulation of progression from G1 to S phase allows the virus to efficiently use the cellular DNA replicating machinery to achieve viral genome replication. E1A protein has both transforming and trans-activating activities. Induces the disassembly of the E2F1 transcription factor from RB1 by direct competition for the same binding site on RB1, with subsequent transcriptional activation of E2F1-regulated S-phase genes and of the E2 region of the adenoviral genome. Release of E2F1 leads to the ARF-mediated inhibition of MDM2 and causes TP53/p53 to accumulate because it is not targeted for degradation by MDM2-mediated ubiquitination anymore. This increase in TP53, in turn, would arrest the cell proliferation and direct its death but this effect is counteracted by the viral protein E1B-55K. Inactivation of the ability of RB1 to arrest the cell cycle is critical for cellular transformation, uncontrolled cellular growth and proliferation induced by viral infection. Interaction with RBX1 and CUL1 inhibits ubiquitination of the proteins targeted by SCF(FBXW7) ubiquitin ligase complex, and may be linked to unregulated host cell proliferation. The tumorigenesis-restraining activity of E1A may be related to the disruption of the host CtBP-CtIP complex through the CtBP binding motif. Interaction with host TMEM173/STING impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta). Promotes the sumoylation of host ZBED1/hDREF with SUMO1 (By similarity). Interacts with host UBE2I; this interaction interferes with polySUMOylation. Interacts with host RB1; this interaction induces the aberrant dissociation of RB1-E2F1 complex thereby disrupting the activity of RB1 and activating E2F1-regulated genes. Interacts with host ATF7; the interaction enhances ATF7-mediated viral transactivation activity which requires the zinc binding domains of both proteins. Isoform early E1A 32 kDa protein and isoform early E1A 26 kDa protein interact (via N-terminus) with CUL1 and E3 ubiquitin ligase RBX1; these interactions inhibit RBX1-CUL1-dependent elongation reaction of ubiquitin chains and attenuate ubiquitination of SCF(FBXW7) target proteins. Interacts (via PXLXP motif) with host ZMYND11/BS69 (via MYND-type zinc finger); this interaction inhibits E1A mediated transactivation. Interacts with host EP300; this interaction stimulates the acetylation of RB1 by recruiting EP300 and RB1 into a multimeric-protein complex. Interacts with host CTBP1 and CTBP2; this interaction seems to potentiate viral replication. Interacts with host DCAF7. Interacts with host DYRK1A. Interacts with host KPNA4; this interaction allows E1A import into the host nucleus. Interacts with host EP400; this interaction stabilizes MYC. Interacts with host TBP protein; this interaction probably disrupts the TBP-TATA complex. Interacts (via LXCXE motif) with host TMEM173/STING; this interaction impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta). Interacts (via C-terminus) with host ZBED1/hDREF (via C-terminus); the interaction is direct (PubMed:25210186). Isoforms are derived from the E1 region of the genome. Belongs to the adenoviridae E1A protein family. +The PR65 subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit. PP2A exists in several trimeric forms, all of which consist of a core composed of a catalytic subunit associated with a 65 kDa regulatory subunit (PR65) (subunit A). The core complex associates with a third, variable subunit (subunit B), which confers distinct properties to the holoenzyme. Interacts with IPO9 (By similarity). Interacts with SGO1 (By similarity). Interacts with RAF1 (By similarity). Each HEAT repeat appears to consist of two alpha helices joined by a hydrophilic region, the intrarepeat loop. The repeat units may be arranged laterally to form a rod-like structure. Belongs to the phosphatase 2A regulatory subunit A family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 2 subfamily. +Catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). The sulfur atoms are provided by the cysteine/cysteine desulfurase (IscS) system. AH2 + ATP + cytidine(32) in tRNA + S-sulfanyl-L-cysteinyl-[cysteine desulfurase] = 2-thiocytidine(32) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[cysteine desulfurase] Binds 1 [4Fe-4S] cluster per subunit. The cluster is chelated by three Cys residues, the fourth Fe has a free coordination site that may bind a sulfur atom transferred from the persulfide of IscS. tRNA modification. Homodimer. The thiolation reaction likely consists of two steps: a first activation step by ATP to form an adenylated intermediate of the target base of tRNA, and a second nucleophilic substitution step of the sulfur (S) atom supplied by the hydrosulfide attached to the Fe-S cluster. Belongs to the TtcA family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +Participates in replication and packaging of the viral genome. Plays a crucial role, together with NSP5, in the formation of virus factories (viroplasms) which are large inclusions in the host cytoplasm where replication intermediates are assembled and viral RNA replication takes place. Displays ssRNA binding, NTPase, RNA triphosphatase (RTPase) and ATP-independent helix-unwinding activities. The unwinding activity may prepare and organize plus-strand RNAs for packaging and replication by removing interfering secondary structures. The RTPase activity plays a role in the removal of the gamma-phosphate from the rotavirus RNA minus strands of dsRNA genome segments. Homooctamer. Interacts with VP1; this interaction is weak. Interacts with NSP5; this interaction leads to up-regulation of NSP5 phosphorylation and formation of viral factories. Found in spherical cytoplasmic structures, called viral factories, that appear early after infection and are the site of viral replication and packaging. Belongs to the rotavirus NSP2 family. +Detected at high levels in the urine of pregnant females (at protein level) and at far lower levels in the urine of nonpregnant females. The order of the peptides shown is unknown. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. The N-terminal domain is an archaea-specific tRNA-editing domain that hydrolyzes incorrectly charged L-seryl-tRNA(Thr). Catalysis of tRNA editing is performed by the charged tRNA itself. Belongs to the class-II aminoacyl-tRNA synthetase family. +Calcium selective cation channel that mediates Ca(2+) uptake in various tissues, including the intestine (PubMed:10428857, PubMed:11287959, PubMed:27296226, PubMed:28878326). Important for normal Ca(2+) ion homeostasis in the body, including bone and skin (By similarity). The channel is activated by low internal calcium level, probably including intracellular calcium store depletion, and the current exhibits an inward rectification (PubMed:10428857, PubMed:11287959, PubMed:27296226). Inactivation includes both a rapid Ca(2+)-dependent and a slower Ca(2+)-calmodulin-dependent mechanism; the latter may be regulated by phosphorylation. In vitro, is slowly inhibited by Mg(2+) in a voltage-independent manner. Heteromeric assembly with TRPV5 seems to modify channel properties. TRPV5-TRPV6 heteromultimeric concatemers exhibit voltage-dependent gating (By similarity). Homotetramer (PubMed:27296226, PubMed:29258289, PubMed:28878326). Probably forms also heterotetramers with TRPV5. Interacts with TRPV5. Interacts with S100A10 and probably with the ANAX2-S100A10 heterotetramer. The interaction with S100A10 is required for the trafficking to the plasma membrane. Interacts with calmodulin. Interacts with BSPRY. Interacts with TCAF1 and TCAF2 (By similarity). Expressed in duodenum, proximal jejunum, cecum, and colon. Glycosylated. Phosphorylation at Tyr-201 and Tyr-202 by SRC leads to an increased calcium influx through the channel. Probably dephosphorylated at these sites by PTPN1. Belongs to the transient receptor (TC 1.A.4) family. TrpV subfamily. TRPV6 sub-subfamily. It is uncertain whether Met-1 or Met-41 is the initiator. In human and mouse, initiation starts at a conserved non-canonical ACG threonine codon decoded as Met-1 upstream of the canonical initiation at Met-41. Unusual initiator. The initiator methionine is coded by a non-canonical ACG threonine codon. +Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide. 6-carboxyhexanoyl-[ACP] + H(+) + L-alanine = (8S)-8-amino-7-oxononanoate + CO2 + holo-[ACP] Cofactor biosynthesis; biotin biosynthesis. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily. +Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 19 (CSTX) family. 04 (U1-Lctx) subfamily. +Shares some antigenic similarities to the smooth muscle protein telokin, but is not similar at the sequence level. +Mediates visceral muscle contractile activity (myotropic activity). Belongs to the periviscerokinin family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL2 family. +Binds 16S rRNA, required for the assembly of 30S particles. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS14 family. +Mediates both low-affinity uptake and efflux of sugar across the plasma membrane. Involved in phloem loading by mediating export from parenchyma cells feeding H(+)-coupled import into the sieve element/companion cell complex, thus contributing to the sucrose migration from sites of synthesis in the mesophyll to the phloem (PubMed:22157085, PubMed:25988582). Contributes to seed filling by triggering sucrose efflux involved in the transfer of sugars from seed coat to embryos (PubMed:25988582). Forms homooligomers and heterooligomers with SWEET5, SWEET11 and SWEET17. Present in the plasma membrane of the phloem. Expressed in leaves, especially in phloem (PubMed:22157085). Expressed in developing seeds (PubMed:25794936). In developing seeds, accumulates specifically at different stages. At globular stage, present in micropylar end of seed coat, in the endosperm and in the embryo suspensor. At the heart stage, confined to the micropylar end of seed coat. From the linear mature cotyledon stage until mature seed, present in the micropylar end of seed coat as well as in the endosperm. Induced by the powdery mildew fungus G.cichoracearum and the pathogenic bacteria P.syringae pv. tomato. Under high-light conditions, plants lacking both SWEET11 and SWEET12 are defective in phloem loading and display slower growth, mild chlorosis, and high levels of starch and sugar accumulation in leaves (PubMed:22157085). In plants lacking SWEET11, SWEET12 and SWEET15, severe seed defects, which include retarded embryo development, reduced seed weight, and reduced starch and lipid content, causing a wrinkled seed phenotype. Altered sucrose efflux involved in the transfer of sugars from seed coat to embryos thus leading to starch accumulation in the seed coat but not in the embryo (PubMed:25794936). Belongs to the SWEET sugar transporter family. +Acts as a chaperone. Belongs to the heat shock protein 70 family. +May help in the organization of the PsaL subunit. Belongs to the PsaI family. +In strains Mu3, Mu50, N315 and Newman, ebh is divided into two ORFs, ebhA and ebhB, which correspond to the C-terminal and N-terminal parts of the full gene, respectively. +Plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis. Belongs to the YciB family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source. ATP + deamido-NAD(+) + NH4(+) = AMP + diphosphate + H(+) + NAD(+) Cofactor biosynthesis; NAD(+) biosynthesis; NAD(+) from deamido-NAD(+) (ammonia route): step 1/1. Homodimer. Belongs to the NAD synthetase family. +Probable transcriptional corepressor which modulates activity of the nuclear hormone receptor daf-12 to regulate the dauer diapause. Isoform d interacts with daf-12. Isoform d is widely expressed: detected in the hypodermis, seam cells, intestine, somatic gonad, neurons, vulval precursors, body wall muscle and pharynx. Isoforms b and d are widely expressed from embryogenesis to adulthood. Isoform d is highly expressed in late L1 and L2 larval stages in XXX neuroendocrine cells. Isoform b is expressed more highly in the embryo and the L1 larval stage. Knockout of isoform d results in defective dauer formation. Eighteen percent of temperature sensitive mutants are embryonic lethal. The surviving animals are small (Sma), clear (Clr), uncoordinated, constipated and sterile. They display variable morphological defects in the main body and pharynx. +Belongs to the MGR3 family. +Belongs to the UPF0374 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +This protein specifically catalyzes the removal of signal peptides from prolipoproteins. Release of signal peptides from bacterial membrane prolipoproteins. Hydrolyzes -Xaa-Yaa-Zaa-|-(S,diacylglyceryl)Cys-, in which Xaa is hydrophobic (preferably Leu), and Yaa (Ala or Ser) and Zaa (Gly or Ala) have small, neutral side chains. Protein modification; lipoprotein biosynthesis (signal peptide cleavage). Belongs to the peptidase A8 family. +High affinity, high specificity proton-dependent sulfate transporter, which mediates sulfate uptake. Provides the sulfur source for the cysteine synthesis pathway. Belongs to the CysZ family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +Contributes to histone modification. May position the N-terminus of histone H3 for efficient trimethylation at 'Lys-4'. As part of the MLL1/MLL complex it is involved in methylation and dimethylation at 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues. May regulate osteoblasts differentiation (By similarity). Interacts with HCFC1. Probable component of complexes involved in histone modification such as the MLL1/MLL complex and the NSL complex. Belongs to the WD repeat WDR5/wds family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +Belongs to the AAE transporter (TC 2.A.81) family. YidE subfamily. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +Fatty acid desaturase involved in the production of chloroplast-specific phosphatidylglycerol molecular species containing 16:1(3E). Catalyzes the formation of a trans double bond introduced close to the carboxyl group of palmitic acid, which is specifically esterified to the sn-2 glyceryl carbon of phosphatidylglycerol. a 1-acyl-2-hexadecanoyl-glycerolipid + 2 H(+) + O2 + 2 reduced [2Fe-2S]-[ferredoxin] = a 1-acyl-2-[(3E)-hexadec-3-enoyl]-glycerolipid + 2 H2O + 2 oxidized [2Fe-2S]-[ferredoxin] Lipid metabolism; fatty acid metabolism. The histidine box domains are involved in binding the catalytic metal ions. No visible phenotype, but missing a chloroplast-specific phosphatidylglycerol molecular species that carries a delta 3-trans-hexadecenoic acid in the sn-2 position of its core glyceryl moiety. Belongs to the fatty acid desaturase CarF family. Truncated N-terminus. +Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uS13 family. +Possible role in transport between endoplasmic reticulum and Golgi. Belongs to the ERGIC family. +Proteasome-associated deubiquitinase which releases ubiquitin from the proteasome targeted ubiquitinated proteins (PubMed:16190881). Ensures the regeneration of ubiquitin at the proteasome. Is a reversibly associated subunit of the proteasome and a large fraction of proteasome-free protein exists within the cell. Required for the degradation of the chemokine receptor CXCR4 which is critical for CXCL12-induced cell chemotaxis. Serves also as a physiological inhibitor of endoplasmic reticulum-associated degradation (ERAD) under the non-stressed condition by inhibiting the degradation of unfolded endoplasmic reticulum proteins via interaction with ERN1 (By similarity). Indispensable for synaptic development and function at neuromuscular junctions (NMJs) (PubMed:19726649). Plays a role in the innate immune defense against viruses by stabilizing the viral DNA sensor CGAS and thus inhibiting its autophagic degradation (By similarity). Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Homodimer (Potential). Associates with the 26S proteasome. Interacts with FANCC, CXCR4 and ERN1. Interacts with TRIM14; this interaction recruits USP14 to cleave ubiquitin chains of CGAS (By similarity). Belongs to the peptidase C19 family. USP14/UBP6 subfamily. +Deglycase that catalyzes the deglycation of the Maillard adducts formed between amino groups of proteins and reactive carbonyl groups of glyoxals. Thus, functions as a protein deglycase that repairs methylglyoxal- and glyoxal-glycated proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteine, arginine and lysine residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of advanced glycation endproducts (AGE) that cause irreversible damage. Also displays proteolytic activity. H2O + N(omega)-(1-hydroxy-2-oxopropyl)-L-arginyl-[protein] = H(+) + L-arginyl-[protein] + lactate H2O + N(6)-(1-hydroxy-2-oxopropyl)-L-lysyl-[protein] = H(+) + L-lysyl-[protein] + lactate H2O + S-(1-hydroxy-2-oxopropyl)-L-cysteinyl-[protein] = H(+) + L-cysteinyl-[protein] + lactate H2O + N(omega)-(1-hydroxy-2-oxoethyl)-L-arginyl-[protein] = glycolate + H(+) + L-arginyl-[protein] H2O + N(6)-(1-hydroxy-2-oxoethyl)-L-lysyl-[protein] = glycolate + H(+) + L-lysyl-[protein] H2O + S-(1-hydroxy-2-oxoethyl)-L-cysteinyl-[protein] = glycolate + H(+) + L-cysteinyl-[protein] Homohexamer formed by a dimer of trimers that assemble into a hollow ring structure. Belongs to the peptidase C56 family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds a dinuclear copper A center per subunit. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Found in a complex with TMEM177, COA6, COX18, COX20, SCO1 and SCO2. Interacts with TMEM177 in a COX20-dependent manner. Interacts with COX20. Interacts with COX16 (By similarity). Belongs to the cytochrome c oxidase subunit 2 family. +Belongs to the UPF0741 family. +Cyclic octapeptide that belongs to the MSDIN-like toxin family responsible for a large number of food poisoning cases and deaths (PubMed:8441706, PubMed:28866879). Cycloaminide B is non-toxic to mammals but shows immunosuppressive activity, probably through the inhibition of the action of interleukin-1 and interleukin-2 (PubMed:8441706). Processed by the macrocyclase-peptidase enzyme POPB to yield a cyclic octapeptide (PubMed:28866879). POPB first removes 10 residues from the N-terminus (By similarity). Conformational trapping of the remaining peptide forces the enzyme to release this intermediate rather than proceed to macrocyclization (By similarity). The enzyme rebinds the remaining peptide in a different conformation and catalyzes macrocyclization of the N-terminal 8 residues (PubMed:28866879). Belongs to the MSDIN fungal toxin family. +May be involved in the metabolism of very long-chain fatty acid-containing phospholipids (VLCFA-PL). Localizes to small particle-like structures, that differ from either the mitochondria, the endoplasmic reticulum near the nucleus, or the peroxisomes. +Structural component of the gap junctions (By similarity). Plays a role in oocyte directional transit in the spermatheca during ovulation by facilitating the directional propagation of the calcium signal in the spermatheca (PubMed:23671426). Plays a role in male tail tip morphogenesis (PubMed:21408209). Expressed in hyp8-11 tail tip cells during the L4 larval stage. RNAi-mediated knockdown causes defective oocyte transit through the spermatheca. Calcium oscillations triggered during ovulation are random resulting in uncoordinated spermatheca constrictions. Oocytes enter the spermatheca normally but change direction several times before returning into the gonad or proceeding into the uterus. RNAi-mediated knockdown disrupts tail tip morphogenesis resulting in retention of the pointed larval tail tip in adult males (also known as the Lep phenotype) (PubMed:21408209). Belongs to the pannexin family. +NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. a ubiquinone + H(+) + n Na(+)(in) + NADH = a ubiquinol + n Na(+)(out) + NAD(+) This reaction is tightly coupled to the Na(+) pumping activity and specifically requires Na(+) for activity. Inhibited by korormicin and 2-N-heptyl-4-hydroxyquinoline N-oxide (HQNO). Composed of six subunits; NqrA, NqrB, NqrC, NqrD, NqrE and NqrF. The N-terminus is blocked. Belongs to the NqrDE/RnfAE family. +Could be involved in septation. Belongs to the SpoVG family. +Aquaporins facilitate the transport of water and small neutral solutes across cell membranes. Expressed in leaves and at lower levels in roots. Aquaporins contain two tandem repeats each containing three membrane-spanning domains and a pore-forming loop with the signature motif Asn-Pro-Ala (NPA). Belongs to the MIP/aquaporin (TC 1.A.8) family. NIP (TC 1.A.8.12) subfamily. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Part of the ABC transporter complex LolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone, LolA. Responsible for the formation of the LolA-lipoprotein complex in an ATP-dependent manner. The complex is composed of two ATP-binding proteins (LolD) and two transmembrane proteins (LolC and LolE). Belongs to the ABC transporter superfamily. Lipoprotein translocase (TC 3.A.1.125) family. +Probably deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs), playing an important role in chemotaxis. H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Belongs to the CheD family. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +ATPase required for the post-translational delivery of tail-anchored (TA) proteins to the endoplasmic reticulum. Recognizes and selectively binds the transmembrane domain of TA proteins in the cytosol. This complex then targets to the endoplasmic reticulum by membrane-bound receptors, where the tail-anchored protein is released for insertion. This process is regulated by ATP binding and hydrolysis. ATP binding drives the homodimer towards the closed dimer state, facilitating recognition of newly synthesized TA membrane proteins. ATP hydrolysis is required for insertion. Subsequently, the homodimer reverts towards the open dimer state, lowering its affinity for the membrane-bound receptor, and returning it to the cytosol to initiate a new round of targeting. Homodimer. Belongs to the arsA ATPase family. +This protein is involved in control of the biosynthesis of threonine. Belongs to the thr operon leader peptide family. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate. ATP + shikimate = 3-phosphoshikimate + ADP + H(+) Binds 1 Mg(2+) ion per subunit. Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 5/7. Monomer. Belongs to the shikimate kinase family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Ubiquitin-like protein that can be covalently attached to proteins as a monomer or as a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex sae1-sae2 and linkage to the E2 enzyme ube2i, and can be promoted by an E3 ligase such as pias1-4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Polymeric sumo2 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins (By similarity). Interacts with sae2 and ube2i. Covalently attached to a number of proteins, including top2 (By similarity). Polymeric chains can be formed through Lys-11 cross-linking. Cleavage of precursor form by a sentrin-specific protease is necessary for function. Belongs to the ubiquitin family. SUMO subfamily. +Bark lectins are storage proteins that probably maintain stocks of nitrogen during dormant period. Self-aggregatable molecules that can bind their own carbohydrate side chains. They could also play a role in the plant's defense against phytophagous invertebrates or herbivorous higher animals. Homotetramer. Weak expression in bark. The lectin accumulates in the inner bark in autumn. Belongs to the leguminous lectin family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity (By similarity). 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +Histone methyltransferase that specifically trimethylates histone H3 to form H3K79me3. This methylation is required for telomere silencing and for the pachytene checkpoint during the meiotic cell cycle by allowing the recruitment of RAD9 to double strand breaks. Nucleosomes are preferred as substrate compared to free histone. L-lysyl(79)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(79)-[histone H3] + 3 S-adenosyl-L-homocysteine Ubiquitination of histone H2B to form H2BK123ub1 is required for efficient DOT1 methyltransferase activity on histone H3. In contrast to other lysine histone methyltransferases, it does not contain a SET domain, suggesting the existence of another mechanism for methylation of lysine residues of histones. Belongs to the class I-like SAM-binding methyltransferase superfamily. DOT1 family. +S-adenosyl-L-methionine + a thiopurine = S-adenosyl-L-homocysteine + a thiopurine S-methylether. Belongs to the class I-like SAM-binding methyltransferase superfamily. TPMT family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Heterodimer of an alpha and a beta chain. Belongs to the bacterial histone-like protein family. +Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction: the enzyme is irreversibly inactivated. The methylated ADA protein acts as a positive regulator of its own synthesis, as well as that of other proteins. The transcription-activating function of the ADA protein resides in its N-terminus. It activates the transcription of alkA, alkB and aidB. a 6-O-methyl-2'-deoxyguanosine in DNA + L-cysteinyl-[protein] = a 2'-deoxyguanosine in DNA + S-methyl-L-cysteinyl-[protein] a 4-O-methyl-thymidine in DNA + L-cysteinyl-[protein] = a thymidine in DNA + S-methyl-L-cysteinyl-[protein] Binds 1 zinc ion per subunit. This enzyme catalyzes only one turnover and therefore is not strictly catalytic. According to one definition, an enzyme is a biocatalyst that acts repeatedly and over many reaction cycles. In the C-terminal section; belongs to the MGMT family. +ATP + pyruvate = ADP + H(+) + phosphoenolpyruvate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 5/5. Belongs to the pyruvate kinase family. In the C-terminal section; belongs to the PEP-utilizing enzyme family. +Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + H(+) + holo-[ACP] Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxD subfamily. +Belongs to the UPF0173 family. +May play a role in cell-cell adhesion. Belongs to the nectin family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Tetramer of two alpha and two beta subunits. Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 2 subfamily. +May play an important role in acrosome formation and nucleus shaping during spermiogenesis. Detected in acrosome of round spermatids and spermatozoa. +Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate. dihydroxyacetone phosphate + iminosuccinate = H(+) + 2 H2O + phosphate + quinolinate Binds 1 [4Fe-4S] cluster per subunit. Inhibited by 4,5 dithiohydroxyphthalic acid (DTHPA) analogs, which bind to the catalytic iron site of the [4Fe-4S] cluster. Cofactor biosynthesis; NAD(+) biosynthesis; quinolinate from iminoaspartate: step 1/1. Belongs to the quinolinate synthase family. Type 2 subfamily. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate. ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterodimer of GatD and GatE. Belongs to the asparaginase 1 family. GatD subfamily. +Expressed by the venom gland. Contains 2 disulfide bonds. Belongs to the scoloptoxin-15 family. +Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act as a core component of the putative HOPS and CORVET endosomal tethering complexes which are proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:11382755, PubMed:23351085, PubMed:24554770, PubMed:25783203). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:25783203). Involved in dendrite development of Pukinje cells (By similarity). Core component of at least two putative endosomal tethering complexes, the homotypic fusion and vacuole protein sorting (HOPS) complex and the class C core vacuole/endosome tethering (CORVET) complex. Their common core is composed of the class C Vps proteins VPS11, VPS16, VPS18 and VPS33A, which in HOPS further associates with VPS39 and VPS41 and in CORVET with VPS8 and TGFBRAP1 (PubMed:23351085, PubMed:25783203, PubMed:23901104). Interacts with RAB5C (By similarity). Interacts with HOOK1 (By similarity). Interacts with STX7, MON1B (PubMed:20434987, PubMed:24554770). Associates with adaptor protein complex 3 (AP-3) and clathrin:AP-3 complexes (By similarity). Interacts with SYNPO2 (PubMed:23434281). Interacts with PLEKHM1 (PubMed:28325809). Cytoplasmic, peripheral membrane protein associated with early endosomes and late endosomes/lysosomes. Ubiquitous. Expression was highest in heart and low in lung. Belongs to the VPS18 family. Unlikely isoform. Aberrant splice sites. Extended N-terminus. +Protein and nucleotide deglycase that catalyzes the deglycation of the Maillard adducts formed between amino groups of proteins or nucleotides and reactive carbonyl groups of glyoxals. Thus, functions as a protein deglycase that repairs methylglyoxal- and glyoxal-glycated proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteine, arginine and lysine residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of Schiff bases and advanced glycation endproducts (AGE). Also functions as a nucleotide deglycase able to repair glycated guanine in the free nucleotide pool (GTP, GDP, GMP, dGTP) and in DNA and RNA. Is thus involved in a major nucleotide repair system named guanine glycation repair (GG repair), dedicated to reversing methylglyoxal and glyoxal damage via nucleotide sanitization and direct nucleic acid repair. Plays an important role in protecting cells from carbonyl stress. H2O + N(omega)-(1-hydroxy-2-oxopropyl)-L-arginyl-[protein] = H(+) + L-arginyl-[protein] + lactate H2O + N(6)-(1-hydroxy-2-oxopropyl)-L-lysyl-[protein] = H(+) + L-lysyl-[protein] + lactate H2O + S-(1-hydroxy-2-oxopropyl)-L-cysteinyl-[protein] = H(+) + L-cysteinyl-[protein] + lactate H2O + N(omega)-(1-hydroxy-2-oxoethyl)-L-arginyl-[protein] = glycolate + H(+) + L-arginyl-[protein] H2O + N(6)-(1-hydroxy-2-oxoethyl)-L-lysyl-[protein] = glycolate + H(+) + L-lysyl-[protein] H2O + S-(1-hydroxy-2-oxoethyl)-L-cysteinyl-[protein] = glycolate + H(+) + L-cysteinyl-[protein] H2O + N(2)-(1-hydroxy-2-oxopropyl)-dGTP = dGTP + H(+) + lactate H2O + N(2)-(1-hydroxy-2-oxopropyl)-GTP = GTP + H(+) + lactate H2O + N(2)-(1-hydroxy-2-oxopropyl)-GDP = GDP + H(+) + lactate H2O + N(2)-(1-hydroxy-2-oxopropyl)-GMP = GMP + H(+) + lactate H2O + N(2)-(1-hydroxy-2-oxoethyl)-dGTP = dGTP + glycolate + H(+) H2O + N(2)-(1-hydroxy-2-oxoethyl)-GTP = glycolate + GTP + H(+) H2O + N(2)-(1-hydroxy-2-oxoethyl)-GDP = GDP + glycolate + H(+) H2O + N(2)-(1-hydroxy-2-oxoethyl)-GMP = glycolate + GMP + H(+) an N(2)-(1-hydroxy-2-oxopropyl)-guanosine in RNA + H2O = a guanosine in RNA + H(+) + lactate an N(2)-(1-hydroxy-2-oxopropyl)-2'-deoxyguanosine in DNA + H2O = a 2'-deoxyguanosine in DNA + H(+) + lactate an N(2)-(1-hydroxy-2-oxoethyl)-guanosine in RNA + H2O = a guanosine in RNA + glycolate + H(+) an N(2)-(1-hydroxy-2-oxoethyl)-2'-deoxyguanosine in DNA + H2O = a 2'-deoxyguanosine in DNA + glycolate + H(+) Homodimer. By heat shock. Belongs to the peptidase C56 family. HchA subfamily. +Essential protein that is involved in the control of cell division, probably through the regulation of ctrA. Its phosphorylation status is regulated by PdhS (By similarity). Interacts with DivL, PleC, DivJ and PdhS. Localized at one pole of the cell. Colocalizes with PdhS (By similarity). +Involved in the metabolism of the antibiotic polyketide bacillaene which is involved in secondary metabolism. The substrate is dihydrobacillaene. Antibiotic biosynthesis; bacillaene biosynthesis. Belongs to the cytochrome P450 family. +Involved in the biogenesis of the 60S ribosomal subunit. May play a part in the quality control of pre-60S particles (By similarity). Component of the pre-66S ribosomal particle. Interacts with NOP7 and RRP1. Interacts with RSA4 (via WD repeats). Belongs to the eukaryotic ribosomal protein eS8 family. Ribosome biogenesis protein NSA2 subfamily. +Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. Endonucleolytic cleavage to 5'-phosphomonoester. Homodimer. Belongs to the ribonuclease III family. +Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine. H(+) + S-adenosyl-L-methionine = CO2 + S-adenosyl 3-(methylsulfanyl)propylamine Binds 1 pyruvoyl group covalently per subunit. Amine and polyamine biosynthesis; S-adenosylmethioninamine biosynthesis; S-adenosylmethioninamine from S-adenosyl-L-methionine: step 1/1. Heterotetramer of two alpha and two beta chains arranged as a dimer of alpha/beta heterodimers. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl group blocking the N-terminus of the alpha chain. Belongs to the prokaryotic AdoMetDC family. Type 1 subfamily. +Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella. Individual Salmonella serotypes usually alternate between the production of 2 antigenic forms of flagella, termed phase 1 and phase 2, each specified by separate structural genes. Belongs to the bacterial flagellin family. +D-mannitol 1-phosphate + NAD(+) = beta-D-fructose 6-phosphate + H(+) + NADH Belongs to the mannitol dehydrogenase family. +Involved in the control of cell fates in the neurectoderm. Acts as a positive regulator of Notch pathway and is required at different levels during development. Belongs to the TM2 family. +Involved in the partitioning of the mitochondrial organelle and mitochondrial DNA (mtDNA) inheritance. Belongs to the misato family. +Displays ATPase and GTPase activities. Belongs to the RapZ-like family. +Biosynthesis of L-glutamate from L-aspartate or L-cysteine. Important regulator of levels of glutamate, the major excitatory neurotransmitter of the vertebrate central nervous system. Acts as a scavenger of glutamate in brain neuroprotection. The aspartate aminotransferase activity is involved in hepatic glucose synthesis during development and in adipocyte glyceroneogenesis. Using L-cysteine as substrate, regulates levels of mercaptopyruvate, an important source of hydrogen sulfide. Mercaptopyruvate is converted into H(2)S via the action of 3-mercaptopyruvate sulfurtransferase (3MST). Hydrogen sulfide is an important synaptic modulator and neuroprotectant in the brain. 2-oxoglutarate + L-aspartate = L-glutamate + oxaloacetate 2-oxoglutarate + L-cysteine = 2-oxo-3-sulfanylpropanoate + L-glutamate (2S)-2-aminobutanoate + 2-oxoglutarate = 2-oxobutanoate + L-glutamate 2-oxoglutarate + 3-sulfino-L-alanine = 3-sulfinopyruvate + L-glutamate Homodimer. In eukaryotes there are cytoplasmic, mitochondrial and chloroplastic isozymes. Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence (By similarity). Belongs to the bacterial ribosomal protein bS1 family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 magnesium ions per subunit. Monomer. Belongs to the DNA polymerase type-Y family. +Involved in peptidoglycan biosynthesis. Transports lipid-linked peptidoglycan precursors from the inner to the outer leaflet of the cytoplasmic membrane. May serve as a defense mechanism against naturally occurring MurJ antagonists. Cell wall biogenesis; peptidoglycan biosynthesis. Transcribed under partial control of SigM ECF sigma factor (PubMed:17434969, PubMed:25918422). Expression is up-regulated in the absence of MurJ (PubMed:25918422). Mutants lacking both murJ and amj have a lethal defect in cell wall synthesis. Belongs to the Amj family. +RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. Also part of the exosome, which is a complex involved in RNA degradation. Acts as a poly(A)-binding protein that enhances the interaction between heteromeric, adenine-rich transcripts and the exosome. ssDNA + n NTP = ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate. Binds two Mg(2+) per subunit. Forms a ternary complex with MCM helicase and DNA. Component of the archaeal exosome complex. Belongs to the archaeal DnaG primase family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Probable neurotoxin. Expressed by the venom duct. The cysteine framework is XXVIII (C-C-C-CC-C-C-C-C-C). Contains 5 disulfide bonds. Belongs to the conotoxin D superfamily. +Transmembrane component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Required for ciliogenesis and sonic hedgehog/SHH signaling. Part of the tectonic-like complex (also named B9 complex). Localizes to the transition zone of primary cilia. Belongs to the TMEM17 family. +May be involved in vacuolar sorting and osmoregulation. Binds 2 Zn(2+) ions per subunit. Belongs to the peptidase M28 family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity and assembly of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 6 family. +Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA). S-adenosyl-L-methionine + uridine(54) in tRNA = 5-methyluridine(54) in tRNA + H(+) + S-adenosyl-L-homocysteine S-adenosyl-L-methionine + uridine(341) in tmRNA = 5-methyluridine(341) in tmRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. TrmA subfamily. +Involved in the active translocation of vitamin B12 (cyanocobalamin) across the outer membrane to the periplasmic space. It derives its energy for transport by interacting with the trans-periplasmic membrane protein TonB. Belongs to the TonB-dependent receptor family. BtuB (TC 1.B.14.3.1) subfamily. +Globally modulates RNA abundance by binding to RNase E (Rne) and regulating its endonucleolytic activity. Can modulate Rne action in a substrate-dependent manner by altering the composition of the degradosome. Interacts with the C-terminal region of Rne. Belongs to the RraB family. Extended N-terminus. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Belongs to the polyribonucleotide nucleotidyltransferase family. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +Acts as a radical domain for damaged PFL and possibly other radical proteins. +Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Binds 1 potassium ion per subunit. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. +Toxic component of a type II toxin-antitoxin (TA) system. Degrades total E.coli RNA, which is partially inhibited by cognate antitoxin VapB15 (PubMed:25450593). Upon expression in M.smegmatis inhibits colony formation, which is neutralized by coexpression with VapB15 (PubMed:20011113). The heterotrimer binds 1 Mg(2+)-Mn(2+) pair while the heterotetramer binds 2 pairs. Both metals are shared by the toxin-antitoxin pair. The heterotrimer binds 1 Mg(2+)-Mn(2+) pair while the heterotetramer binds 2 pairs. Both metals are shared by the toxin-antitoxin pair. RNase activity inhibited by EDTA. Crystallizes as a VapB15-VapC15(2) heterotrimer and as a VapB15(2)-VapC15(2) heterotetramer; each toxin pair forms a homodimer which creates a channel in which the antitoxin binds. Induced by hypoxia. In this enzyme the conserved residue Asp-4 binds Mg(2+) via H(2)O. Belongs to the PINc/VapC protein family. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Cleaves arabinose units from O-2- or O-3-monosubstituted xylose residues, thereby assisting in arabinoxylan (AX) and short-chain arabinoxylo-oligosaccharide (AXOS) degradation. Is more active on wheat bran AXOS than on wheat water-extractable AX and rye water-extractable AX. Does not display endoxylanase, xylosidase or arabinanase activity. Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. Optimum pH is 5.6. Stable from pH 4.4 to 7.6. Optimum temperature is 45 degrees Celsius. Thermostable for 40 min from 4 to 45 degrees Celsius. Glycan degradation; xylan degradation. The CBM6 domain lost its carbohydrate binding capacity. Belongs to the glycosyl hydrolase 43 family. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions (By similarity). 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate H(+) + oxaloacetate = CO2 + pyruvate Divalent metal cation. Homotrimer. Belongs to the class II aldolase/RraA-like family. +Antimicrobial activity against Gram-negative bacterium E.coli. Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Brevinin subfamily. +Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate. dihydroxyacetone phosphate + iminosuccinate = H(+) + 2 H2O + phosphate + quinolinate Binds 1 [4Fe-4S] cluster per subunit. Cofactor biosynthesis; NAD(+) biosynthesis; quinolinate from iminoaspartate: step 1/1. Belongs to the quinolinate synthase family. Type 1 subfamily. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Regulator of short-term neuronal synaptic plasticity in the dentate gyrus. Associates with AMPA receptors (ionotropic glutamate receptors) in synaptic spines and promotes AMPA receptor desensitization at excitatory synapses (By similarity). Component of some AMPA receptors (ionotropic glutamate receptors) complex. Belongs to the shisa family. SHISA9 subfamily. +ATP-binding RNA helicase involved in ribosome assembly. ATP + H2O = ADP + H(+) + phosphate Associates with pre-ribosomal particles. The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis. Belongs to the DEAD box helicase family. DDX27/DRS1 subfamily. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +May function as a nuclear transport receptor. Binds to nucleoporins and the GTP-bound form of Ran. Belongs to the exportin family. +Agglutinogen that binds to eukaryotic cells; a process mediated by the R-G-D sequence. Pertactin may have a role in bacterial adhesion, and thus play a role in virulence. May contribute to the disease state of whooping cough. Monomer. The cleaved C-terminal fragment (autotransporter domain) is localized in the outer membrane. The signal peptide, cleaved at the inner membrane, guides the autotransporter protein to the periplasmic space. Then, insertion of the C-terminal translocator domain in the outer membrane forms a hydrophilic pore for the translocation of the passenger domain to the bacterial cell surface, with subsequent cleavage (By similarity). Synthesized only in the presence of low Mg(2+) concentrations. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the PetN family. +S-adenosyl-L-methionine-dependent protein-lysine N-methyltransferase that mono- and dimethylates elongation factor 1-alpha (TEF1 and TEF2) at 'Lys-316'. May play a role in intracellular transport. Defects at both very early and later stages of endocytic transport in cells. Present with 1620 molecules/cell in log phase SD medium. Belongs to the class I-like SAM-binding methyltransferase superfamily. EFM4 family. +May play a role in neural plasticity. May be involved during axon regeneration. Forms disulfide-linked dimers. EPDs are synthesized in the meninx and secreted in the cerebrospinal fluid. Different glycosylation variants are known as EPD-beta and EPD-gamma. Binds calcium through the terminal sialic acids. Belongs to the ependymin family. +May act as a bridging protein that binds pectin and other cell wall polysaccharides. Probably involved in maintaining esterification of pectins (By similarity). May be involved in the specific O-acetylation of cell wall polymers (By similarity). Contains 2 motifs that are conserved in esterases, but it is unlikely that this protein belongs to the catalytically active pectin esterases. Belongs to the PC-esterase family. TBL subfamily. +Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose. beta-D-ribopyranose = beta-D-ribofuranose Carbohydrate metabolism; D-ribose degradation; D-ribose 5-phosphate from beta-D-ribopyranose: step 1/2. Homodecamer. Belongs to the RbsD / FucU family. RbsD subfamily. +Transcription factor which regulates nonfermentable carbon utilization. Belongs to the ERT1/acuK family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Belongs to the acyltransferase 3 family. +Belongs to the LpqB lipoprotein family. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homodimer. Belongs to the ThiC family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvP family. +The L3 protein is a component of the large subunit of cytoplasmic ribosomes. Belongs to the universal ribosomal protein uL3 family. +Promotes colloidosmotic lysis by binding to the midgut epithelial cells of many lepidopteran larvae. The crystal protein is produced during sporulation and is accumulated both as an inclusion and as part of the spore coat. Introduced by genetic manipulation and expressed in insect-resistant cotton and tomato by Calgene (Monsanto) and in maize by Dekalb Genetics. Toxic segment of the protein is located in the N-terminus. Belongs to the delta endotoxin family. +DNA helicase that possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for heterochromatin organization. ATP + H2O = ADP + H(+) + phosphate Belongs to the SNF2/RAD54 helicase family. +Component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins. Belongs to the bacterial ribosomal protein bL34 family. +Belongs to the bacterial ribosomal protein bS16 family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria. 3-deoxy-alpha-D-manno-oct-2-ulosonate + CTP = CMP-3-deoxy-beta-D-manno-octulosonate + diphosphate Nucleotide-sugar biosynthesis; CMP-3-deoxy-D-manno-octulosonate biosynthesis; CMP-3-deoxy-D-manno-octulosonate from 3-deoxy-D-manno-octulosonate and CTP: step 1/1. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Belongs to the KdsB family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Acyltransferase; part of the gene cluster that mediates the biosynthesis of monakolin K, also known as lovastatin, and which acts as a potent competitive inhibitor of HMG-CoA reductase (PubMed:18578535). Monakolin K biosynthesis is performed in two stages (PubMed:19693441). The first stage is catalyzed by the nonaketide synthase mokA, which belongs to type I polyketide synthases and catalyzes the iterative nine-step formation of the polyketide (PubMed:18578535, PubMed:19693441). This PKS stage is completed by the action of dehydrogenase mokE, which catalyzes the NADPH-dependent reduction of the unsaturated tetra-, penta- and heptaketide intermediates that arise during the mokA-mediated biosynthesis of the nonaketide chain and leads to dihydromonacolin L (PubMed:19693441). Covalently bound dihydromonacolin L is released from mokA by the mokD esterase (By similarity). Conversion of dihydromonacolin L into monacolin L and then monacolin J is subsequently performed with the participation of molecular oxygen and P450 monoogygenase mokC (PubMed:19693441). Finally, mokF performs the conversion of monacoline J to monacoline K through the addition of the side-chain diketide moiety (2R)-2-methylbutanoate produced by the diketide synthase mokB (PubMed:19693441). (S)-2-methylbutanoyl-[2-methylbutanoate polyketide synthase] + monacolin J carboxylate = holo-[2-methylbutanoate polyketide synthase] + lovastatin carboxylate Polyketide biosynthesis; lovastatin biosynthesis. Expression is controlled by the monacolin K cluster transcription regulator mokH (PubMed:19968298). Monacoline K acts as an inhibitor of HMG-CoA reductase involved in cholesterogenesis (PubMed:21821946). Its hypocholesterolemic activity might be useful for lowering cholesterol levels in the blood and reduce artherosclerosis and coronary heart disease (PubMed:21821946). Belongs to the class-A beta-lactamase family. +Regulatory subunit of the condensin complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes. The condensin complex probably introduces positive supercoils into relaxed DNA in the presence of type I topoisomerases and converts nicked DNA into positive knotted forms in the presence of type II topoisomerase. Component of the condensin complex, which contains the XCAP-E/SMC2 and XCAP-C/SMC4 heterodimer, and three non SMC subunits that probably regulate the complex: XCAP-H/NCAPH, XCAP-D2/NCAPD2 and XCAP-G/NCAPG. In interphase cells, the majority of the condensin complex is found in the cytoplasm, while a minority of the complex is associated with chromatin. A subpopulation of the complex however remains associated with chromosome foci in interphase cells. During mitosis, most of the condensin complex is associated with the chromatin. At the onset of prophase, the regulatory subunits of the complex are phosphorylated by CDK1, leading to condensin's association with chromosome arms and to chromosome condensation. Dissociation from chromosomes is observed in late telophase (By similarity). Phosphorylated by cdk1. Its phosphorylation, as well as that of XCAP-D2 and XCAP-H subunits, activates the condensin complex and is required for chromosome condensation. Belongs to the CND3 (condensin subunit 3) family. +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Belongs to the UPF0763 family. +Plays an important role in the control of DNA replication and the maintenance of replication fork stability. Important for cell survival after DNA damage or replication stress. May be required fin the replication checkpoint induced by hydroxyurea or ultraviolet light (By similarity). Interacts with TIMELESS, which impairs TIMELESS self-association. Belongs to the CSM3 family. +Immunity component of one of 6 LXG toxin-immunity modules in this strain. They promote kin selection, mediate competition in biofilms, and drive spatial segregation of different strains, indicating that LXG toxins may help avoid warfare between strains in biofilms. Mediates intercellular competition during biofilm formation; disruption of the operon disadvantages the bacteria, but overexpression of the cognate immunity protein restores growth in competition with wild-type. In situ neutralizes the toxic effect of cognate toxin YokI (PubMed:34280190). Neutralizes the ability to inhibit growth of cognate toxin YokI upon expression in E.coli. Does not have immunity protein activity on other LXG toxins (PubMed:22200572). Probably interacts with cognate toxin YokI but not with other non-cognate toxins. The interaction inhibits the toxic activity of YokI (Probable). Expressed on rich and minimal solid media likely in early stationary phase; not dependent on DegSU. Not expressed in liquid LB, but only under conditions that promote biofilm formation. Deletion of the yokI-yokJ operon has no visible growth phenotype, however it is out-competed by wild-type cells. +Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein. Belongs to the DsbB family. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-methyl-D-erythritol + diphosphate Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. Belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily. +A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis. Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes. Belongs to the type II topoisomerase GyrA/ParC subunit family. +Plays a role in the flagellum-specific transport system. Belongs to the FliP/MopC/SpaP family. +ADP-binding subunit of the dihydroxyacetone kinase, which is responsible for the phosphoenolpyruvate (PEP)-dependent phosphorylation of dihydroxyacetone (PubMed:11350937). DhaL-ADP is converted to DhaL-ATP via a phosphoryl group transfer from DhaM and transmits it to dihydroxyacetone bound to DhaK (PubMed:11350937). DhaL acts also as coactivator of the transcription activator DhaR by binding to the sensor domain of DhaR (PubMed:15616579). In the presence of dihydroxyacetone, DhaL-ADP displaces DhaK and stimulates DhaR activity (PubMed:15616579). In the absence of dihydroxyacetone, DhaL-ADP is converted by the PTS to DhaL-ATP, which does not bind to DhaR (PubMed:15616579). dihydroxyacetone + phosphoenolpyruvate = dihydroxyacetone phosphate + pyruvate kcat is 2.8 sec(-1). Values measured with the DhaKLM complex. Complexation with ADP increases the thermal unfolding temperature from 40 to 65 degrees Celsius. Polyol metabolism; glycerol degradation. Homodimer (PubMed:16647083, PubMed:21209328, PubMed:24440518). The dihydroxyacetone kinase complex is composed of a homodimer of DhaM, a homodimer of DhaK and the subunit DhaL (PubMed:16647083, PubMed:21209328). DhaL also forms a complex with DhaR (PubMed:24440518). Activated by DhaR. Unlike the carbohydrate-specific transporters of the PTS, the complex DhaKML has no transport activity. The tightly bound ADP participates in a double displacement phosphoryl transfer reaction and thus plays the same role as histidines, cysteines and aspartic acids in other phosphoprotein intermediates. +Involved in regulation of the actin cytoskeleton. May regulate WAS actin-bundling activity. Bridges the interaction between ABL1 and PTPN18 leading to ABL1 dephosphorylation. May play a role as a scaffold protein between PTPN12 and WAS and allow PTPN12 to dephosphorylate WAS. Has the potential to physically couple CD2 and CD2AP to WAS. Acts downstream of CD2 and CD2AP to recruit WAS to the T-cell:APC contact site so as to promote the actin polymerization required for synapse induction during T-cell activation. Down-regulates CD2-stimulated adhesion through the coupling of PTPN12 to CD2. Also has a role in innate immunity and the inflammatory response. Recruited to inflammasomes by MEFV. Induces formation of pyroptosomes, large supramolecular structures composed of oligomerized PYCARD dimers which form prior to inflammatory apoptosis. Binding to MEFV allows MEFV to bind to PYCARD and facilitates pyroptosome formation. Regulates endocytosis and cell migration in neutrophils. Homodimer. Homotrimer. Interacts (via coiled-coil domain) with CD2AP, PTPN12 and PTPN18. Interacts (via SH3 domain) with ABL1 and WAS. Interacts (via SH3 and coiled-coil domains) with MEFV (via B-box zinc finger); the interaction allows binding of MEFV to PYCARD and facilitates formation of PYCARD pyroptosomes. Interacts with DNM2 and FASLG (By similarity). Interacts with CD2. Colocalized with PTPN12 in the cytoplasm and the perinuclear region (PubMed:11711533). During interphase, colocalizes with F-actin in the cortical cytoskeleton, lamellipodia, and stress fibers (PubMed:9265651). In dividing cells, colocalizes with the F-actin rich cytokinetic cleavage furrow (PubMed:9265651). Colocalized with CD2AP and WAS in the actin cytoskeleton within the cytoplasm (PubMed:12530983, PubMed:9488710). Colocalized with CD2, CD2AP and WAS at the site of T-cell:APC contact (PubMed:12530983). Mainly cytoplasmic in T cells. Colocalizes in cluster with CD2 near the cell surface membrane in activated T-cells. In monocytes, forms a branched filamentous network in the cytoplasm. In transfected cells, forms relatively straight filaments radiating out from the nucleus. Filament formation requires an intact tubulin cytoskeleton. In migrating neutrophils, colocalizes with PIP5K1C and DNM2 to the trailing edge of the uropod in a actin-dependent manner (By similarity). Highly expressed in adult lung and spleen, and weakly expressed in testis, muscle, kidney, brain and heart. Highly expressed in spleen and thymus, moderately in lung, brain and muscle, and weakly expressed in heart and liver (at protein level). Highly expressed in 7 dpc embryos. The F-BAR domain is important for filament formation. The SH3 domain is not required for filament formation or localization to the uropod (By similarity). Dephosphorylated on Tyr-344 by PTPN18, this event negatively regulates the association of PSTPIP1 with SH2 domain-containing proteins as tyrosine kinase. Phosphorylation of Tyr-344 is probably required for subsequent phosphorylation at other tyrosine residues. Phosphorylation is induced by activation of the EGFR and PDGFR in a ABL1 dependent manner. The phosphorylation regulates the interaction with WAS and with MEFV. +The TFIID basal transcription factor complex plays a major role in the initiation of RNA polymerase II (Pol II)-dependent transcription. TFIID recognizes and binds promoters with or without a TATA box via its subunit tbp, a TATA-box-binding protein, and promotes assembly of the pre-initiation complex (PIC). The TFIID complex consists of tbp and TBP-associated factors (TAFs). Mediates both basal and activator-dependent transcription. Component of the TFIID basal transcription factor complex, composed of TATA-box-binding protein tbp, and a number of TBP-associated factors (TAFs). Belongs to the TAF8 family. +Required for the post-translational delivery of tail-anchored (TA) proteins to the endoplasmic reticulum. Together with CAMLG/GET2, acts as a membrane receptor for soluble GET3/TRC40, which recognizes and selectively binds the transmembrane domain of TA proteins in the cytosol. Required to ensure correct topology and ER insertion of CAMLG. Component of the Golgi to ER traffic (GET) complex, which is composed of GET1, CAMLG/GET2 and GET3. Within the complex, GET1 and CAMLG form a heterotetramer which is stabilized by phosphatidylinositol binding and which binds to the GET3 homodimer. Interacts with CAMLG/GET2 (via C-terminus). GET3 shows a higher affinity for CAMLG than for GET1. Belongs to the WRB/GET1 family. +Pre-60S-associated factor involved in the cytoplasmic maturation of the 60S subunit. Involved in the dissociation and recycling of other late pre-60S factors like ARX1, TIF6 and ALB1 before newly synthesized large ribosomal subunits enter translation. Cooperates with the co-chaperone JJJ1 in the release of the nuclear-export factor ARX1. May act redundantly with REH1 to directly promote a stabilizing structural rearrangement in cytoplasmic 60S subunit maturation independent on ARX1 recycling. Associates with nascent pre-60S particles that have not yet entered the translating pool, and is released from mature 60S subunits. Interacts with pre-60S factors ARX1 and RPL24. Interacts with JJJ1. Present with 830 molecules/cell in log phase SD medium. Belongs to the REI1 family. +Probable guanine nucleotide exchange factor (GEF), which may be involved in the secretion process. Interacts with SEC5. The interaction occurs only in the presence of magnesium or manganese and is stimulated by dCTP or GTP (By similarity). +Integrins alpha-1/beta-1, alpha-2/beta-1, alpha-10/beta-1 and alpha-11/beta-1 are receptors for collagen. Integrins alpha-1/beta-1 and alpha-2/beta-2 recognize the proline-hydroxylated sequence G-F-P-G-E-R in collagen. Integrins alpha-2/beta-1, alpha-3/beta-1, alpha-4/beta-1, alpha-5/beta-1, alpha-8/beta-1, alpha-10/beta-1, alpha-11/beta-1 and alpha-V/beta-1 are receptors for fibronectin. Alpha-4/beta-1 recognizes one or more domains within the alternatively spliced CS-1 and CS-5 regions of fibronectin. Integrin alpha-5/beta-1 is a receptor for fibrinogen. Integrin alpha-1/beta-1, alpha-2/beta-1, alpha-6/beta-1 and alpha-7/beta-1 are receptors for lamimin. Integrin alpha-6/beta-1 (ITGA6:ITGB1) is present in oocytes and is involved in sperm-egg fusion. Integrin alpha-4/beta-1 is a receptor for VCAM1 and recognizes the sequence Q-I-D-S in VCAM1. Integrin alpha-9/beta-1 is a receptor for VCAM1, cytotactin and osteopontin. It recognizes the sequence A-E-I-D-G-I-E-L in cytotactin. Integrin alpha-3/beta-1 is a receptor for epiligrin, thrombospondin and CSPG4. Integrin alpha-3/beta-1 provides a docking site for FAP (seprase) at invadopodia plasma membranes in a collagen-dependent manner and hence may participate in the adhesion, formation of invadopodia and matrix degradation processes, promoting cell invasion. Alpha-3/beta-1 may mediate with LGALS3 the stimulation by CSPG4 of endothelial cells migration. Integrin alpha-V/beta-1 is a receptor for vitronectin. Beta-1 integrins recognize the sequence R-G-D in a wide array of ligands. When associated with alpha-7/beta-1 integrin, regulates cell adhesion and laminin matrix deposition. Involved in promoting endothelial cell motility and angiogenesis. Involved in osteoblast compaction through the fibronectin fibrillogenesis cell-mediated matrix assembly process and the formation of mineralized bone nodules. May be involved in up-regulation of the activity of kinases such as PKC via binding to KRT1. Together with KRT1 and RACK1, serves as a platform for SRC activation or inactivation. Plays a mechanistic adhesive role during telophase, required for the successful completion of cytokinesis (By similarity). ITGA4:ITGB1 binds to fractalkine (CX3CL1) and may act as its coreceptor in CX3CR1-dependent fractalkine signaling. ITGA4:ITGB1 and ITGA5:ITGB1 bind to PLA2G2A via a site (site 2) which is distinct from the classical ligand-binding site (site 1) and this induces integrin conformational changes and enhanced ligand binding to site 1. ITGA5:ITGB1 acts as a receptor for fibrillin-1 (FBN1) and mediates R-G-D-dependent cell adhesion to FBN1. ITGA5:ITGB1 is a receptor for IL1B and binding is essential for IL1B signaling (By similarity). ITGA5:ITGB3 is a receptor for soluble CD40LG and is required for CD40/CD40LG signaling (By similarity). Plays an important role in myoblast differentiation and fusion during skeletal myogenesis (By similarity). Interacts with seprase FAP (seprase); the interaction occurs at the cell surface of invadopodia membrane in a collagen-dependent manner (By similarity). Heterodimer of an alpha and a beta subunit. Beta-1 associates with either alpha-1, alpha-2, alpha-3, alpha-4, alpha-5, alpha-6, alpha-7, alpha-8, alpha-9, alpha-10, alpha-11 or alpha-V. ITGA6:ITGB1 is found in a complex with CD9; interaction takes place in oocytes and is involved in sperm-egg fusion. Binds LGALS3BP and NMRK2, when associated with alpha-7, but not with alpha-5. Interacts with FLNA, FLNB, FLNC and RANBP9. Interacts with KRT1 in the presence of RACK1 and SRC. Interacts with JAML; integrin alpha-4/beta-1 may regulate leukocyte to endothelial cells adhesion by controlling JAML homodimerization. Interacts with RAB21. Interacts (via the cytoplasmic region) with RAB25 (via the hypervariable C-terminal region). Interacts with MYO10. Interacts with ITGB1BP1 (via C-terminal region); the interaction is a prerequisite for focal adhesion disassembly. Interacts with TLN1; the interaction is prevented by competitive binding of ITGB1BP1. Interacts with ACAP1; required for ITGB1 recycling. Interacts with ASAP3. Interacts with FERMT2; the interaction is inhibited in presence of ITGB1BP1. Interacts with DAB2. Interacts with FGR and HCK. Isoform 2 interacts with alpha-7A and alpha-7B in adult skeletal muscle. Isoform 2 interacts with alpha-7B in cardiomyocytes of adult heart. Interacts with EMP2; the interaction may be direct or indirect and ITGB1 has a heterodimer form (By similarity). ITGA5:ITGB1 interacts with CCN3 (By similarity). ITGA4:ITGB1 is found in a ternary complex with CX3CR1 and CX3CL1 (By similarity). ITGA5:ITGB1 interacts with FBN1 (By similarity). ITGA5:ITGB1 interacts with IL1B. Interacts with MDK. ITGA4:ITGB1 interacts with MDK; this interaction mediates MDK-induced osteoblast cells migration through PXN phosphorylation. ITGA6:ITGB1 interacts with MDK; this interaction mediates MDK-induced neurite-outgrowth (By similarity). ITGA5:ITGB1 interacts with ACE2 (By similarity). Interacts with TMEM182 and LAMB1 (By similarity). Enriched preferentially at invadopodia, cell membrane protrusions that correspond to sites of cell invasion, in a collagen-dependent manner. Localized at plasma and ruffle membranes in a collagen-independent manner. Colocalizes with ITGB1BP1 and metastatic suppressor protein NME2 at the edge or peripheral ruffles and lamellipodia during the early stages of cell spreading on fibronectin or collagen. Translocates from peripheral focal adhesions to fibrillar adhesions in an ITGB1BP1-dependent manner (By similarity). Localized in trophoblast basement membrane and basolateral surfaces of uninucleate cells. In cardiac muscle, isoform 2 is found in costameres and intercalated disks. In the developing placenta, expressed during the morula (days 6-7) through the attachment stage (day 21). Expressed in the endoderm of day 14 blastocysts but then is down-regulated in these cells prior to implantation. Expressed on lateral surfaces of trophectodermal cells as attachment proceeded and is particularly intense in migrating binucleate cells at day 24 of development. The cysteine residues are involved in intrachain disulfide bonds. Belongs to the integrin beta chain family. +Binds to the 23S rRNA. Belongs to the bacterial ribosomal protein bL9 family. +Important for reducing fluoride concentration in the cell, thus reducing its toxicity. Belongs to the CrcB (TC 9.B.71) family. +Homodimer and heterodimers. Belongs to the Casparian strip membrane proteins (CASP) family. +May play a role in lysosomes motility. Alternatively, may play a role in chromosome segregation (By similarity). Belongs to the small GTPase superfamily. Arf family. +RNA-binding protein that regulates alternative splicing events by binding to 5'-UGCAUGU-3' elements. Prevents binding of U2AF2 to the 3'-splice site. Regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis (By similarity). Binds to the C-terminus of ATXN2. +Belongs to the FAM90 family. Could be the product of a pseudogene. +Produces ATP from ADP in the presence of a proton gradient across the membrane. Belongs to the V-ATPase E subunit family. +Electron transfer subunit of the terminal reductase during anaerobic growth on various sulfoxide and N-oxide compounds. Binds 4 [4Fe-4S] clusters. The complex consists of three subunits: YnfF, the reductase; YnfG, an electron transfer protein, and YnfH, a membrane anchor protein. +Belongs to the bacterial ribosomal protein bL33 family. +Plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis. Belongs to the YciB family. +Plays a central role in chromosome condensation, segregation and cell cycle progression. Functions as a homodimer, which is essential for chromosome partition. Involved in negative DNA supercoiling in vivo, and by this means organize and compact chromosomes. May achieve or facilitate chromosome segregation by condensation DNA from both sides of a centrally located replisome during cell division. Homodimerization via its hinge domain. Binds to DNA via its C-terminal region. Interacts, and probably forms a ternary complex, with MukE and MukF via its C-terminal region. The complex formation is stimulated by calcium or magnesium. Interacts with tubulin-related protein FtsZ. Restricted to the nucleoid region. The hinge domain, which separates the large intramolecular coiled coil regions, allows the homodimerization, forming a V-shaped homodimer. Belongs to the SMC family. MukB subfamily. +Probably deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs), playing an important role in chemotaxis. H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Belongs to the CheD family. +Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly. Belongs to the UreE family. +Involved in chemotaxis. Part of a chemotaxis signal transduction system that modulates chemotaxis in response to various stimuli. Catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins or MCP) by CheR. Also mediates the irreversible deamidation of specific glutamine residues to glutamic acid. [protein]-L-glutamate 5-O-methyl ester + H2O = H(+) + L-glutamyl-[protein] + methanol H2O + L-glutaminyl-[protein] = L-glutamyl-[protein] + NH4(+) Contains a C-terminal catalytic domain, and an N-terminal region which modulates catalytic activity. Phosphorylated by CheA. Phosphorylation of the N-terminal regulatory domain activates the methylesterase activity. Belongs to the CheB family. +Non-catalytic subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (PubMed:16174750, PubMed:23028982). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (By similarity). Essential for the proper assembly and activity of V-ATPase (By similarity). In renal intercalated cells, mediates secretion of protons (H+) into the urine thereby ensuring correct urinary acidification (PubMed:16174750). Required for optimal olfactory function by mediating the acidification of the nasal olfactory epithelium (PubMed:23028982). V-ATPase is a heteromultimeric enzyme made up of two complexes: the ATP-hydrolytic V1 complex and the proton translocation V0 complex (By similarity). The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H (By similarity). The proton translocation complex V0 consists of the proton transport subunit a, a ring of proteolipid subunits c9c'', rotary subunit d, subunits e and f, and the accessory subunits ATP6AP1/Ac45 and ATP6AP2/PRR (By similarity). Forms a complex with SLC9A3R1 and SCL4A7 (By similarity). Highly expressed in the kidney; found in early distal nephron, encompassing thick ascending limbs and distal convoluted tubules and in the alpha-intercalated cells of the cortical collecting ducts (at protein level) (PubMed:14585495, PubMed:29993276). Expressed in the olfactory epithelium (at protein level) (PubMed:23028982). Expressed at lower levels in the testis (PubMed:14585495). The PDZ-binding motif mediates interactions with SLC9A3R1 and SCL4A7. Mice show a higher urinary pH and a more severe metabolic acidosis after oral acid challenge in comparison to wild-type littermates (PubMed:16174750). Mice show diminished innate avoidance behavior (revealed as a decrease in freezing time and an increase in the number of sniffs in the presence of trimethyl-thiazoline) and diminished innate appetitive behavior (a decrease in time spent investigating the urine of the opposite sex) (PubMed:23028982). Belongs to the ATPase alpha/beta chains family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Cytoplasmic adapter regulating receptors of the signaling lymphocytic activation molecule (SLAM) family such as SLAMF1, CD244, LY9, CD84, SLAMF6 and SLAMF7. In SLAM signaling seems to cooperate with SH2D1B/EAT-2. Initially it has been proposed that association with SLAMF1 prevents SLAMF1 binding to inhibitory effectors including INPP5D/SHIP1 and PTPN11/SHP-2. However, by simultaneous interactions, recruits FYN which subsequently phosphorylates and activates SLAMF1. Positively regulates CD244/2B4- and CD84-mediated natural killer (NK) cell functions. Can also promote CD48-, SLAMF6 -, LY9-, and SLAMF7-mediated NK cell activation. In the context of NK cell-mediated cytotoxicity enhances conjugate formation with target cells (By similarity). May also regulate the activity of the neurotrophin receptors NTRK1, NTRK2 and NTRK3 (By similarity). Interacts with CD84, CD244, LY9, SLAMF1 and FYN. Interacts with NTRK1, NTRK2 and NTRK3 (By similarity). +Transferrins are iron binding transport proteins which bind Fe(3+) ion in association with the binding of an anion, usually bicarbonate. Belongs to the transferrin family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Required for assembly of dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes, which are responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella. Probably acts together with ccdc40 to form a molecular ruler that determines the 96 nanometer (nm) repeat length and arrangements of components in cilia and flagella. Not required for outer dynein arm complexes assembly. Belongs to the CCDC39 family. +Has E3 ubiquitin-protein ligase activity. In the absence of an external substrate, it can catalyze self-ubiquitination. Stimulates ubiquitination of potassium channel KCNJ1, enhancing it's dynamin-dependent and clathrin-independent endocytosis. Acts as a scaffold protein that coordinates with MAPK8IP1/JIP1 in organizing different components of the JNK pathway, including RAC1 or RAC2, MAP3K11/MLK3 or MAP3K7/TAK1, MAP2K7/MKK7, MAPK8/JNK1 and/or MAPK9/JNK2 into a functional multiprotein complex to ensure the effective activation of the JNK signaling pathway. Regulates the differentiation of CD4(+) and CD8(+) T-cells and promotes T-helper 1 (Th1) cell differentiation. Regulates the activation of MAPK8/JNK1 and MAPK9/JNK2 in CD4(+) T-cells and the activation of MAPK8/JNK1 in CD8(+) T-cells. Plays a crucial role in the migration of neocortical neurons in the developing brain. Controls proper cortical neuronal migration and the formation of proximal cytoplasmic dilation in the leading process (PCDLP) in migratory neocortical neurons by regulating the proper localization of activated RAC1 and F-actin assembly. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Interacts with RAC1; in a GTP-dependent manner. Interacts with MAP3K10/MLK2 and MAP3K11/MLK3. Interacts with MAPK8IP; this interaction leads to the PJAC complex (POSH-JIP or SH3RF1/MAPK8IP apoptotic complex) with a 1:1 ratio. Interacts with SIAH1. Interacts with HERP1. Probably part of a signaling complex that may contain SH3RF1, MAPK8IP, DLK1, MAP2K4/MKK4, MAP2K7/MKK7, MAPK8/JNK1, MAPK9/JNK2, AKT1 and AKT2. Found in a complex with RAC2, MAP3K7/TAK1, MAP2K7/MKK7, MAPK8IP1/JIP1, MAPK8/JNK1 and MAPK9/JNK2. Found in a complex with RAC1, MAP3K11/MLK3, MAP2K7/MKK7, MAPK8IP1/JIP1 and MAPK8/JNK1. Interacts with SH3RF2. Colocalizes, with AKT2, in lamellipodia. Colocalizes, with HERP1, in trans-Golgi network. The RING finger domain is required for ubiquitin ligase activity and autoubiquitination. Phosphorylated at Ser-304 by AKT1 and AKT2. When phosphorylated, it has reduced ability to bind Rac. Autoubiquitinated. Ubiquitinated by SH3RF2, leading to proteasome-mediated degradation. Belongs to the SH3RF family. +Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). H(+) + orotidine 5'-phosphate = CO2 + UMP Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. Homodimer. Belongs to the OMP decarboxylase family. Type 1 subfamily. +Acts as an antagonist to SinR. SinI prevents SinR from binding to its target sequence on the gene for AprE (By similarity). Heterodimer with SinR. +Putative taste receptor. TAS1R1/TAS1R3 responds to the umami taste stimulus (the taste of monosodium glutamate). TAS1R2/TAS1R3 recognizes diverse natural and synthetic sweeteners. TAS1R3 is essential for the recognition and response to the disaccharide trehalose (By similarity). Sequence differences within and between species can significantly influence the selectivity and specificity of taste responses. Forms homodimers or heterodimers with TAS1R1 and TAS1R2. Belongs to the G-protein coupled receptor 3 family. TAS1R subfamily. The taste experience - Issue 55 of February 2005 +Phospholipase that hydrolyzes phosphatidic acid, including 1,2-dioleoyl-sn-phosphatidic acid (PubMed:9488669). Required for the organization of the endoplasmic reticulum exit sites (ERES), also known as transitional endoplasmic reticulum (tER) (By similarity). 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O = (9Z)-octadecenoate + 2-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H(+) Forms homooligomers and, to a much smaller extent, heterooligomers with DDHD2. Interacts with SEC23A and SEC24C. The measured range is 1-835. Belongs to the PA-PLA1 family. +Belongs to the RemA family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate. (R)-pantoate + ATP + beta-alanine = (R)-pantothenate + AMP + diphosphate + H(+) Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantothenate from (R)-pantoate and beta-alanine: step 1/1. Homodimer. The reaction proceeds by a bi uni uni bi ping pong mechanism. Belongs to the pantothenate synthetase family. +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Binds 1 zinc ion per subunit. Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +Belongs to the MscS (TC 1.A.23) family. +a uridine in RNA = a pseudouridine in RNA Belongs to the pseudouridine synthase RluA family. +Belongs to the UPF0297 family. +Interconverts simultaneously and stereospecifically pyruvate and lactate with concomitant interconversion of NADH and NAD(+). (S)-lactate + NAD(+) = H(+) + NADH + pyruvate Fermentation; pyruvate fermentation to lactate; (S)-lactate from pyruvate: step 1/1. Homotetramer. Isolates from various regions of the US and Canada show some variations. PubMed:8105474 has sequenced LDH-B isolates called Florida 1A, 1B, 2A and 2B; Georgia 2A and 2B; Maine 2A; New Jersey 121A, 121B, 137A, 137B and 197B; Nova Scotia 1A, 1B, 2A and 2B. Belongs to the LDH/MDH superfamily. LDH family. +Probably functions as a manganese efflux pump. Belongs to the MntP (TC 9.B.29) family. +Catalyzes the radical-mediated synthesis of 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil from 5-amino-6-(D-ribitylamino)uracil and L-tyrosine. 5-amino-6-(D-ribitylamino)uracil + L-tyrosine + S-adenosyl-L-methionine = 2-iminoacetate + 5'-deoxyadenosine + 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil + H(+) + L-methionine Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; coenzyme F0 biosynthesis. Consists of two subunits, CofG and CofH. Belongs to the radical SAM superfamily. CofH family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +Scaffold protein that may play a role in cell adhesion, cell spreading and in the reorganization of the actin cytoskeleton. Plays a role in the regulation of cell proliferation. May act as a tumor suppressor. Inhibits tumor cell growth. Interacts via LIM domain 1 with ZYX. Interacts (via LIM domain 3) with ENAH and VASP. Interacts with ALKBH4, talin, actin, alpha-actinin, GRIP1 and PXN. Interacts (via LIM domain 2) with ACTL7A (via N-terminus). Heterodimer with ACTL7A; the heterodimer interacts with ENAH to form a heterotrimer. Detected along actin stress fibers. Ubiquitous. The N-terminal and the C-terminal halves of the protein can associate with each other, thereby hindering interactions with ZYX. Belongs to the prickle / espinas / testin family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the LeuD family. LeuD type 1 subfamily. +Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol. 2 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) = a cardiolipin + glycerol Belongs to the phospholipase D family. Cardiolipin synthase subfamily. ClsA sub-subfamily. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate. ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterodimer of GatD and GatE. Belongs to the GatB/GatE family. GatE subfamily. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +The physiological role of BioH is to remove the methyl group introduced by BioC when the pimeloyl moiety is complete. It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway through the hydrolysis of the ester bonds of pimeloyl-ACP esters. 6-carboxyhexanoyl-[ACP] methyl ester + H2O = 6-carboxyhexanoyl-[ACP] + H(+) + methanol Cofactor biosynthesis; biotin biosynthesis. Monomer. Belongs to the AB hydrolase superfamily. Carboxylesterase BioH family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Glutarylation at Lys-92 (H4K91glu) destabilizes nucleosomes by promoting dissociation of the H2A-H2B dimers from nucleosomes. Belongs to the histone H4 family. +Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA and the activity is stimulated by poly(A)-binding protein PAB1. PAN deadenylation is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping and subsequent 5'-3' exonucleolytic degradation by XRN1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails. Exonucleolytic cleavage of poly(A) to 5'-AMP. Binds 2 metal cations per subunit in the catalytic exonuclease domain. Positively regulated by the regulatory subunit PAN3. Forms a heterotrimer with an asymmetric homodimer of the regulatory subunit PAN3 to form the poly(A)-nuclease (PAN) deadenylation complex. Contains a pseudo-UCH domain. This ubiquitin C-terminal hydrolase (UCH)-like or ubiquitin specific protease (USP)-like domain is predicted to be catalytically inactive because it lacks the active site catalytic triad characteristic of thiol proteases, with residues at the equivalent structural positions that are incompatible with catalysis, and it cannot bind ubiquitin. It functions as a structural scaffold for intra- and intermolecular interactions in the complex. The linker, or PAN3 interaction domain (PID), between the WD40 repeats and the pseudo-UCH domain mediates interaction with PAN3. Belongs to the peptidase C19 family. PAN2 subfamily. +ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA (By similarity). ATP + H2O = ADP + H(+) + phosphate The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis. Belongs to the DEAD box helicase family. DDX48/FAL1 subfamily. +Involved in the cytoplasmic maturation steps of pre-60S ribosomal particles by promoting the release of shuttling protein RSL24D1/RLP24 from the pre-ribosomal particles. +Down-regulates transcriptional activation by nuclear receptors, such as NR1F2. Interacts with NR1F2, RARA and THRB in a ligand-dependent manner. Expression is restricted to the central nervous system (neurons in the dentate gyrus of the hippocampus, the amygdala, thalamic and hypothalamic regions). +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Mu-conotoxins block voltage-gated sodium channels. This toxin reversibly blocks voltage-gated sodium channel in cephalopods, with no alteration in the voltage dependence of sodium conductance or on the kinetics of inactivation (By similarity). Expressed by the venom duct. The cysteine framework is XII (C-C-C-C-CC-C-C). +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate from glycerone phosphate: step 1/1. Homodimer. Belongs to the triosephosphate isomerase family. +Central component of the spindle assembly checkpoint. Belongs to the MAD1 family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Partially overlaps MES1. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Nuclear transcriptional activator of viral gene expression, that is essential for viral transcription from the LTR promoter and replication. Acts as a sequence-specific molecular adapter, directing components of the cellular transcription machinery to the viral RNA to promote processive transcription elongation by the RNA polymerase II (RNA pol II) complex, thereby increasing the level of full-length transcripts. In the absence of Tat, the RNA Pol II generates short or non-processive transcripts that terminate at approximately 60 bp from the initiation site. Tat associates with the CCNT1/cyclin-T1 component of the P-TEFb complex (CDK9 and CCNT1), which promotes RNA chain elongation. This binding increases Tat's affinity for a hairpin structure at the 5'-end of all nascent viral mRNAs referred to as the transactivation responsive RNA element (TAR RNA) and allows Tat/P-TEFb complex to bind cooperatively to TAR RNA. The CDK9 component of P-TEFb and other Tat-activated kinases hyperphosphorylate the C-terminus of RNA Pol II that becomes stabilized and much more processive. Other factors such as HTATSF1/Tat-SF1, SUPT5H/SPT5, and HTATIP2 are also important for Tat's function. Besides its effect on RNA Pol II processivity, Tat induces chromatin remodeling of proviral genes by recruiting the histone acetyltransferases (HATs) CREBBP, EP300 and PCAF to the chromatin. This also contributes to the increase in proviral transcription rate, especially when the provirus integrates in transcriptionally silent region of the host genome. To ensure maximal activation of the LTR, Tat mediates nuclear translocation of NF-kappa-B by interacting with host RELA. Through its interaction with host TBP, Tat may also modulate transcription initiation. Tat can reactivate a latently infected cell by penetrating in it and transactivating its LTR promoter. In the cytoplasm, Tat is thought to act as a translational activator of HIV-1 mRNAs. Extracellular circulating Tat can be endocytosed by surrounding uninfected cells via the binding to several surface receptors such as CD26, CXCR4, heparan sulfate proteoglycans (HSPG) or LDLR. Neurons are rarely infected, but they internalize Tat via their LDLR. Through its interaction with nuclear HATs, Tat is potentially able to control the acetylation-dependent cellular gene expression. Modulates the expression of many cellular genes involved in cell survival, proliferation or in coding for cytokines or cytokine receptors. Tat plays a role in T-cell and neurons apoptosis. Tat induced neurotoxicity and apoptosis probably contribute to neuroAIDS. Circulating Tat also acts as a chemokine-like and/or growth factor-like molecule that binds to specific receptors on the surface of the cells, affecting many cellular pathways. In the vascular system, Tat binds to ITGAV/ITGB3 and ITGA5/ITGB1 integrins dimers at the surface of endothelial cells and competes with bFGF for heparin-binding sites, leading to an excess of soluble bFGF. Interacts with host CCNT1. Associates with the P-TEFb complex composed at least of Tat, P-TEFb (CDK9 and CCNT1), TAR RNA, RNA Pol II. Recruits the HATs CREBBP, TAF1/TFIID, EP300, PCAF and GCN5L2. Interacts with host KAT5/Tip60; this interaction targets the latter to degradation. Interacts with the host deacetylase SIRT1. Interacts with host capping enzyme RNGTT; this interaction stimulates RNGTT. Binds to host KDR, and to the host integrins ITGAV/ITGB3 and ITGA5/ITGB1. Interacts with host KPNB1/importin beta-1 without previous binding to KPNA1/importin alpha-1. Interacts with EIF2AK2. Interacts with host nucleosome assembly protein NAP1L1; this interaction may be required for the transport of Tat within the nucleus, since the two proteins interact at the nuclear rim. Interacts with host C1QBP/SF2P32; this interaction involves lysine-acetylated Tat. Interacts with the host chemokine receptors CCR2, CCR3 and CXCR4. Interacts with host DPP4/CD26; this interaction may trigger an anti-proliferative effect. Interacts with host LDLR. Interacts with the host extracellular matrix metalloproteinase MMP1. Interacts with host PRMT6; this interaction mediates Tat's methylation. Interacts with, and is ubiquitinated by MDM2/Hdm2. Interacts with host PSMC3 and HTATIP2. Interacts with STAB1; this interaction may overcome SATB1-mediated repression of IL2 and IL2RA (interleukin) in T cells by binding to the same domain than HDAC1. Interacts (when acetylated) with human CDK13, thereby increasing HIV-1 mRNA splicing and promoting the production of the doubly spliced HIV-1 protein Nef.Interacts with host TBP; this interaction modulates the activity of transcriptional pre-initiation complex. Interacts with host RELA. Probably localizes to both nuclear and nucleolar compartments. Nuclear localization is mediated through the interaction of the nuclear localization signal with importin KPNB1. Secretion occurs through a Golgi-independent pathway. Tat is released from infected cells to the extracellular space where it remains associated to the cell membrane, or is secreted into the cerebrospinal fluid and sera. Extracellular Tat can be endocytosed by surrounding uninfected cells via binding to several receptors depending on the cell type. The cell attachment site mediates the interaction with ITGAV/ITGB3 and ITGA5/ITGB1 integrins, leading to vascular cell migration and invasion. This interaction also provides endothelial cells with the adhesion signal they require to grow in response to mitogens. The Cys-rich region may bind 2 zinc ions. This region is involved in binding to KAT5. The transactivation domain mediates the interaction with CCNT1, GCN5L2, and MDM2. The Arg-rich RNA-binding region binds the TAR RNA. This region also mediates the nuclear localization through direct binding to KPNB1 and is involved in Tat's transfer across cell membranes (protein transduction). The same region is required for the interaction with EP300, PCAF, EIF2AK2 and KDR. Asymmetrical arginine methylation by host PRMT6 seems to diminish the transactivation capacity of Tat and affects the interaction with host CCNT1. Acetylation by EP300, CREBBP, GCN5L2/GCN5 and PCAF regulates the transactivation activity of Tat. EP300-mediated acetylation of Lys-50 promotes dissociation of Tat from the TAR RNA through the competitive binding to PCAF's bromodomain. In addition, the non-acetylated Tat's N-terminus can also interact with PCAF. PCAF-mediated acetylation of Lys-28 enhances Tat's binding to CCNT1. Lys-50 is deacetylated by SIRT1. Polyubiquitination by host MDM2 does not target Tat to degradation, but activates its transactivation function and fosters interaction with CCNT1 and TAR RNA. Phosphorylated by EIF2AK2 on serine and threonine residues adjacent to the basic region important for TAR RNA binding and function. Phosphorylation of Tat by EIF2AK2 is dependent on the prior activation of EIF2AK2 by dsRNA. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Expressed in the late stage of the infection cycle, when unspliced viral RNAs are exported to the cytoplasm by the viral Rev protein. Belongs to the lentiviruses Tat family. +Required for assembly of cytochrome c oxidase (complex IV). Component of 250-400 kDa complexes called cytochrome oxidase assembly intermediates or COA complexes. Belongs to the COA3 family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +Part of the capsid inner membrane. +GTP-binding protein involved in transport from the endoplasmic reticulum to the Golgi apparatus. Activated by the guanine nucleotide exchange factor PREB. Involved in the selection of the protein cargo and the assembly of the COPII coat complex (By similarity). Synergizes with the cargo receptor SURF4 to mediate the export of lipoproteins from the endoplasmic reticulum, thereby regulating lipoprotein delivery and the maintenance of lipid homeostasis (By similarity). Homodimer. Binds PREB. Part of the COPII coat complex. Binds to the cytoplasmic tails of target proteins in the endoplasmic reticulum (By similarity). Interacts with SURF4 (By similarity). Associated with the endoplasmic reticulum and Golgi stacks, in particular in the juxta-nuclear Golgi region. Belongs to the small GTPase superfamily. SAR1 family. +Catalyzes the phosphorolysis of diverse nucleosides, yielding D-ribose 1-phosphate and the respective free bases. Can use uridine, adenosine, guanosine, cytidine, thymidine, inosine and xanthosine as substrates. Also catalyzes the reverse reactions. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha-D-ribose 1-phosphate adenosine + phosphate = adenine + alpha-D-ribose 1-phosphate cytidine + phosphate = alpha-D-ribose 1-phosphate + cytosine guanosine + phosphate = alpha-D-ribose 1-phosphate + guanine inosine + phosphate = alpha-D-ribose 1-phosphate + hypoxanthine phosphate + thymidine = 2-deoxy-alpha-D-ribose 1-phosphate + thymine phosphate + uridine = alpha-D-ribose 1-phosphate + uracil phosphate + xanthosine = alpha-D-ribose 1-phosphate + xanthine Belongs to the nucleoside phosphorylase PpnP family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Serine/threonine kinase which acts as an essential component of the MAP kinase signal transduction pathway. MAPK14 is one of the four p38 MAPKs which play an important role in the cascades of cellular responses evoked by extracellular stimuli such as pro-inflammatory cytokines or physical stress leading to direct activation of transcription factors. Accordingly, p38 MAPKs phosphorylate a broad range of proteins and it has been estimated that they may have approximately 200 to 300 substrates each. Some of the targets are downstream kinases which are activated through phosphorylation and further phosphorylate additional targets. RPS6KA5/MSK1 and RPS6KA4/MSK2 can directly phosphorylate and activate transcription factors such as CREB1, ATF1, the NF-kappa-B isoform RELA/NFKB3, STAT1 and STAT3, but can also phosphorylate histone H3 and the nucleosomal protein HMGN1. RPS6KA5/MSK1 and RPS6KA4/MSK2 play important roles in the rapid induction of immediate-early genes in response to stress or mitogenic stimuli, either by inducing chromatin remodeling or by recruiting the transcription machinery. On the other hand, two other kinase targets, MAPKAPK2/MK2 and MAPKAPK3/MK3, participate in the control of gene expression mostly at the post-transcriptional level, by phosphorylating ZFP36 (tristetraprolin) and ELAVL1, and by regulating EEF2K, which is important for the elongation of mRNA during translation. MKNK1/MNK1 and MKNK2/MNK2, two other kinases activated by p38 MAPKs, regulate protein synthesis by phosphorylating the initiation factor EIF4E2. MAPK14 interacts also with casein kinase II, leading to its activation through autophosphorylation and further phosphorylation of TP53/p53. In the cytoplasm, the p38 MAPK pathway is an important regulator of protein turnover. For example, CFLAR is an inhibitor of TNF-induced apoptosis whose proteasome-mediated degradation is regulated by p38 MAPK phosphorylation. In a similar way, MAPK14 phosphorylates the ubiquitin ligase SIAH2, regulating its activity towards EGLN3. MAPK14 may also inhibit the lysosomal degradation pathway of autophagy by interfering with the intracellular trafficking of the transmembrane protein ATG9. Another function of MAPK14 is to regulate the endocytosis of membrane receptors by different mechanisms that impinge on the small GTPase RAB5A. In addition, clathrin-mediated EGFR internalization induced by inflammatory cytokines and UV irradiation depends on MAPK14-mediated phosphorylation of EGFR itself as well as of RAB5A effectors. Ectodomain shedding of transmembrane proteins is regulated by p38 MAPKs as well. In response to inflammatory stimuli, p38 MAPKs phosphorylate the membrane-associated metalloprotease ADAM17. Such phosphorylation is required for ADAM17-mediated ectodomain shedding of TGF-alpha family ligands, which results in the activation of EGFR signaling and cell proliferation. Another p38 MAPK substrate is FGFR1. FGFR1 can be translocated from the extracellular space into the cytosol and nucleus of target cells, and regulates processes such as rRNA synthesis and cell growth. FGFR1 translocation requires p38 MAPK activation. In the nucleus, many transcription factors are phosphorylated and activated by p38 MAPKs in response to different stimuli. Classical examples include ATF1, ATF2, ATF6, ELK1, PTPRH, DDIT3, TP53/p53 and MEF2C and MEF2A. The p38 MAPKs are emerging as important modulators of gene expression by regulating chromatin modifiers and remodelers. The promoters of several genes involved in the inflammatory response, such as IL6, IL8 and IL12B, display a p38 MAPK-dependent enrichment of histone H3 phosphorylation on 'Ser-10' (H3S10ph) in LPS-stimulated myeloid cells. This phosphorylation enhances the accessibility of the cryptic NF-kappa-B-binding sites marking promoters for increased NF-kappa-B recruitment. Phosphorylates CDC25B and CDC25C which is required for binding to 14-3-3 proteins and leads to initiation of a G2 delay after ultraviolet radiation. Phosphorylates TIAR following DNA damage, releasing TIAR from GADD45A mRNA and preventing mRNA degradation. The p38 MAPKs may also have kinase-independent roles, which are thought to be due to the binding to targets in the absence of phosphorylation. Protein O-Glc-N-acylation catalyzed by the OGT is regulated by MAPK14, and, although OGT does not seem to be phosphorylated by MAPK14, their interaction increases upon MAPK14 activation induced by glucose deprivation. This interaction may regulate OGT activity by recruiting it to specific targets such as neurofilament H, stimulating its O-Glc-N-acylation. Required in mid-fetal development for the growth of embryo-derived blood vessels in the labyrinth layer of the placenta. Also plays an essential role in developmental and stress-induced erythropoiesis, through regulation of EPO gene expression. Phosphorylates S100A9 at 'Thr-113' (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by cell stresses such as DNA damage, heat shock, osmotic shock, anisomycin and sodium arsenite, as well as pro-inflammatory stimuli such as bacterial lipopolysaccharide (LPS) and interleukin-1. Activation occurs through dual phosphorylation of Thr-180 and Tyr-182 by either of two dual specificity kinases, MAP2K3/MKK3 or MAP2K6/MKK6, and potentially also MAP2K4/MKK4, as well as by TAB1-mediated autophosphorylation. MAPK14 phosphorylated on both Thr-180 and Tyr-182 is 10-20-fold more active than MAPK14 phosphorylated only on Thr-180, whereas MAPK14 phosphorylated on Tyr-182 alone is inactive. whereas Thr-180 is necessary for catalysis, Tyr-182 may be required for auto-activation and substrate recognition. Phosphorylated at Tyr-323 by ZAP70 in an alternative activation pathway in response to TCR signaling in T-cells. This alternative pathway is inhibited by GADD45A. Inhibited by dual specificity phosphatases, such as DUSP1, DUSP10, and DUSP16. Specifically inhibited by the binding of pyridinyl-imidazole compounds, which are cytokine-suppressive anti-inflammatory drugs (CSAID). SB203580 is an inhibitor of MAPK14. Component of a signaling complex containing at least AKAP13, PKN1, MAPK14, ZAK and MAP2K3. Within this complex, AKAP13 interacts directly with PKN1, which in turn recruits MAPK14, MAP2K3 and ZAK (By similarity). Binds to a kinase interaction motif within the protein tyrosine phosphatase, PTPRR (By similarity). This interaction retains MAPK14 in the cytoplasm and prevents nuclear accumulation (By similarity). Interacts with SPAG9 and GADD45A (By similarity). Interacts with CDC25B, CDC25C, DUSP1, DUSP10, DUSP16, NP60, SUPT20H and TAB1. Interacts with casein kinase II subunits CSNK2A1 and CSNK2B. Interacts with PPM1D. Interacts with CDK5RAP3; recruits PPM1D to MAPK14 and may regulate its dephosphorylation (By similarity). Interacts with DUSP2; this interaction does not lead to catalytic activation of DUSP2 and dephosphrylation of MAPK14 (PubMed:16288922). Macrophages, monocytes, T- and B-lymphocytes. Isoform 2 is specifically expressed in kidney and liver. The TXY motif contains the threonine and tyrosine residues whose phosphorylation activates the MAP kinases. Dually phosphorylated on Thr-180 and Tyr-182 by the MAP2Ks MAP2K3/MKK3, MAP2K4/MKK4 and MAP2K6/MKK6 in response to inflammatory cytokines, environmental stress or growth factors, which activates the enzyme. Dual phosphorylation can also be mediated by TAB1-mediated autophosphorylation. TCR engagement in T-cells also leads to Tyr-323 phosphorylation by ZAP70. Dephosphorylated and inactivated by DUPS1, DUSP10 and DUSP16. PPM1D also mediates dephosphorylation and inactivation of MAPK14 (By similarity). Acetylated at Lys-53 and Lys-152 by KAT2B and EP300. Acetylation at Lys-53 increases the affinity for ATP and enhances kinase activity. Lys-53 and Lys-152 are deacetylated by HDAC3 (By similarity). Ubiquitinated. Ubiquitination leads to degradation by the proteasome pathway (By similarity). Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. MAP kinase subfamily. +Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP). diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 1/2. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrE subfamily. +Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ). 5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphooxyethyl)-thiazole + ADP + H(+) Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-methyl-5-(2-phosphoethyl)-thiazole from 5-(2-hydroxyethyl)-4-methylthiazole: step 1/1. Belongs to the Thz kinase family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily. Extended N-terminus. +Involved in the synthesis of meso-diaminopimelate (m-DAP or DL-DAP), required for both lysine and peptidoglycan biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate. (2S,6S)-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydrodipicolinate + H(+) + H2O + L-glutamate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route): step 1/1. Homodimer. Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. LL-diaminopimelate aminotransferase subfamily. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. ATP + NAD(+) = ADP + H(+) + NADP(+) Belongs to the NAD kinase family. +Plays an important role in the de novo pathway and in the salvage pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP (By similarity). GTP + IMP + L-aspartate = GDP + 2 H(+) + N(6)-(1,2-dicarboxyethyl)-AMP + phosphate Binds 1 Mg(2+) ion per subunit. Purine metabolism; AMP biosynthesis via de novo pathway; AMP from IMP: step 1/2. Homodimer. Belongs to the adenylosuccinate synthetase family. +Methionine-sulfoxide reductase that specifically reduces methionine (R)-sulfoxide back to methionine. While in many cases, methionine oxidation is the result of random oxidation following oxidative stress, methionine oxidation is also a post-translational modification that takes place on specific residue. Acts as a regulator of actin assembly by reducing methionine (R)-sulfoxide mediated by MICALs (MICAL1, MICAL2 or MICAL3) on actin, thereby promoting filament repolymerization. Plays a role in innate immunity by reducing oxidized actin, leading to actin repolymerization in macrophages. [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(R)-S-oxide-[protein] [thioredoxin]-disulfide + H2O + L-methionine = [thioredoxin]-dithiol + L-methionine (R)-S-oxide Binds 1 zinc ion per subunit. Truncated MSRB1/SEPX1 proteins produced by failed UGA/Sec decoding are ubiquitinated by the CRL2(FEM1C) E3 ubiquitin-protein ligase complex. Belongs to the MsrB Met sulfoxide reductase family. Truncated C-terminus. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Feedback inhibited by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Belongs to the ATP phosphoribosyltransferase family. Long subfamily. +Belongs to the eukaryotic ribosomal protein eS6 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Pectinolytic enzymes consist of four classes of enzymes: pectin lyase, polygalacturonase, pectin methylesterase and rhamnogalacturonase. Among pectinolytic enzymes, pectin lyase is the most important in depolymerization of pectin, since it cleaves internal glycosidic bonds of highly methylated pectins (By similarity). Eliminative cleavage of (1->4)-alpha-D-galacturonan methyl ester to give oligosaccharides with 4-deoxy-6-O-methyl-alpha-D-galact-4-enuronosyl groups at their non-reducing ends. Belongs to the polysaccharide lyase 1 family. +Catalyzes the covalent attachment of the prokaryotic ubiquitin-like protein modifier Pup to the proteasomal substrate proteins, thereby targeting them for proteasomal degradation. This tagging system is termed pupylation. The ligation reaction involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a substrate lysine. ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N(6)-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine. Protein degradation; proteasomal Pup-dependent pathway. Protein modification; protein pupylation. The reaction mechanism probably proceeds via the activation of Pup by phosphorylation of its C-terminal glutamate, which is then subject to nucleophilic attack by the substrate lysine, resulting in an isopeptide bond and the release of phosphate as a good leaving group. Belongs to the Pup ligase/Pup deamidase family. Pup-conjugating enzyme subfamily. +May play a role in filopodium movement. Belongs to the CFAP53 family. +Dermonecrotic toxins cleave the phosphodiester linkage between the phosphate and headgroup of certain phospholipids (sphingolipid and lysolipid substrates), forming an alcohol (often choline) and a cyclic phosphate (By similarity). This toxin acts on sphingomyelin (SM) (By similarity). It may also act on ceramide phosphoethanolamine (CPE), lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE), but not on lysophosphatidylserine (LPS), and lysophosphatidylglycerol (LPG) (By similarity). It acts by transphosphatidylation, releasing exclusively cyclic phosphate products as second products (By similarity). Induces dermonecrosis, hemolysis, increased vascular permeability, edema, inflammatory response, and platelet aggregation (By similarity). an N-(acyl)-sphingosylphosphocholine = an N-(acyl)-sphingosyl-1,3-cyclic phosphate + choline an N-(acyl)-sphingosylphosphoethanolamine = an N-(acyl)-sphingosyl-1,3-cyclic phosphate + ethanolamine a 1-acyl-sn-glycero-3-phosphocholine = a 1-acyl-sn-glycero-2,3-cyclic phosphate + choline a 1-acyl-sn-glycero-3-phosphoethanolamine = a 1-acyl-sn-glycero-2,3-cyclic phosphate + ethanolamine Binds 1 Mg(2+) ion per subunit. Expressed by the venom gland. Belongs to the arthropod phospholipase D family. Class II subfamily. The most common activity assay for dermonecrotic toxins detects enzymatic activity by monitoring choline release from substrate. Liberation of choline from sphingomyelin (SM) or lysophosphatidylcholine (LPC) is commonly assumed to result from substrate hydrolysis, giving either ceramide-1-phosphate (C1P) or lysophosphatidic acid (LPA), respectively, as a second product. However, two studies from Lajoie and colleagues (2013 and 2015) report the observation of exclusive formation of cyclic phosphate products as second products, resulting from intramolecular transphosphatidylation. Cyclic phosphates have vastly different biological properties from their monoester counterparts, and they may be relevant to the pathology of brown spider envenomation. +Involved in the degradation of phospho-AI-2, thereby terminating induction of the lsr operon and closing the AI-2 signaling cycle. Catalyzes the conversion of (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione (P-DPD) to 3-hydroxy-5-phosphonooxypentane-2,4-dione (P-HPD). (2S)-2-hydroxy-3,4-dioxopentyl phosphate = 3-hydroxy-2,4-dioxopentyl phosphate Homodimer. Belongs to the LsrG family. +Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Binds 2 divalent ions per subunit. Binds 1 potassium ion per subunit. Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Homotetramer; dimer of dimers. Belongs to the AdoMet synthase family. +Belongs to the AB hydrolase superfamily. AB hydrolase 4 family. +Belongs to the universal ribosomal protein uL29 family. +Belongs to the bacterial ribosomal protein bL34 family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr). L-histidyl-[protein] + phosphoenolpyruvate = N(pros)-phospho-L-histidyl-[protein] + pyruvate Homodimer. The N-terminal domain contains the HPr binding site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the pyruvate binding site. The reaction takes place in three steps, mediated by a phosphocarrier histidine residue located on the surface of the central domain. The two first partial reactions are catalyzed at an active site located on the N-terminal domain, and the third partial reaction is catalyzed at an active site located on the C-terminal domain. For catalytic turnover, the central domain swivels from the concave surface of the N-terminal domain to that of the C-terminal domain. Belongs to the PEP-utilizing enzyme family. +Catalyzes the desaturation of acyl-CoAs to 2-trans-enoyl-CoAs. First enzyme of the fatty acid beta-oxidation pathway. a 2,3-saturated acyl-CoA + O2 = a (2E)-enoyl-CoA + H2O2 Belongs to the acyl-CoA oxidase family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the 50S ribosomal subunit. Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Forms a heptameric L10(L12)2(L12)2(L12)2 complex, where L10 forms an elongated spine to which the L12 dimers bind in a sequential fashion. Belongs to the universal ribosomal protein uL10 family. +Co-chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Seems to help targeting proteins to be folded toward HscA. Interacts with HscA and stimulates its ATPase activity. Interacts with IscU. Belongs to the HscB family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Catalyzes the specific phosphorylation of arginine residues in a large number of proteins. Is part of the bacterial stress response system. Protein arginine phosphorylation has a physiologically important role and is involved in the regulation of many critical cellular processes, such as protein homeostasis, motility, competence, and stringent and stress responses, by regulating gene expression and protein activity. ATP + L-arginyl-[protein] = ADP + H(+) + N(omega)-phospho-L-arginyl-[protein] Appears to be allosterically activated by the binding of pArg-containing polypeptides to the pArg-binding pocket localized in the C-terminal domain of McsB. Belongs to the ATP:guanido phosphotransferase family. +Allows bacterial pathogens to use the host heme as an iron source. Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring to the oxo-bilirubin chromophore staphylobilin (a mixture of the linear tetrapyrroles 5-oxo-delta-bilirubin and 15-oxo-beta-bilirubin) in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron. 5 AH2 + 2 H(+) + heme b + 4 O2 = 5 A + delta-staphylobilin + Fe(2+) + formaldehyde + 4 H2O 5 AH2 + 2 H(+) + heme b + 4 O2 = 5 A + beta-staphylobilin + Fe(2+) + formaldehyde + 4 H2O Homodimer. Belongs to the antibiotic biosynthesis monooxygenase family. Heme-degrading monooxygenase IsdG subfamily. +Endosomal protein that may be involved in endocytosis (PubMed:16103374). Involved in the trafficking of proteins from prevacuolar compartments (PVCs) to vacuoles (PubMed:23682115, PubMed:24824487). May activate the MON1-CCZ1 complex which acts as guanine nucleotide exchange factors (GEF) for Rab7 protein family, and serves as a link between Rab5 and Rab7 families in PVCs, and mediates PVC maturation (PubMed:24824487). Involved in vacuolar transport of storage proteins with EREX as effector. Regulates membrane trafficking to protein storage vacuoles (PSVs) (PubMed:27288222). Regulated by guanine nucleotide exchange factors (GEFs) which promote the exchange of bound GDP for free GTP. Interacts with VPS9A homodimer (PubMed:18055610, PubMed:20833725). Interacts with TCTP1 (PubMed:20736351). Interacts with MON1 (PubMed:24824487). Interacts with EREX (via PX domain) (PubMed:27288222). Binds to VPS3 (PubMed:29463724). Strong co-localization with VPS3 and VPS18 in cytoplasmic puncta. Expressed in roots and actively dividing cells. Expressed during pollen germination and pollen tube growth. Activated by VPS9A. Over-expression of the constitutively active GTP-bound mutant of Leu-69 induces the formation of large ring-like structures of 1-2 micrometers in diameter. Belongs to the small GTPase superfamily. Rab family. +Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P). an N-acyl-D-glucosamine 6-phosphate = an N-acyl-D-mannosamine 6-phosphate Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 3/5. Belongs to the NanE family. +Usually encoded in the trnK tRNA gene intron. Probably assists in splicing its own and other chloroplast group II introns. Belongs to the intron maturase 2 family. MatK subfamily. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. This subunit is found at the monomer-monomer interface and is required for correct PSII assembly and/or dimerization. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbL family. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +Global transcriptional regulator that plays a key role in stress response and exerts either positive or negative regulation of genes. Acts by interacting with the C-terminal domain of the alpha subunit of the RNA polymerase (RNAP). This interaction can enhance binding of RNAP to the promoter region of target genes and stimulate their transcription, or block interaction of RNAP with activator. Interacts with the C-terminal domain of the alpha subunit of the RNAP. Belongs to the ArsC family. Spx subfamily. +Belongs to the UPF0223 family. +Probable neurotoxin with unknown target. Possibly targets ion channels. Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser) ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec) Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. Homodimer. The tRNA molecule binds across the dimer. Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily. +Catalyzes the dehydration of methylthioribulose-1-phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P). S-methyl-5-thio-D-ribulose 1-phosphate = 5-methylsulfanyl-2,3-dioxopentyl phosphate + H2O Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 2/6. Homotetramer. Belongs to the aldolase class II family. MtnB subfamily. +Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. Binds 3 Zn(2+) ions. Belongs to the AP endonuclease 2 family. +Member of the two-component regulatory system CitT/CitS. Phosphorylated by CitS. +May play a role in hematopoietic cell proliferation or differentiation. Potential mediator of neuronal apoptosis. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by phosphorylation on Thr-173. Ubiquitously expressed in all tissues examined with highest levels in the brain and testis. Strongly expressed in the pyramidal and granule neurons of the hippocampus and also in the cerebellum. Weakly expressed in the cerebellum by E20, levels increase until 28 days after birth. Autophosphorylated. Phosphorylation on Thr-173 by STK11/LKB1 in complex with STE20-related adapter-alpha (STRADA) pseudo kinase and CAB39 (By similarity). Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system. The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon. Belongs to the TatA/E family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Belongs to the UPF0259 family. +A number of isoforms are produced. According to EST sequences. Belongs to the eukaryotic ribosomal protein eS10 family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex. Belongs to the complex I 30 kDa subunit family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Plays a role in regulating the structure of the Golgi apparatus. Interacts with DLG1 (PubMed:11602598). Interacts with ARF6 (GTP-bound form) (By similarity). Recruited to tight junctions (TJ) during late stages of maturation of the TJ complexes. Excluded from adherens junctions and desmosomes. Ubiquitously expressed. +Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine. [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(S)-S-oxide-[protein] [thioredoxin]-disulfide + H2O + L-methionine = [thioredoxin]-dithiol + L-methionine (S)-S-oxide Belongs to the MsrA Met sulfoxide reductase family. +Catalyzes the phosphorylation of D-glycero-D-manno-heptose 7-phosphate at the C-1 position to selectively form D-glycero-beta-D-manno-heptose-1,7-bisphosphate. Catalyzes the ADP transfer from ATP to D-glycero-beta-D-manno-heptose 1-phosphate, yielding ADP-D-glycero-beta-D-manno-heptose. ATP + D-glycero-beta-D-manno-heptose 7-phosphate = ADP + D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H(+) ATP + D-glycero-beta-D-manno-heptose 1-phosphate + H(+) = ADP-D-glycero-beta-D-manno-heptose + diphosphate Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate: step 1/4. Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate: step 3/4. Homodimer. In the N-terminal section; belongs to the carbohydrate kinase PfkB family. In the C-terminal section; belongs to the cytidylyltransferase family. +Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. PetG is required for either the stability or assembly of the cytochrome b6-f complex. The 4 large subunits of the cytochrome b6-f complex are cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are PetG, PetL, PetM and PetN. The complex functions as a dimer. Belongs to the PetG family. +Belongs to the SCO1/2 family. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. Heterodimer of HisH and HisF. Belongs to the HisA/HisF family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity (By similarity). Belongs to the universal ribosomal protein uS4 family. +Secreted subtilisin-like serine protease with keratinolytic activity that contributes to pathogenicity. Belongs to the peptidase S8 family. +GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel. Binds UBQLN1 (By similarity). Generally pentameric. There are five types of GABA(A) receptor chains: alpha, beta, gamma, delta, and rho. Belongs to the ligand-gated ion channel (TC 1.A.9) family. Gamma-aminobutyric acid receptor (TC 1.A.9.5) subfamily. GABRA6 sub-subfamily. Forbidden fruit - Issue 56 of March 2005 +Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S pre-initiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B. EIF2S1/eIF-2-alpha is a key component of the integrated stress response (ISR), required for adaptation to various stress: phosphorylation by metabolic-stress sensing protein kinases in response to stress converts EIF2S1/eIF-2-alpha in a global protein synthesis inhibitor, leading to a attenuation of cap-dependent translation, while concomitantly initiating the preferential translation of ISR-specific mRNAs, such as the transcriptional activators ATF4 and QRICH1. Activity is regulated by phosphorylation at Ser-49 and Ser-52, which stabilizes the eIF-2/GDP/eIF-2B complex and prevents the eIF-2B-mediated exchange of GDP for GTP, thereby preventing the formation of the 43S pre-initiation complex (PIC). This results in the global attenuation of 5' cap-dependent protein synthesis and concomitant translation of ISR-specific mRNAs that contain a short upstream open reading frame (uORF) in their 5' UTR. Heterotrimer composed of an alpha, a beta and a gamma chain. Phosphorylation at Ser-49 and Ser-52 stabilizes the eIF-2/GDP/eIF-2B complex and prevents GDP/GTP exchange reaction, thus impairing the recycling of eIF-2 between successive rounds of initiation and leading to global inhibition of translation, while concomitantly initiating the preferential translation of integrated stress response (ISR)-specific mRNAs. Belongs to the eIF-2-alpha family. Truncated C-terminus. +S-adenosyl-L-methionine + a thiopurine = S-adenosyl-L-homocysteine + a thiopurine S-methylether. Belongs to the class I-like SAM-binding methyltransferase superfamily. TPMT family. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Belongs to the UPF0301 (AlgH) family. +Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. ATP + dTMP = ADP + dTDP Belongs to the thymidylate kinase family. +Tuberculosinyl transferase that catalyzes the condensation of adenosine and tuberculosinyl diphosphate (TbPP) to generate 1-tuberculosinyladenosine (1-TbAd), which acts as an antiacid that directly protects M.tuberculosis from acid pH and physically remodels M.tuberculosis phagolysosomes (PubMed:24516143, PubMed:31427817). In addition, acts as a phosphatase that catalyzes the diphosphate-removal from TbPP to produce both tuberculosinol (TOH) and isotuberculosinol (iso-TOH) (PubMed:21228491, PubMed:24475925). Has broad substrate specificity, and can also use the 3 labdadienyl diphosphates, copalyl diphosphate (CDP), ent-CDP and syn-CDP in vitro (PubMed:21290071). adenosine + H(+) + tuberculosinyl diphosphate = 1-tuberculosinyladenosine + diphosphate H2O + tuberculosinyl diphosphate = diphosphate + tuberculosinol H2O + tuberculosinyl diphosphate = (13R)-edaxadiene + diphosphate H2O + tuberculosinyl diphosphate = (13S)-edaxadiene + diphosphate (+)-copalyl diphosphate + H2O = (+)-copalol + diphosphate (+)-copalyl diphosphate + H2O = diphosphate + manool (+)-copalyl diphosphate + H2O = 13-epi-manool + diphosphate ent-copalyl diphosphate + H2O = (-)-ent-copalol + diphosphate ent-copalyl diphosphate + H2O = diphosphate + ent-manool 9alpha-copalyl diphosphate + H2O = diphosphate + syn-copalol 9alpha-copalyl diphosphate + H2O = (13S)-vitexifolin A + diphosphate Can also use Fe(2+), Cu(2+), Mn(2+), Zn(2+) and Ni(2+). Inhibited by the bisphosphonate inhibitor BPH-629. kcat is 0.031 min(-1) with tuberculosinyl diphosphate as substrate. Optimum pH is 7. It is active in a pH range of 5.5-9.0. Optimum temperature is 45 degrees Celsius. No activity is detected above 50 degrees Celsius. Homodimer. Deletion of the gene abolishes 1-TbAd biosynthesis and decreases the formation of swollen phagosomes. 1-TbAd is highly prevalent among patient-derived M.tuberculosis strains, where it is among the most abundant lipids produced. Belongs to the diterpene synthase family. +Displays ATPase and GTPase activities. Belongs to the RapZ-like family. +May participate in the maintenance of segment identity in the hindbrain and pituitary development, and maturation or maintenance of the overall structure of the nervous system. May function as a regulatory subunit of ion channels. Abundant in 18-24 week old fetal brain. Postnatally its expression decline and only minimal levels were present in adulthood. Belongs to the neuronatin family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Probably part of a binding-protein-dependent transport system for an amino acid. Probably responsible for the translocation of the substrate across the membrane. Belongs to the binding-protein-dependent transport system permease family. HisMQ subfamily. +Gastrin stimulates the stomach mucosa to produce and secrete hydrochloric acid and the pancreas to secrete its digestive enzymes. It also stimulates smooth muscle contraction and increases blood circulation and water secretion in the stomach and intestine. Sulfation on Tyr-87 enhances proteolytic processing, and blocks peptide degradation. Levels of sulfation differ between proteolytically-cleaved gastrins and between tissues (By similarity). Belongs to the gastrin/cholecystokinin family. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Thiol protease. Probably an important virulence factor. Inactive below 20 degrees Celsius and pH 6.0. Inhibited by divalent cations. Belongs to the peptidase C2 family. +Modifies, by uridylylation and deuridylylation, the PII regulatory proteins (GlnB and homologs), in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen assimilation and metabolism. [protein-PII]-L-tyrosine + UTP = [protein-PII]-uridylyl-L-tyrosine + diphosphate [protein-PII]-uridylyl-L-tyrosine + H2O = [protein-PII]-L-tyrosine + H(+) + UMP Uridylyltransferase (UTase) activity is inhibited by glutamine, while glutamine activates uridylyl-removing (UR) activity. Has four distinct domains: an N-terminal nucleotidyltransferase (NT) domain responsible for UTase activity, a central HD domain that encodes UR activity, and two C-terminal ACT domains that seem to have a role in glutamine sensing. Belongs to the GlnD family. +Methyltransferase; part of the gene cluster that mediates the biosynthesis of the tetrahydroxanthone dimer secalonic acid D (PubMed:30996871, PubMed:33891392). The pathway begins with the synthesis of atrochrysone thioester by the polyketide synthase AacuL (Probable). The atrochrysone carboxyl ACP thioesterase AacuM then breaks the thioester bond and releases the atrochrysone carboxylic acid from AacuL (Probable). Atrochrysone carboxylic acid is decarboxylated by the decarboxylase AacuI, and oxidized by the anthrone oxygenase AacuG to yield emodin (Probable). Emodin is then reduced to emodin hydroquinone by a yet unidentified oxidoreductase (Probable). A-ring reduction by the short chain dehydrogenase AacuN, dehydration by the scytalone dehydratase-like protein AacuK and probable spontaneous re-oxidation, results in overall deoxygenation to chrysophanol (PubMed:33891392). Baeyer-Villiger oxidation by the Baeyer-Villiger monooxygenase (BVMO) AacuH then yields monodictyphenone (PubMed:33891392). Monodictyphenone is transformed into compounds with the tetrahydroxanthone skeleton via methylesterification by the methyltransferase AacuQ, followed by the action of the flavin-dependent monooxygenase AacuC, the isomerase AacuP, and the short chain dehydrogenase/reductase AacuF or AacuD (PubMed:33891392). AacuF and AacuD should accept the same compound as a substrate but perform the ketoreduction with a different stereoselectivity, thus yielding blennolides B and A, respectively (PubMed:33891392). In the final step of the biosynthesis, the cytochrome P450 monooxygenase AacuE accepts blennolide B and/or blennolide A to conduct the dimerization reaction to furnish the tetrahydroxanthone dimers, secalonic acids D, B, and F (PubMed:33891392). Secondary metabolite biosynthesis. Secalonic acids show unprecedented anticancer activities against various human cancer cells and might be interesting for further derivatization, targeting diseases such as cancer. Belongs to the methyltransferase superfamily. +Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP. Allosterically activated by GTP. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uracil: step 1/1. Belongs to the UPRTase family. +Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The NB-protein (ChlN-ChlB) is the catalytic component of the complex. 2 ADP + chlorophyllide a + oxidized 2[4Fe-4S]-[ferredoxin] + 2 phosphate = 2 ATP + 2 H2O + protochlorophyllide a + reduced 2[4Fe-4S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per heterodimer. The cluster is bound at the heterodimer interface by residues from both subunits. Porphyrin-containing compound metabolism; chlorophyll biosynthesis (light-independent). Protochlorophyllide reductase is composed of three subunits; ChlL, ChlN and ChlB. Forms a heterotetramer of two ChlB and two ChlN subunits. Belongs to the BchN/ChlN family. +Belongs to the poxviridae F6 protein family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase delta chain family. +Tyrosine protein phosphatase which functions as a dosage-dependent inducer of mitotic progression. Directly dephosphorylates CDK1 and stimulates its kinase activity. Also dephosphorylates CDK2 in complex with cyclin E, in vitro (By similarity). Phosphorylation by PIM1 leads to an increase in phosphatase activity (By similarity). H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate Stimulated by B-type cyclins. Stimulated by PIM1-mediated phosphorylation (By similarity). Interacts with CCNB1/cyclin B1. Interacts with YWHAE/14-3-3 epsilon when phosphorylated. Interacts with CUL1 specifically when CUL1 is neddylated and active. Interacts with BTRC/BTRCP1 and FBXW11/BTRCP2. Interactions with CUL1, BTRC and FBXW11 are enhanced upon DNA damage. Interacts with PIM1. Interacts with CHEK2; mediates CDC25A phosphorylation and degradation in response to infrared-induced DNA damages (By similarity). Interacts with HSP90AB1; prevents heat shock-mediated CDC25A degradation and contributes to cell cycle progression (By similarity). Ubiquitously expressed in most developing tissue. High levels in the testis and lower levels in the ovary, particularly in germ cells. Lower levels also in kidney, liver, heart and muscle. First detected at the blastocyst stage. The phosphodegron motif mediates interaction with specific F-box proteins when phosphorylated. Putative phosphorylation sites at Ser-78 and Ser-81 appear to be essential for this interaction (By similarity). Phosphorylated by CHEK1 on Ser-75, Ser-123, Ser-172, Ser-271, Ser-284 and Thr-497 during checkpoint mediated cell cycle arrest. Also phosphorylated by CHEK2 on Ser-123, Ser-271, and Ser-284 during checkpoint mediated cell cycle arrest. Phosphorylation on Ser-172 and Thr-497 creates binding sites for YWHAE/14-3-3 epsilon which inhibits CDC25A. Phosphorylation on Ser-75, Ser-123, Ser-172, Ser-271 and Ser-284 may also promote ubiquitin-dependent proteolysis of CDC25A by the SCF complex. Phosphorylation of CDC25A at Ser-75 by CHEK1 primes it for subsequent phosphorylation at Ser-75, Ser-81 and Ser-87 by NEK11. Phosphorylation by NEK11 is required for BTRC-mediated polyubiquitination and degradation. Phosphorylation by PIM1 leads to an increase in phosphatase activity. Phosphorylated by PLK3 following DNA damage, leading to promote its ubiquitination and degradation (By similarity). Ubiquitinated by the anaphase promoting complex/cyclosome (APC/C) ubiquitin ligase complex that contains FZR1/CDH1 during G1 phase leading to its degradation by the proteasome. Ubiquitinated by a SCF complex containing BTRC and FBXW11 during S phase leading to its degradation by the proteasome. Deubiquitination by USP17L2/DUB3 leads to its stabilization (By similarity). Belongs to the MPI phosphatase family. +Vesicle trafficking protein that functions in the secretory pathway. Part of the t-SNARE complex. Belongs to the syntaxin family. +Required during biogenesis of c-type cytochromes (cytochrome c6 and cytochrome f) at the step of heme attachment. May interact with CcsA. Belongs to the Ccs1/CcsB family. +In presence of calcium ions, it binds to surfactant phospholipids and contributes to lower the surface tension at the air-liquid interface in the alveoli of the mammalian lung and is essential for normal respiration. Enhances the expression of MYO18A/SP-R210 on alveolar macrophages. Oligomeric complex of 6 set of homotrimers. Pulmonary surfactant consists of 90% lipid and 10% protein. There are 4 surfactant-associated proteins: 2 collagenous, carbohydrate-binding glycoproteins (SP-A and SP-D) and 2 small hydrophobic proteins (SP-B and SP-C). Belongs to the SFTPA family. +Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. (2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 4/5. Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface. Belongs to the enolase family. +Plays a role in the initiation of viral DNA replication. A dimer of E2 interacts with a dimer of E1 in order to improve specificity of E1 DNA binding activity. Once the complex recognizes and binds DNA at specific sites, the E2 dimer is removed from DNA. E2 also regulates viral transcription through binding to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory regions of the viral genome. Activates or represses transcription depending on E2RE's position with regards to proximal promoter elements including the TATA-box. Repression occurs by sterically hindering the assembly of the transcription initiation complex. Binds DNA as homodimer. Interacts with protein E1; this interaction greatly increases E1 DNA-binding activity. Interacts with protein L1; this interaction enhances E2-dependent replication and transcription activation. Interacts with protein L2; this interaction inhibits E2 transcriptional activity but not DNA replication function E2. Interacts with protein E7; this interaction inhibits E7 oncogenic activity. Interacts with host TAF1; this interaction modulates E2-dependent transcriptional regulation. Interacts with host BRD4; this interaction mediates E2 transcriptional activation function. Additionally, the interaction with host BRD4 on mitotic chromosomes mediates tethering of the viral genome. Interacts with host TOPBP1; this interaction is required for optimal viral DNA replication. Phosphorylated. Belongs to the papillomaviridae E2 protein family. +Specifically cleaves olefinic bonds in cyclic enones (PubMed:11094980). Involved in the biosynthesis of jasmonic acid (JA) and perhaps in biosynthesis or metabolism of other oxylipin signaling moleclules (PubMed:29291349, PubMed:10872231, PubMed:10973494). Required for the spatial and temporal regulation of JA levels during dehiscence of anthers, promoting the stomium degeneration program (PubMed:10899973, PubMed:10973494). In vitro, reduces 9S,13S-12-oxophytodienoic acid (9S,13S-OPDA) and 9R,13R-OPDA to 9S,13S-OPC-8:0 and 9R,13R-OPC-8:0, respectively (PubMed:10872231). Can detoxify the explosive 2,4,6-trinitrotoluene (TNT) in vitro by catalyzing its nitroreduction to form hydroxylamino-dinitrotoluene (HADNT) (PubMed:19605548). NADP(+) + OPC-8 = (10Z,15Z)-12-oxophytodienoate + H(+) + NADPH Optimum pH is 7-8. Active from pH 5.0 to 8.5. Lipid metabolism; oxylipin biosynthesis. Expressed in green seedling, leaves, flowers (anthers, pistil, petal and stamen), and to a lower extent in roots and siliques. Specifically expressed in filament during anther dehiscence initiation. At the initiation time of the stomium degeneration program, expressed in all floral organs. Later, transcripts levels increase in pistil, petal, stamen filament, and in vascular region close to the stamen filament. When the anther dehiscence is initiated, levels of transcripts decrease, except within the vascular tissues. Induction mediated by wounding and methyl JA (MeJA) needs COI1. Also induced by BR (24-epibrassinolide), UV LIGHT, wind, touch, and the detergent Sapogenat T-110. Seems to not be influenced by salicylic acid, cold and heat treatments (PubMed:11094980, Ref.4). Induced by infection with the fungal pathogens Botritys cinerea and Alternaria brassicicola, insect feeding with Spodoptera littoralis, and wounding (PubMed:29291349). Male sterility (PubMed:10973494, PubMed:19765234, PubMed:29291349). Fertility can be restored by exogenous jasmonate but not by 12-oxophytodienoic acid (PubMed:10973494, PubMed:19765234, PubMed:29291349). Large petals with altered vein patterning (PubMed:19765234). Belongs to the NADH:flavin oxidoreductase/NADH oxidase family. +Involved in pre-mRNA splicing as a component of the splicing factor SF3A complex that contributes to the assembly of the 17S U2 snRNP, and the subsequent assembly of the pre-spliceosome 'E' complex and the pre-catalytic spliceosome 'A' complex. Involved in pre-mRNA splicing as a component of pre-catalytic spliceosome 'B' complexes, including the Bact complex. Interacts directly with the duplex formed by U2 snRNA and the intron. Component of splicing factor SF3A which is composed of three subunits; SF3A3/SAP61, SF3A2/SAP62 and SF3A1/SAP114. SF3A1 functions as scaffold that interacts directly with both SF3A2 and SF3A3. SF3A associates with the splicing factor SF3B and a 12S RNA unit to form the mature 17S U2 small nuclear ribonucleoprotein complex (17S U2 snRNP). Identified in the spliceosome 'E' complex, a precursor of the spliceosome 'A' complex. Identified in the spliceosome 'A' and 'B' complexes. Identified in the spliceosome 'C' complex. Interacts with HTATSF1. Belongs to the SF3A2 family. +Part of a complex that catalyzes the reversible cleavage of acetyl-CoA, allowing autotrophic growth from CO(2). The alpha-epsilon complex generates CO from CO(2), while the beta subunit (this protein) combines the CO with CoA and a methyl group to form acetyl-CoA. The methyl group, which is incorporated into acetyl-CoA, is transferred to the beta subunit by a corrinoid iron-sulfur protein (the gamma-delta complex). acetyl-CoA + Co(I)-[corrinoid Fe-S protein] + H(+) = CO + CoA + methyl-Co(III)-[corrinoid Fe-S protein] Binds 1 [Ni-Fe-S] cluster. Monomer. The ACDS complex is made up of alpha, epsilon, beta, gamma and delta chains with a probable stoichiometry of (alpha(2)epsilon(2))(4)-beta(8)-(gamma(1)delta(1))(8) (Potential). Belongs to the CdhC family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +(6S)-5,6,7,8-tetrahydrofolate + ATP + formate = (6S)-10-formyltetrahydrofolate + ADP + phosphate One-carbon metabolism; tetrahydrofolate interconversion. Belongs to the formate--tetrahydrofolate ligase family. +Belongs to the clarin family. +Plays an important role in promoting lung pathology in both primary viral infection and secondary bacterial infection. Promotes alteration of mitochondrial morphology, dissipation of mitochondrial membrane potential, and cell death. Alternatively, inhibits the production of interferon in the infected cell at the level of host mitochondrial antiviral signaling MAVS. Its level of expression differs greatly depending on which cell type is infected, in a manner that is independent of the levels of expression of other viral proteins. Monocytic cells are more affected than epithelial cells. Seems to disable virus-infected monocytes or other host innate immune cells. During early stage of infection, predisposes the mitochondria to permeability transition through interaction with host SLC25A6/ANT3 and VDAC1. These proteins participate in the formation of the permeability transition pore complex (PTPC) responsible of the release of mitochondrial products that triggers apoptosis. Oligomer. Interacts with human SLC25A6/ANT3 and VDAC1. Interacts with host MAVS. Inner mitochondrial membrane in most cells types. Otherwise is detected in the nucleus and cytosol. Is not encoded in all strains, and seems to be dispensable for replication. Belongs to the influenza viruses PB1-F2 family. +Involved in iron-sulfur (Fe-S) cluster assembly. May act as a regulator of Fe-S biogenesis. Belongs to the frataxin family. +Catalyzes the last two steps in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34. 5-aminomethyl-2-thiouridine(34) in tRNA + S-adenosyl-L-methionine = 5-methylaminomethyl-2-thiouridine(34) in tRNA + H(+) + S-adenosyl-L-homocysteine In the N-terminal section; belongs to the methyltransferase superfamily. tRNA (mnm(5)s(2)U34)-methyltransferase family. In the C-terminal section; belongs to the DAO family. +Snake venom serine protease that hydrolyzes specific chromogenic substrate S-2302 suggesting that AHP-Ka is a plasma kallikrein. Has esterase activity on alpha-N-benzoyl-L-arginine ethyl ester hydrochloride (BAEE) and amidolytic activity. Inhibited by PMSF, Fe(3+), Fe(2+), Cu(2+), Cd(2+), Mn(2+), and Al(3+). Not inhibited by Ca(2+) and Mg(2+) and EDTA. Optimum pH is 7-8. Optimum temperature is 30-40 degrees Celsius. Monomer. Expressed by the venom gland. N-glycosylated. Cleavage of N-glycans reduces the catalytic enzymatic efficiency. Belongs to the peptidase S1 family. Snake venom subfamily. +Endo-inulinase involved in utilization of the plant storage polymer inulin, consisting of fructooligosaccharides with a degree of polymerization (DP) value from 2 to 60. Endohydrolysis of (2->1)-beta-D-fructosidic linkages in inulin. Expression is induced in presence of sucrose or inulin and controlled by the catabolite repressor creA and by the inulinolytic genes regulator inuR. Plays an important role in biofuel production. Pure nonhydrolyzed inulin can be directly converted to ethanol in a simultaneous saccharification and fermentation process when combining A.niger and S.cerevisiae. Endoinulinase can digest fructooligosaccharides with high degree of polymerization (DP) values (>20) into short molecules that may be readily hydrolyzed by S.cerevisiae SUC2. Thus, introduction of an endoinulinase gene into S.cerevisiae will improve its inulin utilization and ethanol fermentation through collaboration between the heterologous endoinulinase and the invertase SUC2. Belongs to the glycosyl hydrolase 32 family. Strain CBS 513.88 / FGSC A1513 contains only one gene encoding for an extracellular endo-inulinase (inuA), contrary to other strains containing two genes (inuA and inuB). Driving on fumes - Issue 164 of September 2014 +Belongs to the TEX13 family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase delta chain family. +Catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates. Cleaves off the terminal sialic acids on the glycosylated HA during virus budding to facilitate virus release. Additionally helps virus spread through the circulation by further removing sialic acids from the cell surface. These cleavages prevent self-aggregation and ensure the efficient spread of the progeny virus from cell to cell. Otherwise, infection would be limited to one round of replication. Described as a receptor-destroying enzyme because it cleaves a terminal sialic acid from the cellular receptors. May facilitate viral invasion of the upper airways by cleaving the sialic acid moieties on the mucin of the airway epithelial cells. Likely to plays a role in the budding process through its association with lipid rafts during intracellular transport. May additionally display a raft-association independent effect on budding. Plays a role in the determination of host range restriction on replication and virulence. Sialidase activity in late endosome/lysosome traffic seems to enhance virus replication. Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates. Inhibited by the neuraminidase inhibitors zanamivir (Relenza) and oseltamivir (Tamiflu). These drugs interfere with the release of progeny virus from infected cells and are effective against all influenza strains. Resistance to neuraminidase inhibitors is quite rare. Homotetramer. Preferentially accumulates at the apical plasma membrane in infected polarized epithelial cells, which is the virus assembly site. Uses lipid rafts for cell surface transport and apical sorting. In the virion, forms a mushroom-shaped spike on the surface of the membrane. Intact N-terminus is essential for virion morphogenesis. Possesses two apical sorting signals, one in the ectodomain, which is likely to be a glycan, and the other in the transmembrane domain. The transmembrane domain also plays a role in lipid raft association. N-glycosylated. The influenza A genome consist of 8 RNA segments. Genetic variation of hemagglutinin and/or neuraminidase genes results in the emergence of new influenza strains. The mechanism of variation can be the result of point mutations or the result of genetic reassortment between segments of two different strains. Belongs to the glycosyl hydrolase 34 family. +2 H(+) + H2O + urea = CO2 + 2 NH4(+) Binds 2 nickel ions per subunit. Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Carboxylation allows a single lysine to coordinate two nickel ions. Belongs to the metallo-dependent hydrolases superfamily. Urease alpha subunit family. +Probable protease subunit of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of the SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. In the complex, it probably acts as the catalytic center that mediates the cleavage of Nedd8 from cullins. It however has no metalloprotease activity by itself and requires the other subunits of the CSN complex (By similarity). The CSN complex is involved in repression of photomorphogenesis in darkness by regulating the activity of COP1-containing Ubl ligase complexes. The complex is also required for degradation of PSIAA6 by regulating the activity of the Ubl ligase SCF-TIR complex. Not involved in CSN's deneddylation/derubylation activity (PubMed:15486099, PubMed:17307927). Essential for the structural integrity of the CSN holocomplex (PubMed:17307927). Component of the CSN complex, probably composed of CSN1, CSN2, CSN3, CSN4, CSN5 (CSN5A or CSN5B), CSN6 (CSN6A or CSN6B), CSN7 and CSN8 (PubMed:9811788, PubMed:12615944, PubMed:15486099). CSN5A or CSN5B are present within distinct CSN complexes each containing only one copy of CSN5 (PubMed:15486099). Interacts with itself (PubMed:9811788). In the complex, it is located in the center and probably interacts directly with CSN4 and CSN6A or CSN6B (PubMed:9811788, PubMed:12615944). Also exists as monomeric form (PubMed:9811788). Interacts with CYT1 in vitro and in planta (PubMed:23424245). Interacts with FLZ3 (Ref.11). Ubiquitously expressed. Highly expressed in flowers and roots. Expressed at lower level in seedlings and siliques. The JAMM motif is essential for the protease activity of the CSN complex resulting in deneddylation of cullins. It constitutes the catalytic center of the complex (By similarity). No visible phenotype and no effect on the derubylation of CUL1 (PubMed:15486099, PubMed:17307927). Csn5a and csn5b double mutants are lethal at the seedling stage (PubMed:17307927). Belongs to the peptidase M67A family. CSN5 subfamily. +Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds, a reaction that is part of a thiamine salvage pathway. Thus, catalyzes the conversion of 4-amino-5-aminomethyl-2-methylpyrimidine to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). Is also able to catalyze the hydrolytic cleavage of thiamine; however, this thiaminase activity may not be physiologically relevant. Therefore, is probably involved in the regeneration of the thiamine pyrimidine from thiamine degraded products present in the environment, rather than in thiamine degradation. 4-amino-5-aminomethyl-2-methylpyrimidine + H2O = 4-amino-5-hydroxymethyl-2-methylpyrimidine + NH4(+) H2O + thiamine = 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole + H(+) Cofactor biosynthesis; thiamine diphosphate biosynthesis. Homotetramer. Belongs to the TenA family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +Probably mediates the hydrolysis of some nucleoside diphosphate derivatives. Belongs to the Nudix hydrolase family. PCD1 subfamily. +Serine/threonine kinase which acts as an essential component of the MAP kinase signal transduction pathway. MAPK14 is one of the four p38 MAPKs which play an important role in the cascades of cellular responses evoked by extracellular stimuli such as pro-inflammatory cytokines or physical stress leading to direct activation of transcription factors. Accordingly, p38 MAPKs phosphorylate a broad range of proteins and it has been estimated that they may have approximately 200 to 300 substrates each. Some of the targets are downstream kinases which are activated through phosphorylation and further phosphorylate additional targets. RPS6KA5/MSK1 and RPS6KA4/MSK2 can directly phosphorylate and activate transcription factors such as CREB1, ATF1, the NF-kappa-B isoform RELA/NFKB3, STAT1 and STAT3, but can also phosphorylate histone H3 and the nucleosomal protein HMGN1. RPS6KA5/MSK1 and RPS6KA4/MSK2 play important roles in the rapid induction of immediate-early genes in response to stress or mitogenic stimuli, either by inducing chromatin remodeling or by recruiting the transcription machinery. On the other hand, two other kinase targets, MAPKAPK2/MK2 and MAPKAPK3/MK3, participate in the control of gene expression mostly at the post-transcriptional level, by phosphorylating ZFP36 (tristetraprolin) and ELAVL1, and by regulating EEF2K, which is important for the elongation of mRNA during translation. MKNK1/MNK1 and MKNK2/MNK2, two other kinases activated by p38 MAPKs, regulate protein synthesis by phosphorylating the initiation factor EIF4E2. MAPK14 interacts also with casein kinase II, leading to its activation through autophosphorylation and further phosphorylation of TP53/p53. In the cytoplasm, the p38 MAPK pathway is an important regulator of protein turnover. For example, CFLAR is an inhibitor of TNF-induced apoptosis whose proteasome-mediated degradation is regulated by p38 MAPK phosphorylation. In a similar way, MAPK14 phosphorylates the ubiquitin ligase SIAH2, regulating its activity towards EGLN3. MAPK14 may also inhibit the lysosomal degradation pathway of autophagy by interfering with the intracellular trafficking of the transmembrane protein ATG9. Another function of MAPK14 is to regulate the endocytosis of membrane receptors by different mechanisms that impinge on the small GTPase RAB5A. In addition, clathrin-mediated EGFR internalization induced by inflammatory cytokines and UV irradiation depends on MAPK14-mediated phosphorylation of EGFR itself as well as of RAB5A effectors. Ectodomain shedding of transmembrane proteins is regulated by p38 MAPKs as well. In response to inflammatory stimuli, p38 MAPKs phosphorylate the membrane-associated metalloprotease ADAM17. Such phosphorylation is required for ADAM17-mediated ectodomain shedding of TGF-alpha family ligands, which results in the activation of EGFR signaling and cell proliferation. Another p38 MAPK substrate is FGFR1. FGFR1 can be translocated from the extracellular space into the cytosol and nucleus of target cells, and regulates processes such as rRNA synthesis and cell growth. FGFR1 translocation requires p38 MAPK activation. In the nucleus, many transcription factors are phosphorylated and activated by p38 MAPKs in response to different stimuli. Classical examples include ATF1, ATF2, ATF6, ELK1, PTPRH, DDIT3, TP53/p53 and MEF2C and MEF2A. The p38 MAPKs are emerging as important modulators of gene expression by regulating chromatin modifiers and remodelers. The promoters of several genes involved in the inflammatory response, such as IL6, IL8 and IL12B, display a p38 MAPK-dependent enrichment of histone H3 phosphorylation on 'Ser-10' (H3S10ph) in LPS-stimulated myeloid cells. This phosphorylation enhances the accessibility of the cryptic NF-kappa-B-binding sites marking promoters for increased NF-kappa-B recruitment. Phosphorylates CDC25B and CDC25C which is required for binding to 14-3-3 proteins and leads to initiation of a G2 delay after ultraviolet radiation. Phosphorylates TIAR following DNA damage, releasing TIAR from GADD45A mRNA and preventing mRNA degradation. The p38 MAPKs may also have kinase-independent roles, which are thought to be due to the binding to targets in the absence of phosphorylation. Protein O-Glc-N-acylation catalyzed by the OGT is regulated by MAPK14, and, although OGT does not seem to be phosphorylated by MAPK14, their interaction increases upon MAPK14 activation induced by glucose deprivation. This interaction may regulate OGT activity by recruiting it to specific targets such as neurofilament H, stimulating its O-Glc-N-acylation. Required in mid-fetal development for the growth of embryo-derived blood vessels in the labyrinth layer of the placenta. Also plays an essential role in developmental and stress-induced erythropoiesis, through regulation of EPO gene expression (By similarity). Phosphorylates S100A9 at 'Thr-113' (By similarity). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by cell stresses such as DNA damage, heat shock, osmotic shock, anisomycin and sodium arsenite, as well as pro-inflammatory stimuli such as bacterial lipopolysaccharide (LPS) and interleukin-1. Activation occurs through dual phosphorylation of Thr-180 and Tyr-182 by either of two dual specificity kinases, MAP2K3/MKK3 or MAP2K6/MKK6, and potentially also MAP2K4/MKK4, as well as by TAB1-mediated autophosphorylation. MAPK14 phosphorylated on both Thr-180 and Tyr-182 is 10-20-fold more active than MAPK14 phosphorylated only on Thr-180, whereas MAPK14 phosphorylated on Tyr-182 alone is inactive. whereas Thr-180 is necessary for catalysis, Tyr-182 may be required for auto-activation and substrate recognition. Phosphorylated at Tyr-323 by ZAP70 in an alternative activation pathway in response to TCR signaling in T-cells. This alternative pathway is inhibited by GADD45A. Inhibited by dual specificity phosphatases, such as DUSP1, DUSP10, and DUSP16. Specifically inhibited by the binding of pyridinyl-imidazole compounds, which are cytokine-suppressive anti-inflammatory drugs (CSAID). SB203580 is an inhibitor of MAPK14 (By similarity). Component of a signaling complex containing at least AKAP13, PKN1, MAPK14, ZAK and MAP2K3. Within this complex, AKAP13 interacts directly with PKN1, which in turn recruits MAPK14, MAP2K3 and ZAK (By similarity). Binds to a kinase interaction motif within the protein tyrosine phosphatase, PTPRR (By similarity). This interaction retains MAPK14 in the cytoplasm and prevents nuclear accumulation (By similarity). Interacts with SPAG9 and GADD45A (By similarity). Interacts with CDC25B, CDC25C, DUSP1, DUSP10, DUSP16, NP60, SUPT20H and TAB1. Interacts with casein kinase II subunits CSNK2A1 and CSNK2B. Interacts with PPM1D. Interacts with CDK5RAP3; recruits PPM1D to MAPK14 and may regulate its dephosphorylation (By similarity). Interacts with DUSP2; this interaction does not lead to catalytic activation of DUSP2 and dephosphrylation of MAPK14 (By similarity). The TXY motif contains the threonine and tyrosine residues whose phosphorylation activates the MAP kinases. Dually phosphorylated on Thr-180 and Tyr-182 by the MAP2Ks MAP2K3/MKK3, MAP2K4/MKK4 and MAP2K6/MKK6 in response to inflammatory citokines, environmental stress or growth factors, which activates the enzyme. Dual phosphorylation can also be mediated by TAB1-mediated autophosphorylation. TCR engagement in T-cells also leads to Tyr-323 phosphorylation by ZAP70. Dephosphorylated and inactivated by DUPS1, DUSP10 and DUSP16 (By similarity). PPM1D also mediates dephosphorylation and inactivation of MAPK14 (By similarity). Acetylated at Lys-53 and Lys-152 by KAT2B and EP300. Acetylation at Lys-53 increases the affinity for ATP and enhances kinase activity. Lys-53 and Lys-152 are deacetylated by HDAC3 (By similarity). Ubiquitinated. Ubiquitination leads to degradation by the proteasome pathway (By similarity). Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. MAP kinase subfamily. +Endo-1,5-alpha-L-arabinanase involved in degradation of pectin. Its preferred substrate is linear 1,5-alpha-L-arabinan (By similarity). Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans. Glycan metabolism; L-arabinan degradation. Belongs to the glycosyl hydrolase 43 family. +Splice factor regulating alternative splice site selection for certain mRNA precursors. Mediates regulation of pre-mRNA splicing in a PKA-dependent manner. Monomer. Component of the spliceosome. Interacts with ZRANB2 and SFRS1/ASF through its Arg/Ser-rich domain. Interacts with RI and RII subunits of PKA. Widely expressed. Found in heart, brain, lung, liver, skeletal muscle, kidney and pancreas. Expressed in activated B-cells and placenta. Expressed in all cell lines tested including Jurkat-TAg, U-937 and HEK293 cells. RI-alpha binding site, predicted to form an amphipathic helix, could participate in protein-protein interactions with a complementary surface on the R-subunit dimer. The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Was originally thought to be a cell surface protein involved in B-cell activation. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Involved in homologous recombination where it functions at an early stage of recombination in a pre-recombinogenic complex with rlp1 and sws1. Also has a role at a later stage of recombination in association with the rhp55-rhp57 complex. Interacts with rlp1 and sws1. +Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis. H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-[ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Belongs to the IspH family. +Antimicrobial peptide. Expressed by the skin glands. Belongs to the frog skin active peptide (FSAP) family. Brevinin subfamily. +Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell. Homopentamer. Belongs to the MscL family. +Belongs to the bacterial ribosomal protein bL28 family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be a menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 4L family. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Transfers the sialyl group (N-acetyl-alpha-neuraminyl or NeuAc) from CMP-NeuAc onto glycoproteins and glycolipids, forming an alpha-2,6-linkage. Produces branched type disialyl structures by transfer of a sialyl group onto the GalNAc or GlcNAc residue inside backbone core chains having a terminal sialic acid with an alpha-2,3-linkage on Gal. ST6GalNAcVI prefers glycolipids to glycoproteins, predominantly catalyzing the biosynthesis of ganglioside GD1alpha from GM1b (PubMed:12668675, PubMed:17123352). Besides GMb1, MSGG and other glycolipids, it shows activity towards sialyl Lc4Cer generating disialyl Lc4Cer, which can lead to the synthesis of disialyl Lewis a (Le(a)), suggested to be a cancer-associated antigen (PubMed:12668675). Also has activity toward GD1a and GT1b, and can generate DSGG (disialylgalactosylgloboside) from MSGG (monosialylgalactosylgloboside) (By similarity). CMP-N-acetyl-beta-neuraminate + ganglioside GM1b (d18:1(4E)) = a ganglioside GD1alpha (d18:1(4E)) + CMP + H(+) CMP-N-acetyl-beta-neuraminate + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->3)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-N-acyl-sphing-4-enine = CMP + H(+) + N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->3)-[N-acetyl-alpha-neuraminosyl-(2->6)]-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-N-acyl-sphing-4-enine CMP-N-acetyl-beta-neuraminate + globoside MSGG = CMP + globoside DSGG + H(+) CMP-N-acetyl-beta-neuraminate + ganglioside GD1a (d18:1(4E)) = CMP + ganglioside GT1aalpha (d18:1(4E)) + H(+) CMP-N-acetyl-beta-neuraminate + ganglioside GT1b (d18:1(4E)) = CMP + ganglioside GQ1b alpha (d18:1(4E)) + H(+) 3-O-[alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-alpha-D-GalNAc]-L-Ser-[protein] + CMP-N-acetyl-beta-neuraminate = 3-O-{alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-[alpha-Neu5Ac-(2->6)]-alpha-D-GalNAc}-L-Ser-[protein] + CMP + H(+) 3-O-[alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-alpha-D-GalNAc]-L-Thr-[protein] + CMP-N-acetyl-beta-neuraminate = 3-O-{alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-[alpha-Neu5Ac-(2->6)]-alpha-D-GalNAc}-L-Thr-[protein] + CMP + H(+) Expressed in kidney, in proximal tubule epithelial cells. Expressed in colon cell lines. Down-regulated in renal cancers. The carbohydrate antigen disialyl Lewis a, which is at least partly synthesized by ST6GALNAC6, is a normal counterpart of sialyl Lewis a, better known as CA19-9, an antigen widely used as a serum marker for diagnosis of cancers in the digestive track. Disialyl Lewis a is predominantly expressed in non-malignant epithelial cells of the digestive organs, while sialyl Lewis a is preferentially expressed in cancers. Disialyl Lewis a in normal epithelial cells serves as a ligand for immunosuppressive receptors, such as SIGLEC7 and SIGLEC9, expressed on resident monocytes/macrophages and maintains immunological homeostasis of mucosal membranes in digestive organs. Sialyl Lewis a, as well as its positional isomer sialyl Lewis x, serves as a ligand for vascular cell adhesion molecule E-selectin and facilitates hematogenous metastasis through mediating adhesion of circulating cancer cells to vascular endothelium (PubMed:17760270). Belongs to the glycosyltransferase 29 family. ST6GalNAc VI +This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL5 family. +One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS17 family. +An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes. Binds ribosomal protein S19. The PRC barrel domain binds ribosomal protein S19. Belongs to the RimM family. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Binds 1 potassium ion per subunit. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Contributes to the nuclear transport of the viral transcriptional activator VP16 during the early phase of infection. Therefore, participates indirectly in the regulation of the immediate-early gene expression. Additionally, seems to be important for efficient nuclear targeting of capsids. The UL51-UL14 complex regulates final viral envelopment for efficient viral replication (PubMed:27440890). Interacts with UL51. Phosphorylated. Belongs to the alphaherpesvirinae HHV-1 UL14 protein family. +Required for the first step of diphthamide biosynthesis, the transfer of 3-amino-3-carboxypropyl from S-adenosyl-L-methionine to a histidine residue. Diphthamide is a post-translational modification of histidine which occurs in elongation factor 2 (By similarity). Protein modification; peptidyl-diphthamide biosynthesis. The DPH-type metal-binding (MB) domain can bind either zinc or iron ions. Belongs to the DPH4 family. +Plays a role in the initiation of viral DNA replication. A dimer of E2 interacts with a dimer of E1 in order to improve specificity of E1 DNA binding activity. Once the complex recognizes and binds DNA at specific sites, the E2 dimer is removed from DNA. E2 also regulates viral transcription through binding to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory regions of the viral genome. Activates or represses transcription depending on E2RE's position with regards to proximal promoter elements including the TATA-box. Repression occurs by sterically hindering the assembly of the transcription initiation complex. Binds DNA as homodimer. Interacts with protein E1; this interaction greatly increases E1 DNA-binding activity. Interacts with protein L1; this interaction enhances E2-dependent replication and transcription activation. Interacts with protein L2; this interaction inhibits E2 transcriptional activity but not DNA replication function E2. Interacts with protein E7; this interaction inhibits E7 oncogenic activity. Interacts with host TAF1; this interaction modulates E2-dependent transcriptional regulation. Interacts with host BRD4; this interaction mediates E2 transcriptional activation function. Additionally, the interaction with host BRD4 on mitotic chromosomes mediates tethering of the viral genome. Interacts with host TOPBP1; this interaction is required for optimal viral DNA replication. Phosphorylated. Belongs to the papillomaviridae E2 protein family. +Belongs to the UPF0391 family. +Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate. S-adenosyl-L-methionine + trans-aconitate = (E)-3-(methoxycarbonyl)pent-2-enedioate + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. Tam family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Serine/threonine-protein kinase involved in the control of the eukaryotic cell cycle, whose activity is controlled by an associated cyclin. Acts as a cell-cycle regulator of Wnt signaling pathway during G2/M phase by mediating the phosphorylation of LRP6 at 'Ser-1490', leading to the activation of the Wnt signaling pathway. Acts as a regulator of cell cycle progression and cell proliferation via its interaction with CCDN3. Phosphorylates RB1 in vitro, however the relevance of such result remains to be confirmed in vivo. May also play a role in meiosis, neuron differentiation and may indirectly act as a negative regulator of insulin-responsive glucose transport. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Serine/threonine-protein kinase activity is promoted by associated cyclins CCDN3 and CCNY and repressed by CDKN1A. Found in a complex with LRP6, CCNY and CAPRIN2 during G2/M stage; CAPRIN2 functions as a scaffold for the complex by binding to CCNY via its N terminus and to CDK14 via its C terminus (PubMed:27821587). Interacts with CCNY; CCNY mediates its recruitment to the plasma membrane and promotes phosphorylation of LRP6 (PubMed:20059949, PubMed:19524571). Interacts with CCDN3 and CDKN1A (PubMed:17517622). Interacts with SEPT8 (PubMed:12098780). Interacts with 14-3-3 proteina YWHAB, YWHAE, YWHAH and YWHAQ (PubMed:16775625). Recruited to the cell membrane by CCNY. Highly expressed in brain, pancreas, kidney, heart, testis and ovary. Also detected at lower levels in other tissues except in spleen and thymus where expression is barely detected. Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily. +Dephosphorylates 26S nuclear proteasomes, thereby decreasing their proteolytic activity. The dephosphorylation may prevent assembly of the core and regulatory particles (CP and RP) into mature 26S proteasome (By similarity). H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Colocalizes with nuclear proteasomes. The Ubiquitin-like domain mediates interaction with proteasomes. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Acts upon elastin. Hydrolysis of proteins, including elastin. Preferential cleavage: Ala-|-Xaa. Binds 1 Ca(2+) ion per subunit. Belongs to the peptidase S1 family. Elastase subfamily. +One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Forms part of the polypeptide exit tunnel. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL4 family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine. [thioredoxin]-disulfide + H2O + L-methionyl-[protein] = [thioredoxin]-dithiol + L-methionyl-(S)-S-oxide-[protein] [thioredoxin]-disulfide + H2O + L-methionine = [thioredoxin]-dithiol + L-methionine (S)-S-oxide Belongs to the MsrA Met sulfoxide reductase family. +Involved in oxygen transport from gills to the various peripheral tissues. Hb2 is a heterotetramer of two alpha-2 chains and two beta-1 chains; Hb3 is a heterotetramer of two alpha-2 chains and two beta-2 chains. Red blood cells. Hb2 displays a low, effector-enhanced Bohr effect and no Root effect. Hb3 displays pronounced Bohr and Root effects, accompanied by strong organophosphate regulation. Belongs to the globin family. +Master enzyme that delivers sulfur to a number of partners involved in Fe-S cluster assembly, tRNA modification or cofactor biosynthesis. Catalyzes the removal of elemental sulfur atoms from cysteine to produce alanine. Functions as a sulfur delivery protein for Fe-S cluster synthesis onto IscU, an Fe-S scaffold assembly protein, as well as other S acceptor proteins. [sulfur carrier]-H + L-cysteine = [sulfur carrier]-SH + L-alanine Cofactor biosynthesis; iron-sulfur cluster biosynthesis. Homodimer. Forms a heterotetramer with IscU, interacts with other sulfur acceptors. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. NifS/IscS subfamily. +Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. Binds to the N-terminal domain of the chaperone ClpA. Belongs to the ClpS family. +Belongs to the eukaryotic ribosomal protein eS8 family. +Acts on oxaloacetate, sulfopyruvate but not on pyruvate. Has a higher selectivity for the coenzyme NADH than for NADPH. (S)-malate + NAD(+) = H(+) + NADH + oxaloacetate (S)-malate + NADP(+) = H(+) + NADPH + oxaloacetate (2S)-3-sulfolactate + NAD(+) = 3-sulfopyruvate + H(+) + NADH Homodimer. Belongs to the LDH2/MDH2 oxidoreductase family. +Involved in the final reduction of the elongation cycle of fatty acid synthesis (FAS II). Catalyzes the reduction of a carbon-carbon double bond in an enoyl moiety that is covalently linked to an acyl carrier protein (ACP). a 2,3-saturated acyl-[ACP] + NAD(+) = a (2E)-enoyl-[ACP] + H(+) + NADH Lipid metabolism; fatty acid biosynthesis. Monomer. Belongs to the TER reductase family. +Mediates activation of long-chain fatty acids for both synthesis of cellular lipids, and degradation via beta-oxidation (PubMed:26893370, PubMed:29739804). Probably by regulating lipid storage and catabolism, plays a role in neuronal function (PubMed:25409104). a long-chain fatty acid + ATP + CoA = a long-chain fatty acyl-CoA + AMP + diphosphate Results in neurodegeneration in the central nervous system including degeneration of lamina and retina, defects in the fenestrated basement membrane, ommatidial disarray, locomotor defects and shortened lifespan (PubMed:26893370, PubMed:29739804). The phenotype is exacerbated in constant light conditions and improves in total darkness (PubMed:29739804). Effects are probably due to elevated levels of very long chain fatty acids (VLCFAs) (PubMed:29739804). Feeding the fly mutant with medium-chain fatty acids, blocks the accumulation of excess VLCFAs as well as development of the pathology (PubMed:29739804). Simultaneous knockout of bgm results in enhanced retinal degeneration and altered fatty acids metabolism (PubMed:26893370). RNAi-mediated knockdown in the adult results in reduction of triglycerides and altered neuronal function, including altered sleep rebound following sleep deprivation (PubMed:25409104). In Norse mythology, Heimdall is the fictional character that for ages guarded the bridge to Asgard without sleeping and without the consequences of sleep deprivation. Belongs to the ATP-dependent AMP-binding enzyme family. Bubblegum subfamily. Truncated C-terminus. +NDH-1 shuttles electrons from an unknown electron donor, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH-1 can be composed of about 15 different subunits; different subcomplexes with different compositions have been identified which probably have different functions. Belongs to the complex I NdhL subunit family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +Specifically methylates guanosine-37 in various tRNAs. guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase TrmD family. +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase. Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Prokaryotic type I sub-subfamily. +Belongs to the UPF0301 (AlgH) family. +This protein is probably a component of a manganese permease, a binding protein-dependent, ATP-driven transport system. Probably responsible for energy coupling to the transport system (By similarity). Belongs to the ABC transporter superfamily. +ATP-binding (A) component of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component). Belongs to the ABC transporter superfamily. Energy-coupling factor EcfA family. +Contributes to the regulation of the Wnt signaling pathway. Down-regulates CTNNB1-mediated transcriptional activation of target genes, such as CCND1, and may thereby act as tumor suppressor. May be involved in dendritic cell and neuron differentiation (By similarity). Interacts with CTNNB1. In neurons, seems to concentrate at axonal growth cone. Perinuclear in neurons (By similarity). Belongs to the NDRG family. +Synthesizes amides which are involved in stress response in the cell wall. Catalyzes the synthesis of hydroxycinnamic acid amides from hydroxycinnamoyl-CoA thioesters and various hydroxyphenylethylamines such as 4-coumaroyl-CoA and sinapoyl-CoA. (E)-feruloyl-CoA + tyramine = CoA + H(+) + N-[(E)-feruloyl]tyramine Inhibited by (2-hydroxyphenyl)amino sulfinyl acetic acid 1,1-dimethylethyl ester, by DEPC and by N-ethylmaleimide. Homodimer. Belongs to the acetyltransferase family. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvA. Belongs to the RuvB family. +May play a role in plant defense. Probably has no oxalate oxidase activity even if the active site is conserved. Oligomer (believed to be a pentamer but probably hexamer). Belongs to the germin family. +Adds the third glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. Transfers glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Glc(2)Man(9)GlcNAc(2)-PP-Dol. a dolichyl beta-D-glucosyl phosphate + alpha-D-Glc-(1->3)-alpha-D-Glc-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphosphodolichol = a dolichyl phosphate + alpha-D-Glc-(1->2)-alpha-D-Glc-(1->3)-alpha-D-Glc-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphosphodolichol + H(+) Protein modification; protein glycosylation. Belongs to the ALG10 glucosyltransferase family. +Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell by interacting with host ITGA4/ITGB1 (By similarity). The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures (By similarity). Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation. Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry. Structural peptide 2 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability (By similarity). Capsid protein VP2 is a homotrimer. A central divalent metal stabilizes the VP2 trimer, possibly calcium. Capsid protein VP3 is a homodimer. Capsid protein VP2 interacts with host ITGA4/ITGB1. Capsid protein VP3 interacts (via C-terminus) with VP1 in the cytoplasm. Capsid VP3 interacts with VP2 (By similarity). Specific enzymatic cleavages yield mature proteins. The capsid assembly seems to be regulated by polyprotein processing. The protease VP4 cleaves itself off the polyprotein, thus releasing pre-VP2 and VP3 within the infected cell. During capsid assembly, the C-terminus of pre-VP2 is further processed by VP4, giving rise to VP2, the external capsid protein and three small peptides that all stay closely associated with the capsid (By similarity). The sequence shown is that of isolate CEF94. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase gamma chain family. +Regulates membrane-cell wall junctions and localized cell wall deposition. Required for establishment of the Casparian strip membrane domain (CSD) and the subsequent formation of Casparian strips, a cell wall modification of the root endodermis that determines an apoplastic barrier between the intraorganismal apoplasm and the extraorganismal apoplasm and prevents lateral diffusion (By similarity). Homodimer and heterodimers. Very restricted localization following a belt shape within the plasma membrane which coincides with the position of the Casparian strip membrane domain in the root endodermis. Belongs to the Casparian strip membrane proteins (CASP) family. +Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. Directly interacts with SKP1 and CUL1. +Allows photoautotrophic growth on dimethyl sulfide (DMS) as the sole electron donor. dimethyl sulfide + 2 Fe(III)-[cytochrome c2] + H2O = dimethyl sulfoxide + 2 Fe(II)-[cytochrome c2] + 2 H(+) Binds 1 [4Fe-4S] cluster. Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit. Heterotrimer of alpha, beta and gamma subunits. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven. Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. +Belongs to the herpesviridae U4 family. +Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +Involved in protein N-glycosylation. Essential for the second step of the dolichol-linked oligosaccharide pathway (By similarity). Heterodimer with ALG13 to form a functional enzyme. Belongs to the ALG14 family. +Part of an ABC transporter complex involved in glucose import. The complex is composed of two ATP-binding proteins (TsgD13), two transmembrane proteins (TsgB13 and TsgC13) and a solute-binding protein (TsgA13). Belongs to the BMP lipoprotein family. +Monothiol glutaredoxin involved in the biogenesis of iron-sulfur clusters (By similarity). Binds one iron-sulfur cluster per dimer. The iron-sulfur cluster is bound between subunits, and is complexed by a bound glutathione and a cysteine residue from each subunit (By similarity). Homodimer. Belongs to the glutaredoxin family. Monothiol subfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. Binds 3 Zn(2+) ions. Belongs to the AP endonuclease 2 family. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Catalyzes the conversion of homogentisate to maleylacetoacetate. homogentisate + O2 = 4-maleylacetoacetate + H(+) Optimum pH is 6.1. Amino-acid degradation; L-phenylalanine degradation; acetoacetate and fumarate from L-phenylalanine: step 4/6. Homohexamer arranged as a dimer of trimers. Defects in Hgd are the cause of alkaptonuria (aku). Aku is an autosomal recessive error of metabolism which is characterized by an increase in the level of homogentisic acid. Belongs to the homogentisate dioxygenase family. +Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate. (2R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (2S)-2-acetolactate + H(+) + NADPH (2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP(+) = (S)-2-ethyl-2-hydroxy-3-oxobutanoate + H(+) + NADPH Binds 2 magnesium ions per subunit. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 2/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 2/4. Belongs to the ketol-acid reductoisomerase family. +The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpB family. +Component of the Rcs signaling system, which controls transcription of numerous genes. Binds to DNA to regulate expression of genes. Belongs to the RcsA family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +Strongly expressed in 2-cell embryos with weak expression detected in other embryonic stages. Also weakly expressed in adult testis. Belongs to the Tdpoz family. +Acts coordinately with atgl-1 within the lipolytic cascade to distribute stored energy to tissues during nutritional deprivation. Interacts with atgl-1. Forms ring-like structures on the surface of lipid droplets. RNAi-mediated knockdown suppresses fasting-induced oxygen consumption. Belongs to the peptidase S33 family. ABHD4/ABHD5 subfamily. +Modulator of adipocyte lipid metabolism. Coats lipid storage droplets to protect them from breakdown by hormone-sensitive lipase (HSL). Its absence may result in leanness (By similarity). Plays a role in unilocular lipid droplet formation by activating CIDEC. Their interaction promotes lipid droplet enlargement and directional net neutral lipid transfer. May modulate lipolysis and triglyceride levels. Interacts with ABHD5 (PubMed:15292255). Interacts with CIDEC (PubMed:23481402). Interacts with AQP7 (By similarity). Lipid droplet surface-associated. Major cAMP-dependent protein kinase-substrate in adipocytes, also dephosphorylated by PP1. When phosphorylated, may be maximally sensitive to HSL and when unphosphorylated, may play a role in the inhibition of lipolysis, by acting as a barrier in lipid droplet (By similarity). Belongs to the perilipin family. Fat, wonderful fat - Issue 10 of May 2001 +(6S)-5,6,7,8-tetrahydrofolate + ATP + formate = (6S)-10-formyltetrahydrofolate + ADP + phosphate One-carbon metabolism; tetrahydrofolate interconversion. Belongs to the formate--tetrahydrofolate ligase family. +Expressed by the venom gland. Is classified as a P-type cytotoxin, since a proline residue stands at position 51 (Pro-31 in standard classification). Belongs to the snake three-finger toxin family. Short-chain subfamily. Orphan group XV sub-subfamily. +Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile) Binds 1 zinc ion per subunit. Monomer. IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily. +Probably involved in the organization of the actin cytoskeleton. May act downstream of CDC42 to induce actin filament assembly leading to cell shape changes. Induces pseudopodia formation in fibroblasts in a CDC42-dependent manner (By similarity). Interacts with CDC42 and RHOQ in a GTP-dependent manner, and with SEPT7. The CRIB domain mediates interaction with CDC42. Belongs to the BORG/CEP family. +H(+) + NADP(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADPH + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Homodimer. Belongs to the ferredoxin--NADP reductase type 2 family. +May act as a neurotransmitter or neuromodulator. Belongs to the allatostatin family. +Belongs to the eukaryotic ribosomal protein eS28 family. +(S)-2,3,4,5-tetrahydrodipicolinate + H2O + succinyl-CoA = (S)-2-succinylamino-6-oxoheptanedioate + CoA Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route): step 1/3. Belongs to the transferase hexapeptide repeat family. +Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps. H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+) Binds 1 dipyrromethane group covalently. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. Monomer. The porphobilinogen subunits are added to the dipyrromethane group. Belongs to the HMBS family. +5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + ATP + L-aspartate = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate: step 1/2. Belongs to the SAICAR synthetase family. +(R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Belongs to the prokaryotic pantothenate kinase family. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Belongs to the cyclophilin-type PPIase family. +Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln). Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by the MOCS3 homolog UBA4. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Prior mcm(5) tRNA modification by the elongator complex is required for 2-thiolation. Also acts as a ubiquitin-like protein (UBL) that is covalently conjugated via an isopeptide bond to lysine residues of target proteins such as AHP1. The thiocarboxylated form serves as substrate for conjugation and oxidative stress specifically induces the formation of UBL-protein conjugates. tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis. C-terminal thiocarboxylation occurs in 2 steps, it is first acyl-adenylated (-COAMP) via the hesA/moeB/thiF part of UBA4, then thiocarboxylated (-COSH) via the rhodanese domain of UBA4. Belongs to the URM1 family. +Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Belongs to the Nudix hydrolase family. RppH subfamily. +Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX. coproporphyrinogen III + 2 H(+) + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; protoporphyrinogen-IX from coproporphyrinogen-III (O2 route): step 1/1. Homodimer. Belongs to the aerobic coproporphyrinogen-III oxidase family. +Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel. Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL. Belongs to the GroES chaperonin family. +Binds and retains class I heavy chains in the endoplasmic reticulum during the early period of virus infection, thereby impairing their transport to the cell surface. Also delays the expression of class I alleles that it cannot affect by direct retention. Binds transporters associated with antigen processing (TAP) and acts as a tapasin inhibitor, preventing class I/TAP association. In consequence, infected cells are masked for immune recognition by cytotoxic T-lymphocytes (By similarity). Expressed at early period of virus infection. The lumenal domain binds directly to the peptide-binding domain of class I molecules. The di-lysine motif confers endoplasmic reticulum localization for type I membrane proteins. Both disulfide bonds are absolutely critical for the interaction with MHC antigens. N-glycosylated; high-mannose. Belongs to the adenoviridae E19 family. +On the 2D-gel the determined MW of this unknown protein is: 70 kDa. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Catalyzes the conversion of 2-hydroxypentadienoic acid (enolic form of 2-oxopent-4-enoate) to 4-hydroxy-2-ketopentanoic acid. (S)-4-hydroxy-2-oxopentanoate = (2Z)-2-hydroxypenta-2,4-dienoate + H2O Aromatic compound metabolism; 3-phenylpropanoate degradation. Belongs to the hydratase/decarboxylase family. MhpD subfamily. +Belongs to the major facilitator superfamily. DHA1 family. MdtH (TC 2.A.1.2.21) subfamily. +The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active -transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The EIIB domain is phosphorylated by phospho-EIIA on a cysteinyl or histidyl residue, depending on the transported sugar. Then, it transfers the phosphoryl group to the sugar substrate concomitantly with the sugar uptake processed by the EIIC domain. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Acetylation is generally linked to gene activation. Methylation at Lys-5 is linked to gene activation. Methylation at Lys-10 is linked to gene repression (By similarity). Belongs to the histone H3 family. +Catalyzes the transfer of the L-Ara4N moiety of the glycolipid undecaprenyl phosphate-alpha-L-Ara4N to lipid A. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. 4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + lipid IVA = lipid IIA + di-trans,octa-cis-undecaprenyl phosphate. Lipopolysaccharide metabolism; 4-amino-4-deoxy-beta-L-arabinose-lipid A biosynthesis. Belongs to the glycosyltransferase 83 family. +RNA-directed RNA polymerase that catalyzes the transcription of viral mRNAs, their capping and polyadenylation. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The viral polymerase binds to the genomic RNA at the 3' leader promoter, and transcribes subsequently all viral mRNAs with a decreasing efficiency. The first gene is the most transcribed, and the last the least transcribed. The viral phosphoprotein acts as a processivity factor. Capping is concommitant with initiation of mRNA transcription. Indeed, a GDP polyribonucleotidyl transferase (PRNTase) adds the cap structure when the nascent RNA chain length has reached few nucleotides. Ribose 2'-O methylation of viral mRNA cap precedes and facilitates subsequent guanine-N-7 methylation, both activities being carried by the viral polymerase. Polyadenylation of mRNAs occur by a stuttering mechanism at a slipery stop site present at the end viral genes. After finishing transcription of a mRNA, the polymerase can resume transcription of the downstream gene. RNA-directed RNA polymerase that catalyzes the replication of viral genomic RNA. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The replicase mode is dependent on intracellular N protein concentration. In this mode, the polymerase replicates the whole viral genome without recognizing transcriptional signals, and the replicated genome is not caped or polyadenylated. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + 2 S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + H(+) + 2 S-adenosyl-L-homocysteine a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-methionine = a 5'-end (5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + H(+) + S-adenosyl-L-homocysteine a 5'-end triphospho-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + GDP + H(+) = a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + diphosphate a 5'-end (5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-homocysteine GTP + H2O = GDP + H(+) + phosphate May form homodimer. Interacts with the P protein. L and P are packaged asymmetrically towards the blunt end of the virus. Belongs to the rhabdoviridae protein L family. +May be involved in transcriptional regulation. Predominant expression in testis. Belongs to the krueppel C2H2-type zinc-finger protein family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +Inhibits phosphatase activities of protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A) complexes. Highly expressed in cerebellum. Substrate for cGMP-dependent protein kinase. Phosphorylated by PRKG1 isoform alpha. Phosphorylation of Thr-68 and Thr-119 is required for its phosphatase activity (By similarity). Substrate for cGMP-dependent protein kinase. +NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADH NADP(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + H(+) + NADPH Membrane lipid metabolism; glycerophospholipid metabolism. Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family. +Regulatory subunit of the histone acetylase B (HAT-B) complex. The complex acetylates 'Lys-12' of histone H4 which is required for telomeric silencing. Component of the HAT-B complex composed of at least HAT1 and HAT2. The HAT-B complex binds to histone H4 tail. Belongs to the WD repeat RBAP46/RBAP48/MSI1 family. +Reticulophagy receptor required for autophagosomal sequestration of endoplasmic reticulum (ER) membranes during ER stress (Ref.5). Confers resistance to ER stress by promoting the autophagic degradation of the ER (ER-phagy or reticulophagy) (Ref.5). Acts as a bridging molecule to mediate the association between atg8 on the autophagic membrane and the vesicle-associated membrane protein-associated proteins (VAPs) scs2 and scs22 on the ER (Ref.5). May play a role in meiosis (PubMed:16303567). Interacts (via the AIM motif) with atg8 (Ref.5). Interacts (via the FFAT motif) with the vesicle-associated membrane protein-associated protein (VAP) family proteins scs2 and scs22 (Ref.5). Accumulates at the preautophagosomal structure when autophagy occurs. Expression is up-regulated during ER stress by the unfolded protein response (UPR) regulator ire1. The atg8-interaction motif (AIM) is required for the association with atg8. The FFAT motif (AIM) is required for the association with the vesicle-associated membrane protein-associated proteins (VAPs) scs2 and scs22. Does not affect growth neither nitrogen starvation-induced ER-phagy, but abolishes DTT-induced ER-phagy. +Belongs to the UPF0324 family. +Component of the large ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Component of the large ribosomal subunit. Belongs to the eukaryotic ribosomal protein eL24 family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates. Cleaves off the terminal sialic acids on the glycosylated HA during virus budding to facilitate virus release. Additionally helps virus spread through the circulation by further removing sialic acids from the cell surface. These cleavages prevent self-aggregation and ensure the efficient spread of the progeny virus from cell to cell. Otherwise, infection would be limited to one round of replication. Described as a receptor-destroying enzyme because it cleaves a terminal sialic acid from the cellular receptors. May facilitate viral invasion of the upper airways by cleaving the sialic acid moieties on the mucin of the airway epithelial cells. Likely to plays a role in the budding process through its association with lipid rafts during intracellular transport. May additionally display a raft-association independent effect on budding. Plays a role in the determination of host range restriction on replication and virulence. Sialidase activity in late endosome/lysosome traffic seems to enhance virus replication. Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates. Binds 1 Ca(2+) ion per subunit. Inhibited by the neuraminidase inhibitors zanamivir (Relenza) and oseltamivir (Tamiflu). These drugs interfere with the release of progeny virus from infected cells and are effective against all influenza strains. Resistance to neuraminidase inhibitors is quite rare. Homotetramer. Preferentially accumulates at the apical plasma membrane in infected polarized epithelial cells, which is the virus assembly site. Uses lipid rafts for cell surface transport and apical sorting. In the virion, forms a mushroom-shaped spike on the surface of the membrane. Intact N-terminus is essential for virion morphogenesis. Possesses two apical sorting signals, one in the ectodomain, which is likely to be a glycan, and the other in the transmembrane domain. The transmembrane domain also plays a role in lipid raft association. N-glycosylated. The influenza B genome consist of 8 RNA segments. Genetic variation of hemagglutinin and/or neuraminidase genes results in the emergence of new influenza strains. The mechanism of variation can be the result of point mutations or the result of genetic reassortment between segments of two different strains. Belongs to the glycosyl hydrolase 34 family. +Catalyzes the NAD(H)-dependent interconversion of D-fructose and D-mannitol in the mannitol metabolic pathway. D-mannitol + NAD(+) = D-fructose + H(+) + NADH Monomer. Belongs to the mannitol dehydrogenase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine One-carbon metabolism; tetrahydrofolate interconversion. Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Mediates the translocation of RNA and DNA across the lysosomal membrane during RNA and DNA autophagy (RDA), a process in which RNA or DNA is directly imported into lysosomes in an ATP-dependent manner, and degraded. Involved in the uptake of single-stranded oligonucleotides by living cells, a process called gymnosis (By similarity). In vitro, mediates the uptake of linear DNA more efficiently than that of circular DNA, but exhibits similar uptake efficacy toward RNA and DNA. Binds long double-stranded RNA (dsRNA) (500 - 700 base pairs), but not dsRNA shorter than 100 bp (By similarity). Interacts with adapter protein complex 1 (AP-1) and AP-2, but not AP-3 and AP-4 (By similarity). Interacts with LAMP2 (By similarity). Mainly localizes to lysosomes and only partly to the plasma membrane (By similarity). Lysosomal localization is required for SIDT2-mediated intracellular degradation of endogenous RNA (By similarity). Highly expressed in the liver, brain, kidney and intestine (at protein level). Glycosylated. Belongs to the SID1 family. +Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor. (S)-dihydroorotate + NAD(+) = H(+) + NADH + orotate Binds 1 FMN per subunit. Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (NAD(+) route): step 1/1. Heterotetramer of 2 PyrK and 2 PyrD type B subunits. Belongs to the dihydroorotate dehydrogenase family. Type 1 subfamily. +Interferon-induced, dsRNA-activated antiviral enzyme which plays a critical role in cellular innate antiviral response. In addition, it may also play a role in other cellular processes such as apoptosis, cell growth, differentiation and gene regulation. Synthesizes preferentially dimers of 2'-5'-oligoadenylates (2-5A) from ATP which then bind to the inactive monomeric form of ribonuclease L (RNase L) leading to its dimerization and subsequent activation. Activation of RNase L leads to degradation of cellular as well as viral RNA, resulting in the inhibition of protein synthesis, thus terminating viral replication. Can mediate the antiviral effect via the classical RNase L-dependent pathway or an alternative antiviral pathway independent of RNase L. Displays antiviral activity against Chikungunya virus (CHIKV), Dengue virus, Sindbis virus (SINV) and Semliki forest virus (SFV). 3 ATP = 5'-triphosphoadenylyl-(2'->5')-adenylyl-(2'->5')-adenosine + 2 diphosphate Produced as a latent enzyme which is activated by dsRNA generated during the course of viral infection (Probable). Strongly activated by long dsRNAs at least 50 nucleotides in length (PubMed:25775560). ssRNA does not activate the enzyme (PubMed:25775560). Monomer. Present at high level in placenta trophoblast. By type I interferon (IFN) and viruses. OAS domain 3 is catalytically active. OAS domain 1 has no catalytic activity but is essential for recognition of long dsRNAs. Belongs to the 2-5A synthase family. +Plays a role in pre-mRNA splicing and 3'-end processing. By recruiting PRPF19 and the PRP19C/Prp19 complex/NTC/Nineteen complex to the RNA polymerase II C-terminal domain (CTD), and thereby pre-mRNA, may couple transcription to splicing. Required for the export of mRNA out of the nucleus, even if the mRNA is encoded by an intron-less gene. Positively regulates pre-mRNA 3'-end processing by recruiting the CFIm complex to cleavage and polyadenylation signals. Interacts with U2AF1L4 (PubMed:16819553). Heterodimer with U2AF1. Binds unphosphorylated SF1. Interacts with SCAF11 and SNW1. Interacts with ZRSR2/U2AF1-RS2. Interacts with RBM17. Interacts with PRPF19; the interaction is direct. Interacts with POLR2A (via the C-terminal domain); Interacts with PRPF19; the interaction is direct. Interacts with POLR2A (via the C-terminal domain); recruits PRPF19 and the Prp19 complex to the pre-mRNA. Interacts with KHDC4 (Isoform 2). Interacts with ZRSR2. Interacts with the SF3B complex composed of SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6 and PHF5A (By similarity). Interacts (via N-terminus) with CPSF7 (via C-terminus); this interaction stimulates pre-mRNA 3'-end processing by promoting the recruitment of the CFIm complex to cleavage and polyadenylation signals (By similarity). Lysyl-hydroxylation at Lys-15 and Lys-276 affects the mRNA splicing activity of the protein, leading to regulate some, but not all, alternative splicing events. Belongs to the splicing factor SR family. +Seems to play a role in the dimerization of PSII. Belongs to the PsbT family. +Responsible for RNA synthesis (replicase and transcriptase), cap addition, and cap methylation. Performs also the polyadenylation of subgenomic mRNAs by a stuttering mechanism at a slipery stop site present at the end of viral genes. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The viral polymerase binds to the genomic RNA at two differents sites in the 3' leader promoter thereby initiating either genome replication or mRNA transcription. In the transcription mode, the polymerase performs the sequential transcription of all mRNAs using a termination-reinitiation mechanism responding to gene start and gene end signals. Some polymerase disengage from the template at each gene junction, resulting in a decreasing abundance of transcripts from the 3' to the 5' end of the genome. The first gene is the most transcribed, and the last the least transcribed. Needs as cofactors the phosphoprotein for processivity and the M2-1 anti-termination protein. Polyribonucleotidyl transferase (PRNTase) adds the cap structure when the nascent RNA chain length has reached few nucleotides (By similarity). Ribose 2'-O methylation of viral mRNA cap precedes and facilitates subsequent guanine-N-7 methylation (By similarity). In the replication mode, the polymerase replicates the whole viral genome without recognizing the gene end transcriptional signals. The ability of the polymerase to override the gene end signals as it is producing the antigenome is probably due to replicative RNA becoming encapsidated with nucleoprotein as it is synthesized (By similarity). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) GTP + H2O = GDP + H(+) + phosphate a 5'-end triphospho-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + GDP + H(+) = a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + diphosphate a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + 2 S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + H(+) + 2 S-adenosyl-L-homocysteine a 5'-end (5'-triphosphoguanosine)-adenylyl-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-methionine = a 5'-end (5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + H(+) + S-adenosyl-L-homocysteine a 5'-end (5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyladenylyl)-adenylyl-cytidylyl-adenosine in mRNA + S-adenosyl-L-homocysteine For RNA-directed RNA polymerase activity. Mn(2+) can stimulate de novo initiation but it is inefficient at supporting elongation of de novo initiated RNA. Interacts with the phosphoprotein (via C-terminus); the association of P and L forms the polymerase complex. Localizes in cytoplasmic inclusion bodies. Contains an RNA-dependent RNA polymerase (RdRp) domain, a polyribonucleotidyl transferase (PRNTase or capping) domain and a methyltransferase (MTase) domain. Belongs to the paramyxovirus L protein family. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Nucleoside triphosphate pyrophosphatase that hydrolyzes dTTP and UTP. May have a dual role in cell division arrest and in preventing the incorporation of modified nucleotides into cellular nucleic acids. dTTP + H2O = diphosphate + dTMP + H(+) H2O + UTP = diphosphate + H(+) + UMP Belongs to the Maf family. YhdE subfamily. +Produces nitric oxide (NO) which is a messenger molecule with diverse functions throughout the body. The production of NO in the salivary gland is used as a vasodilator for blood sucking. H(+) + 2 L-arginine + 3 NADPH + 4 O2 = 4 H2O + 2 L-citrulline + 3 NADP(+) + 2 nitric oxide Binds 1 FAD. Binds 1 FMN. Stimulated by calcium/calmodulin. Belongs to the NOS family. +Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source. ATP + deamido-NAD(+) + NH4(+) = AMP + diphosphate + H(+) + NAD(+) Cofactor biosynthesis; NAD(+) biosynthesis; NAD(+) from deamido-NAD(+) (ammonia route): step 1/1. Homodimer. Belongs to the NAD synthetase family. +Auxiliary protein of the large-conductance, voltage and calcium-activated potassium channel (BK alpha). Modulates gating properties by producing a marked shift in the BK channel's voltage dependence of activation in the hyperpolarizing direction, and in the absence of calcium. KCNU1 channel auxiliary protein. May modulate KCNU1 gating properties. May interact with KCNU1; this interaction may be required for LRRC52 stability and may change the channel gating properties (By similarity). Interacts with KCNMA1. Expression at the cell surface may require the presence of KCNU1. Mainly expressed in testis and skeletal muscle. The transmembrane domain is necessary for interaction with KCNMA1. N-glycosylated. +Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units. Binds 1 Ca(2+) ion per subunit. Monomer. Belongs to the glycosyl hydrolase 13 family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The main subunits of complex b-c1 are: cytochrome b, cytochrome c1 and the Rieske protein. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +This protein binds specifically to 23S rRNA. The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase. Exhibits a low intrinsic GTPase activity, which is essential for nickel insertion. Homodimer. Belongs to the SIMIBI class G3E GTPase family. HypB/HupM subfamily. +Anti-sigma factor for SigI7. Negatively regulates SigI7 activity through direct interaction. Interacts (via RsgI N-terminal anti-sigma domain) with SigI7. Up-regulated in pretreated yellow poplar (PYP)-grown cells. +Mannose-binding lectin which recognizes specific carbohydrate structures and agglutinates a variety of animal cells by binding to cell-surface glycoproteins and glycolipids. May be a calcium-dependent lectin (By similarity). Expressed by the venom gland. Belongs to the true venom lectin family. +ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity. ATP + L-cysteine + L-glutamate = ADP + gamma-L-glutamyl-L-cysteine + H(+) + phosphate Belongs to the glutamate--cysteine ligase type 2 family. YbdK subfamily. +Belongs to the universal ribosomal protein uS9 family. +Plays a regulatory role in calcium-dependent exocytosis and neurotransmitter release (By similarity). Inhibits membrane fusion between transport vesicles and the plasma membrane. May modulate the assembly of trans-SNARE complexes between transport vesicles and the plasma membrane. Competes with STXBP1 for STX1 binding. Inhibits translocation of GLUT4 from intracellular vesicles to the plasma membrane. Part of a complex that contains STX1, STXBP5, SNAP25 and SYT1 (By similarity). Interacts with STX1A and STX4A via its v-SNARE homology domain. Part of a complex that contains STXBP5, STX4A and SNAP23. Cytoplasmic, and associated with vesicular membranes and the plasma membrane. Detected in heart, spleen, lung, skeletal muscle, liver and kidney (at protein level). Detected in brain, particularly in the olfactory bulb and in hippocampus. Detected in the tenia tecta and in the piriform layer of the brain cortex. Belongs to the WD repeat L(2)GL family. +Transcription factor that acts as a transcriptional activator (By similarity). May function as a switch in neuronal development (PubMed:7748786). Low level expression is seen in undifferentiated proliferating cells of the neural epithelium. Greater expression is seen in the maturing neurons after they leave the neural epithelium. Also expressed in the embryonic gut epithelium and adrenal medulla. Expression is maximal at stages 24-31, then begins to decline. Expression is low by stage 37 and disappears by stage 39. Does not appear to be expressed in adults. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type beta chain is a regulatory subunit. Belongs to the ATPase alpha/beta chains family. +Involved in the response to variation in environmental oxygen levels by inhibiting hif-1-mediated gene transcription in a vhl-1-independent manner (PubMed:16980385). Plays a role in susceptibility to killing mediated by P.aeruginosa and by pore-forming toxins produced by B.thuringiensis (PubMed:20011506, PubMed:20865124). Probably by preventing hif-1 transcriptional activity, regulates behavioral responses, such as locomotion speed following acute reoxygenation (PubMed:22405203). Plays a role in normal egg-laying probably by regulating spermatogenesis and in body morphogenesis (PubMed:16980385). Expressed in intestine, some sensory neurons in the head, body wall muscles and socket cells. In L4 stage, expressed in vulva, ventral nerve cord, tail and at higher levels in hypodermis. Induced by hypoxia. Impaired acute acceleration of locomotion speed upon rapid increase in oxygen levels (from 0% to 5-20% oxygen). In double mutants for both rhy-1 and hif-1, normal increase in locomotion speed is restored. +beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Binds 2 magnesium ions per subunit. Carbohydrate biosynthesis; gluconeogenesis. Homotetramer. Belongs to the FBPase class 1 family. +Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP. Allosterically activated by GTP. Pyrimidine metabolism; UMP biosynthesis via salvage pathway; UMP from uracil: step 1/1. Belongs to the UPRTase family. +Belongs to the heat shock protein 70 family. +S-adenosyl-L-methionine-dependent 2'-O-ribose methyltransferase that catalyzes the formation of 2'-O-methylguanosine at position 1370 (Gm1370) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl transferase domain of the mtLSU rRNA. guanosine(1370) in 16S rRNA + S-adenosyl-L-methionine = 2'-O-methylguanosine(1370) in 16S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family. +Participates in the translocation of lipoproteins from the inner membrane to the outer membrane. Only forms a complex with a lipoprotein if the residue after the N-terminal Cys is not an aspartate (The Asp acts as a targeting signal to indicate that the lipoprotein should stay in the inner membrane). Monomer. Belongs to the LolA family. +Defense against chitin-containing fungal pathogens. Binds the hyphal tips of fungi and degrades nascent chitin. Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins. Optimum pH is about 5.0. Stable between pH 4-8. Enzyme activity is retained almost fully under 40 degrees Celsius and completely destroyed at 70 degrees Celsius. At 60 degrees Celsius the activity was 15-30% compared to the untreated enzyme. Localized to the starchy endoderm of the seed May localize to other parts of the seed including the aleurone cells (at protein level). Levels increase from 23 to 40 days after flowering, and are maintained until maturation (at protein level). Belongs to the glycosyl hydrolase 19 family. Chitinase class II subfamily. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Acts as a chemokine-like protein by regulating cell proliferation and migration through activation of G protein-coupled receptors (GPCRs), such as S1PR2 and FPR2 (PubMed:29453251). Stimulates chemotactic migration of macrophages mediated by the MAPK3/ERK1 and AKT1 pathway (By similarity). Blocks TNFSF11/RANKL-induced osteoclast formation from macrophages by inhibiting up-regulation of osteoclast fusogenic and differentiation genes (By similarity). Stimulation of macrophage migration and inhibition of osteoclast formation is mediated through the GPCR FPR2 (By similarity). Acts as a adipokine by negatively regulating vascular smooth muscle cell (VSMC) proliferation and migration in response to platelet-derived growth factor stimulation via GPCR S1PR2 and G protein GNA12/GNA13-transmitted RHOA signaling (PubMed:29453251). Inhibits injury-induced cell proliferation and neointima formation in the femoral arteries (PubMed:29453251). Expressed in the epididymal adipose tissue, in aortic adventitial fibroblasts and low expression in vascular smooth muscle cells (at protein level) (PubMed:29453251). Expressed in the central nervous system, highly expressed in the hypothalamic paraventricular nucleus (PubMed:29453251). Repressed in adipocytes after stimulation with Tnfa, Il6 and Ins1 (PubMed:29453251). Specifically down-regulated in the hypothalamic paraventricular nucleus following water deprivation (PubMed:29453251). Belongs to the TAFA family. +Release of N-terminal glutamate (and to a lesser extent aspartate) from a peptide. Binds 2 divalent metal cations per subunit. Belongs to the peptidase M42 family. +Mediates transport of starch oligosaccharides from the surface of the outer membrane to the periplasm for subsequent degradation. Glycan degradation; starch degradation. Interacts with SusD. By maltose. Abolished ability to grow on starch. Belongs to the TonB-dependent receptor family. +Receptor for abscisic acid (ABA) required for ABA-mediated responses such as stomatal closure and germination inhibition. Inhibits the activity of group-A protein phosphatases type 2C (PP2Cs) when activated by ABA (PubMed:22579247, PubMed:23844015, PubMed:21658606). Can be activated by both (-)-ABA and (+)-ABA (PubMed:23844015). Homodimer and monomer (PubMed:21658606). Binds ABA on one subunit only. ABA-binding favors monomer and trans-homodimer intermediate, and increases PP2C inhibitor activity (PubMed:22579247, PubMed:23844015). Binds both (-)-ABA and (+)-ABA (PubMed:23844015). Binds to CARs protein in an ABA-independent manner, both at the plasma membrane and in the nucleus (By similarity). Interacts with HAB1, ABI1 and ABI2, and possibly with other PP2Cs (PubMed:19407142, PubMed:19898420, PubMed:22579247, PubMed:23844015). Localizes at the plasma membrane in the presence of a CAR protein. Upon interaction with ABA, the 'latch' and 'gate' loops change in conformation leading to a tight dimerization and the creation a surface that enables the receptor to dock into and inhibit the PP2C active site. The synthetic growth inhibitor pyrabactin inhibits ABA-binding and subsequent PP2Cs inhibitor properties. Belongs to the PYR/PYL/RCAR abscisic acid intracellular receptor family. Probable cloning artifact. +This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA. dUTP + H2O = diphosphate + dUMP + H(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 2/2. Belongs to the dUTPase family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate Heterotrimer of A, B and C subunits. Belongs to the amidase family. GatA subfamily. +Cell division protein that may be involved in stabilizing or promoting the assembly of the division complex. Localizes to the division septum. Belongs to the FtsQ/DivIB family. DivIB subfamily. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG (By similarity). Occurs in many kinds of cells as a complex with monomeric actin in a 1:1 ratio (By similarity). Interacts with PFN2 (By similarity). Belongs to the profilin family. +Microtubule-binding protein required to ensure proper cell division and nuclear envelope reassembly by sequestering the endoplasmic reticulum away from chromosomes during mitosis. Probably acts by clearing the endoplasmic reticulum membrane from metaphase chromosomes. Expressed in circumvallate papillae and testis. Belongs to the DP1 family. +Deposition-and-exchange histone chaperone specific for H2AZ1, specifically chaperones H2AZ1 and deposits it into nucleosomes. As component of the SRCAP complex, mediates the ATP-dependent exchange of histone H2AZ1/H2B dimers for nucleosomal H2A/H2B, leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the NuA4 histone acetyltransferase complex which contains the catalytic subunit KAT5/TIP60 and the subunits EP400, TRRAP/PAF400, BRD8/SMAP, EPC1, DMAP1/DNMAP1, RUVBL1/TIP49, RUVBL2, ING3, actin, ACTL6A/BAF53A, MORF4L1/MRG15, MORF4L2/MRGX, MRGBP, YEATS4/GAS41 and VPS72/YL1. Component of a NuA4-related complex which contains EP400, TRRAP/PAF400, SRCAP, BRD8/SMAP, EPC1, DMAP1/DNMAP1, RUVBL1/TIP49, RUVBL2, actin, ACTL6A/BAF53A, VPS72 and YEATS4/GAS41. Also part of a multiprotein complex which contains SRCAP and which binds to H2AZ1/H2AZ. Interacts (via N-terminal domain) with H2AZ1. In all tissues examined, most abundantly in brain and thymus. Belongs to the VPS72/YL1 family. +One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. +May be involved in repressing heterocyst differentiation and may be essential for preventing all vegetative cells from differentiating. Belongs to the short-chain dehydrogenases/reductases (SDR) family. +Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)). 7-carboxy-7-deazaguanine + ATP + NH4(+) = 7-cyano-7-deazaguanine + ADP + H(+) + H2O + phosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. Belongs to the QueC family. +Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. cyanate + 3 H(+) + hydrogencarbonate = 2 CO2 + NH4(+) Belongs to the cyanase family. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +(S)-malate + a quinone = a quinol + oxaloacetate Carbohydrate metabolism; tricarboxylic acid cycle; oxaloacetate from (S)-malate (quinone route): step 1/1. Belongs to the MQO family. +D-glutamate cyclase that converts D-glutamate to 5-oxo-D-proline. D-glutamate = 5-oxo-D-proline + H2O Accumulation of D-glutamate in heart. Mice develop normally and do not display any visible phenotype under normal conditions. Belongs to the D-glutamate cyclase family. +There are 3 tandem-duplicated genes coding for this protein in S.cerevisiae (YLR156W, YLR159W and YLR161W). Additionally, a fourth copy has been disrupted by a Ty1 retrotransposon, which led to the prediction of the 2 dubious ORFs YLR157W-D and YLR157W-E. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +Part of the oxygenase component of the biphenyl dioxygenase system that catalyzes the stereospecific dihydroxylation of the aromatic ring of biphenyl, yielding a dihydrodiol compound. Is essential for biphenyl degradation and growth of Rhodococcus sp. strain RHA1 on biphenyl as the sole source of carbon and energy. Can also use naphtalene and 4-chlorobiphenyl (4-CB) as substrates, as well as some polychlorinated biphenyls (PCB) such as 2,2'-dichlorobiphenyl, 2,3-dichlorobiphenyl and 2,5,2'-trichlorobiphenyl. Exhibits weak activity toward dibenzofuran and dibenzo-p-dioxin. Electrons are transferred from NADH to the [2Fe-2S] cluster in BphA1 via FAD of BphA4 and [2Fe-2S] cluster of BphA3. biphenyl + H(+) + NADH + O2 = (2R,3S)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD(+) Binds 1 [2Fe-2S] cluster per subunit. Binds 1 Fe cation per subunit. Xenobiotic degradation; biphenyl degradation; 2-hydroxy-2,4-pentadienoate and benzoate from biphenyl: step 1/4. Heterohexamer consisting of three BphA1 subunits and three BphA2 subunits. The multicomponent biphenyl dioxygenase system is composed of a ferredoxin reductase (BphA4), a ferredoxin (BphA3), and a terminal oxygenase (BphA1A2). Transcription is up-regulated by aromatic compounds including biphenyl, ethylbenzene, benzene, toluene, xylene, cumene, cymene, and chlorinated benzenes. Is under the control of the BphST two-component regulatory system. Cells lacking this gene lose their ability to grow on biphenyl. Belongs to the bacterial ring-hydroxylating dioxygenase alpha subunit family. +Component of the nexin-dynein regulatory complex (N-DRC) a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. Plays a critical role in the assembly of N-DRC and also stabilizes the assembly of multiple inner dynein arms and radial spokes. Coassembles with CCDC65/DRC2 to form a central scaffold needed for assembly of the N-DRC and its attachment to the outer doublet microtubules. Component of the nexin-dynein regulatory complex (N-DRC). Belongs to the DRC1 family. Truncated C-terminus. +Involved in the degradation of glucose and galactose via the Entner-Doudoroff pathway. Catalyzes the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxygluconate (KDG) forming pyruvate and glyceraldehyde 3-phosphate or glyceraldehyde, respectively. It is also able to catalyze the reversible cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) and 2-keto-3-deoxygalactonate (KDGal). 2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-phosphate + pyruvate 2-dehydro-3-deoxy-6-phospho-D-galactonate = D-glyceraldehyde 3-phosphate + pyruvate Carbohydrate acid metabolism; 2-dehydro-3-deoxy-D-gluconate degradation; D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate: step 2/2. Homotetramer; dimer of dimers. Belongs to the DapA family. KDPG aldolase subfamily. +Light-emitting reaction in luminous bacteria. a long-chain fatty aldehyde + FMNH2 + O2 = a long-chain fatty acid + FMN + 2 H(+) + H2O + hnu Heterodimer of an alpha and a beta chain. +Required for efficient export of polyadenylated RNA. Acts as component of the THO subcomplex of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and which specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. Component of the THO subcomplex of the transcription/export (TREX) complex which seems to have a dynamic structure involving ATP-dependent remodeling. Belongs to the THOC7 family. +Belongs to the UPF0057 (PMP3) family. +Belongs to the universal ribosomal protein uS9 family. +Could be the product of a pseudogene. +Involved in the biosynthesis of UDP-glucuronic acid (UDP-GlcA), providing nucleotide sugars for cell-wall polymers. H2O + 2 NAD(+) + UDP-alpha-D-glucose = 3 H(+) + 2 NADH + UDP-alpha-D-glucuronate Nucleotide-sugar biosynthesis; UDP-alpha-D-glucuronate biosynthesis; UDP-alpha-D-glucuronate from UDP-alpha-D-glucose: step 1/1. Belongs to the UDP-glucose/GDP-mannose dehydrogenase family. +Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP). D-erythrose 4-phosphate + H2O + phosphoenolpyruvate = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 1/7. Belongs to the class-I DAHP synthase family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Belongs to the AIM11 family. +Could influence the NAM7/UPF1 function, possibly at the level of mRNA turnover. Participates in mitochondrial biogenesis (By similarity). Belongs to the ISF1/MBR1 family. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Together with LptD, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Required for the proper assembly of LptD. Binds LPS and may serve as the LPS recognition site at the outer membrane. Component of the lipopolysaccharide transport and assembly complex. Interacts with LptD. Belongs to the LptE lipoprotein family. +Catalyzes, although with low efficiency, the sulfur transfer reaction from thiosulfate to cyanide. hydrogen cyanide + thiosulfate = 2 H(+) + sulfite + thiocyanate Belongs to the GlpE family. +Plays a role in peptidoglycan recycling by cleaving the terminal beta-1,4-linked N-acetylglucosamine (GlcNAc) from peptide-linked peptidoglycan fragments, giving rise to free GlcNAc, anhydro-N-acetylmuramic acid and anhydro-N-acetylmuramic acid-linked peptides. Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. Cell wall biogenesis; peptidoglycan recycling. Belongs to the glycosyl hydrolase 3 family. NagZ subfamily. +ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl-tRNA(Gln) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Acts as a NAD(+) hydrolase (NADase): in response to activation, catalyzes cleavage of NAD(+) into ADP-D-ribose (ADPR) and nicotinamide; NAD(+) cleavage triggering a defense system that promotes cell death (PubMed:31439793). In addition to ADPR, also generates a cyclization variant of cyclic ADPR (cADPR), termed v-cADPR, for which the cyclizing bond is unknown (PubMed:31439793). Also able to hydrolyze NADP(+), but not other NAD(+)-related molecules (PubMed:31439793). v-cADPR activates ThsA, an NAD(+) hydrolase in B.cereus (PubMed:34853457). H2O + NAD(+) = ADP-D-ribose + H(+) + nicotinamide H2O + NADP(+) = ADP-D-ribose 2'-phosphate + H(+) + nicotinamide The TIR domain catalyzes the NAD(+) cleavage (NADase) activity (PubMed:31439793). In contrast to classical TIR-NB-LRR receptor-like proteins, only contains a TIR domain (Probable). +Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate + RNA(n) Belongs to the polyribonucleotide nucleotidyltransferase family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine = ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurCDEF family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Homotetramer. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) Binds 1 Ca(2+) ion per subunit. Homotrimer. Expressed by the venom gland. Is not neurotoxic. Belongs to the phospholipase A2 family. Group I subfamily. D49 sub-subfamily. Extended N-terminus. +Catalyzes the reversible interconversion of serine and glycine with tetrahydromethanopterin (H4MPT) serving as the one-carbon carrier. Also exhibits a pteridine-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. 5,10-methylenetetrahydromethanopterin + glycine + H2O = 5,6,7,8-tetrahydromethanopterin + L-serine Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1. Homodimer. Belongs to the SHMT family. +Catalyzes the condensation of pyruvate and acetyl-coenzyme A to form (R)-citramalate. acetyl-CoA + H2O + pyruvate = (3R)-citramalate + CoA + H(+) Amino-acid biosynthesis; L-isoleucine biosynthesis; 2-oxobutanoate from pyruvate: step 1/3. Homodimer. Belongs to the alpha-IPM synthase/homocitrate synthase family. +Integrin alpha-V/beta-3 (ITGAV:ITGB3) is a receptor for cytotactin, fibronectin, laminin, matrix metalloproteinase-2, osteopontin, osteomodulin, prothrombin, thrombospondin, vitronectin and von Willebrand factor. Integrin alpha-IIB/beta-3 (ITGA2B:ITGB3) is a receptor for fibronectin, fibrinogen, plasminogen, prothrombin, thrombospondin and vitronectin. Integrins alpha-IIB/beta-3 and alpha-V/beta-3 recognize the sequence R-G-D in a wide array of ligands. Integrin alpha-IIB/beta-3 recognizes the sequence H-H-L-G-G-G-A-K-Q-A-G-D-V in fibrinogen gamma chain. Following activation integrin alpha-IIB/beta-3 brings about platelet/platelet interaction through binding of soluble fibrinogen. This step leads to rapid platelet aggregation which physically plugs ruptured endothelial surfaces. Fibrinogen binding enhances SELP expression in activated platelets (By similarity). ITGAV:ITGB3 binds to fractalkine (CX3CL1) and acts as its coreceptor in CX3CR1-dependent fractalkine signaling. ITGAV:ITGB3 binds to NRG1 (via EGF domain) and this binding is essential for NRG1-ERBB signaling. ITGAV:ITGB3 binds to FGF1 and this binding is essential for FGF1 signaling. ITGAV:ITGB3 binds to FGF2 and this binding is essential for FGF2 signaling (By similarity). ITGAV:ITGB3 binds to IGF1 and this binding is essential for IGF1 signaling (By similarity). ITGAV:ITGB3 binds to IGF2 and this binding is essential for IGF2 signaling (By similarity). ITGAV:ITGB3 binds to IL1B and this binding is essential for IL1B signaling (By similarity). ITGAV:ITGB3 binds to PLA2G2A via a site (site 2) which is distinct from the classical ligand-binding site (site 1) and this induces integrin conformational changes and enhanced ligand binding to site 1 (By similarity). ITGAV:ITGB3 acts as a receptor for fibrillin-1 (FBN1) and mediates R-G-D-dependent cell adhesion to FBN1 (By similarity). In brain, plays a role in synaptic transmission and plasticity. Involved in the regulation of the serotonin neurotransmission, is required to localize to specific compartments within the synapse the serotonin receptor SLC6A4 and for an appropriate reuptake of serotonin (By similarity). Controls excitatory synaptic strength by regulating GRIA2-containing AMPAR endocytosis, which affects AMPAR abundance and composition (PubMed:18549786). ITGAV:ITGB3 acts as a receptor for CD40LG (By similarity). Heterodimer of an alpha and a beta subunit (By similarity). Beta-3 (ITGB3) associates with either alpha-IIB (ITGA2B) or alpha-V (ITGAV). Interacts with FLNB and COMP (By similarity). Interacts with PDIA6 following platelet stimulation (By similarity). Interacts with SYK; upon activation by ITGB3 promotes platelet adhesion (By similarity). Interacts with MYO10 (By similarity). Interacts with DAB2. Interacts with FERMT2. Integrin ITGAV:ITGB3 interacts with FBLN5 (via N-terminus) (By similarity). Interacts with EMP2; regulates the levels of the heterodimer ITGA5:ITGB3 integrin expression on the plasma membrane (By similarity). ITGAV:ITGB3 interacts with CCN3 (By similarity). ITGAV:ITGB3 interacts with AGRA2 (By similarity). ITGAV:ITGB3 is found in a ternary complex with CX3CR1 and CX3CL1. ITGAV:ITGB3 is found in a ternary complex with NRG1 and ERBB3. ITGAV:ITGB3 is found in a ternary complex with FGF1 and FGFR1. ITGAV:ITGB3 interacts with FGF2; it is likely that FGF2 can simultaneously bind ITGAV:ITGB3 and FGF receptors (By similarity). ITGAV:ITGB3 binds to IL1B (By similarity). ITGAV:ITGB3 is found in a ternary complex with IGF1 and IGF1R (By similarity). ITGAV:ITGB3 interacts with IGF2 (By similarity). ITGAV:ITGB3 interacts with FBN1 (By similarity). ITGAV:ITGB3 interacts with CD9, CD81 and CD151 (via second extracellular domain) (By similarity). Interacts (via the allosteric site (site 2)) with CXCL12 in a CXCR4-independent manner (By similarity). Interacts with MXRA8/DICAM; the interaction inhibits ITGAV:ITGB3 heterodimer formation (By similarity). ITGAV:ITGB3 interacts with PTN. Forms a complex with PTPRZ1 and PTN that stimulates endothelial cell migration through ITGB3 Tyr-772 phosphorylation (By similarity). ITGAV:ITGB3 interacts with SLC6A4 (By similarity). ITGA2B:ITGB3 interacts with PPIA/CYPA; the interaction is ROS and PPIase activity-dependent and is increased in the presence of thrombin (By similarity). Phosphorylated on tyrosine residues in response to thrombin-induced platelet aggregation. Probably involved in outside-in signaling. Belongs to the integrin beta chain family. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. Belongs to the DNA mismatch repair MutS family. +Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Belongs to the UPF0026 family. +Provides the (R)-glutamate required for cell wall biosynthesis. L-glutamate = D-glutamate Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the aspartate/glutamate racemases family. +DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate. Belongs to the endonuclease V family. +Thiolesterase that catalyzes the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid. an S-(2-hydroxyacyl)glutathione + H2O = a 2-hydroxy carboxylate + glutathione + H(+) (R)-S-lactoylglutathione + H2O = (R)-lactate + glutathione + H(+) Binds 2 Zn(2+) ions per subunit. Secondary metabolite metabolism; methylglyoxal degradation; (R)-lactate from methylglyoxal: step 2/2. Monomer. Testis. Produced by alternative splicing. Also produced by alternative initiation at Met-49 of isoform 1. Alternative initiation has been proven in human. Belongs to the metallo-beta-lactamase superfamily. Glyoxalase II family. Only one single gene encoding glyoxalase II has been identified in vertebrates. In yeast and higher plants, separate genes encode the cytosolic and mitochondrial forms of glyoxalase II. +Facilitates L-arginine uptake, as part of the AaxABC system. The arginine uptake by the bacterium in the macrophage may be a virulence factor against the host innate immune response (By similarity). Belongs to the OprB family. +The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. Belongs to the RecF family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Belongs to the universal stress protein B family. +Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I. di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 4 family. MraY subfamily. +As part of the heme biosynthetic pathway, catalyzes the sequential polymerization of four molecules of porphobilinogen to form hydroxymethylbilane, also known as preuroporphyrinogen. Catalysis begins with the assembly of the dipyrromethane cofactor by the apoenzyme from two molecules of porphobilinogen or from preuroporphyrinogen. The covalently linked cofactor acts as a primer, around which the tetrapyrrole product is assembled. In the last step of catalysis, the product, preuroporphyrinogen, is released, leaving the cofactor bound to the holodeaminase intact. H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4(+) Binds 1 dipyrromethane group covalently. Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 2/4. Monomer. Belongs to the HMBS family. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 3 family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +Found in functional membrane microdomains (FMM) that may be equivalent to eukaryotic membrane rafts. FMMs are highly dynamic and increase in number as cells age. Flotillins are thought to be important factors in membrane fluidity. Homooligomerizes. Belongs to the flotillin-like FloA family. +NAD(+) + prephenate = 3-(4-hydroxyphenyl)pyruvate + CO2 + NADH Amino-acid biosynthesis; L-tyrosine biosynthesis; (4-hydroxyphenyl)pyruvate from prephenate (NAD(+) route): step 1/1. Belongs to the prephenate/arogenate dehydrogenase family. +Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to TFIIK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. In transcription, TFIIH has an essential role in transcription initiation. When the pre-initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module TFIIK controls the initiation of transcription. Component of the 7-subunit TFIIH core complex composed of XPB/SSL2, XPD/RAD3, SSL1, TFB1, TFB2, TFB4 and TFB5, which is active in NER. The core complex associates with the 3-subunit CTD-kinase module TFIIK composed of CCL1, KIN28 and TFB3 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription. Belongs to the TFB4 family. +CoA + 2 oxidized [2Fe-2S]-[ferredoxin] + pyruvate = acetyl-CoA + CO2 + H(+) + 2 reduced [2Fe-2S]-[ferredoxin] 3-methyl-2-oxobutanoate + CoA + 2 oxidized [2Fe-2S]-[ferredoxin] = 2-methylpropanoyl-CoA + CO2 + H(+) + 2 reduced [2Fe-2S]-[ferredoxin] Heterotetramer of one alpha, one beta, one delta and one gamma chain. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +hexadecanoyl-CoA + L-cysteinyl-[protein] = CoA + S-hexadecanoyl-L-cysteinyl-[protein] The DHHC domain is required for palmitoyltransferase activity. Belongs to the DHHC palmitoyltransferase family. +GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel. Generally pentameric. There are five types of GABA(A) receptor chains: alpha, beta, gamma, delta, and rho. Forms a ternary complex with SQSTM1 and PRKCZ. Retina. Belongs to the ligand-gated ion channel (TC 1.A.9) family. Gamma-aminobutyric acid receptor (TC 1.A.9.5) subfamily. GABRR3 sub-subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Catalyzes the conversion of N-acetyl-diaminopimelate to diaminopimelate and acetate. H2O + N-acetyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-2,6-diaminoheptanedioate + acetate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (acetylase route): step 3/3. Belongs to the peptidase M20A family. N-acetyldiaminopimelate deacetylase subfamily. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a 'molecular matchmaker', a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex. Belongs to the DNA mismatch repair MutL/HexB family. +Regulates the transcription of the arc operon, involved in arginine catabolism. Amino-acid degradation; L-arginine degradation via ADI pathway. Belongs to the ArgR family. +Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. ATP + cytidine(34) in tRNA(Ile2) + L-lysine = AMP + diphosphate + H(+) + lysidine(34) in tRNA(Ile2) The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a P-loop motif involved in ATP binding. Belongs to the tRNA(Ile)-lysidine synthase family. +Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-aspartyl-tRNA(Asx) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseA family. +RNA-binding protein that is involved in various steps of RNA biogenesis and processing. Preferentially binds, via its two RNA recognition motifs RRM1 and RRM2, to GU-repeats on RNA molecules predominantly localized within long introns and in the 3'UTR of mRNAs. In turn, regulates the splicing of many non-coding and protein-coding RNAs including proteins involved in neuronal survival, as well as mRNAs that encode proteins relevant for neurodegenerative diseases. Plays a role in maintaining mitochondrial homeostasis by regulating the processing of mitochondrial transcripts. Regulates also mRNA stability by recruiting CNOT7/CAF1 deadenylase on mRNA 3'UTR leading to poly(A) tail deadenylation and thus shortening. In response to oxidative insult, associates with stalled ribosomes localized to stress granules (SGs) and contributes to cell survival (By similarity). Participates also in the normal skeletal muscle formation and regeneration, forming cytoplasmic myo-granules and binding mRNAs that encode sarcomeric proteins (PubMed:30464263). Plays a role in the maintenance of the circadian clock periodicity via stabilization of the CRY1 and CRY2 proteins in a FBXL3-dependent manner (PubMed:27123980). Negatively regulates the expression of CDK6 (By similarity). Regulates the expression of HDAC6, ATG7 and VCP in a PPIA/CYPA-dependent manner (PubMed:25678563). Homodimer. Homooligomer (via its N-terminal domain) (By similarity). Interacts with BRDT (PubMed:22570411). Binds specifically to pyrimidine-rich motifs of TAR DNA and to single stranded TG repeated sequences. Binds to RNA, specifically to UG repeated sequences with a minimum of six contiguous repeats. Interacts with ATXN2; the interaction is RNA-dependent. Interacts with MATR3. Interacts with UBQLN2. Interacts with HNRNPA2B1 (By similarity). Interacts with ZNF106 (PubMed:28072389). Interacts with CNOT7/CAF1 (By similarity). Interacts with CRY2 (PubMed:27123980). Interacts with PPIA/CYPA; the interaction is dependent on RNA-binding activity of TARDBP and PPIase activity of PPIA/CYPA (PubMed:25678563). Acetylation of PPIA/CYPA at 'Lys-125' favors the interaction of TARDBP with PPIA/CYPA (By similarity). Continuously travels in and out of the nucleus. Localizes to stress granules in response to oxidative stress. A small subset localizes in mitochondria. The RRM domains can bind to both DNA and RNA. Hyperphosphorylated. Ubiquitinated. TARDBP depletion leads to atrophy of spinal motor neurons. Affects motor axon, neuromuscular junction and skeletal muscle. +Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate. ATP + L-glutamate = ADP + L-glutamyl 5-phosphate Amino-acid biosynthesis; L-proline biosynthesis; L-glutamate 5-semialdehyde from L-glutamate: step 1/2. Belongs to the glutamate 5-kinase family. +Part of the 50S ribosomal subunit. Contacts protein L32. Belongs to the bacterial ribosomal protein bL17 family. +Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position. Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain. Glycan biosynthesis; glycogen biosynthesis. Monomer. Belongs to the glycosyl hydrolase 13 family. GlgB subfamily. +Member of the two-component regulatory system GtcS/GtcR which may act in the control of the transcription of the grs operon which encodes the multienzymes involved in the biosynthesis of the peptide antibiotic gramicidin S. Phosphorylated by GtcS. +Stimulates the secretion of gonadotropins. Midbrain and hindbrain. Expressed at significantly higher levels during hibernation and post-breeding. Not expressed in pituitary. Belongs to the GnRH family. +Lipid transfer protein that, together with LTPG1, binds to lipids and functions as a component of the cuticular lipid export machinery that performs extensive export of intracellular lipids (e.g. C29 alkane) from epidermal cells to the surface to build the cuticular wax layer and silique walls (PubMed:22891199). Contributes to pre-invasive defense against some non-host powdery mildew pathogens by preventing the penetration of the epidermal cell wall by the fungal agents (e.g. Blumeria graminis f. sp. hordei (Bgh)) (PubMed:30102837). Involved in seed and ovule maturation and development, probably by regulating the fatty acids homeostasis during suberin and sporopollenin biosynthesis or deposition (PubMed:24460633). Targeted to the plasma membrane via the vesicular trafficking system. Up-regulated in the epidermis of top stems. Expressed in roots, cotyledons, seedlings, leaves, stems, buds, flower and silique walls (PubMed:23893219). Preferentially expressed in the shoot apical meristem and the root meristem (PubMed:21558309). Also detected in expanding leaves and petals, developing flowers, and elongating pistils, stamens and siliques (PubMed:21558309). Accumulates in seeds after imbibition (PubMed:23893219). Mainly present in elongating or expanding tissues (PubMed:21558309). Strongly expressed in the aerial portions and root tips of seedlings. Present in stem and leaf epidermis, including the trichomes, leaf mesophyll cells, and stem cortex and xylem. In flowers, observed in the upper portion of the styles, anther filament, and veins of the sepals and petals, silique walls and developing seeds (PubMed:23893219). O-glycosylated on hydroxyprolines; noncontiguous hydroxylproline residues are glycosylated with arabinogalactan. Reduced cuticular wax load on the stem surface and in silique walls, with altered cuticular lipid composition (especially C29 alkane) associated with diffuse cuticular layer structure (PubMed:22891199). Increased susceptibility to penetration of the epidermal cell wall by the non-host mildew fungal agent Blumeria graminis f. sp. hordei (Bgh) (PubMed:30102837). Some early aborted seeds and infertile ovules, and increased salt permeability in seeds (PubMed:24460633). Belongs to the plant LTP family. +Belongs to the SDO1/SBDS family. +With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex. Belongs to the universal ribosomal protein uS12 family. +Catalyzes the oxidation of glycolate to glyoxylate, with a reduction of O2 to H2O2. Is a key enzyme in photorespiration in green plants. glycolate + O2 = glyoxylate + H2O2 Photosynthesis; photorespiration; glycine from 2-phosphoglycolate: step 2/3. Homotetramer. Belongs to the FMN-dependent alpha-hydroxy acid dehydrogenase family. +Cysteine methyltransferase effector that inhibits host cell NF-kappa-B activation by preventing nuclear translocation of host protein RELA/p65 (PubMed:20485572). Acts by mediating cysteine methylation of host proteins TAB2 and TAB3: methylation of a conserved cysteine residue of the RanBP2-type zinc finger (NZF) of TAB2 and TAB3 disrupts zinc-binding, thereby inactivating the ubiquitin chain-binding activity of TAB2 and TAB3, leading to NF-kappa-B inactivation (PubMed:27445336). Also mediates cysteine methylation of host protein ZRANB3, inactivating its ability to bind ubiquitin chains (PubMed:27445336). L-cysteinyl-[protein] + S-adenosyl-L-methionine = H(+) + S-adenosyl-L-homocysteine + S-methyl-L-cysteinyl-[protein] Monomer. Secreted via the type III secretion system (TTSS). Mainly localizes in the cytoplasm of the infected cells, and occasionaly in the host nucleus. Belongs to the NleE/OspZ family. +Part of a complex that provides reducing equivalents for heterodisulfide reductase. The F420-non-reducing hydrogenase is composed of three subunits; MvhA, MvhD and MvhG. It forms a complex with the heterodisulfide reductase (hdr) (By similarity). Belongs to the [NiFe]/[NiFeSe] hydrogenase small subunit family. +DNA-binding protein that regulates the transcription of several genes and is involved in heart development and limb pattern formation (PubMed:10079235). May bind to the core DNA motif of promoters (By similarity). Monomer. Homodimer (via the T-box); binds DNA as homodimer. Shuttles between the cytoplasm and the nucleus. Expressed exclusively in the developing heart and eye. Expression begins within a subset of cardioblasts at neurula stages and continues within the heart during morphogenesis at later tadpole stages. Within the heart tube, expressed in all but the most anterior domain, the bulbus cordis. The T-Box domain binds to double-stranded DNA. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +May be involved in the transport of PQQ or its precursor to the periplasm. Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. Belongs to the PqqB family. +Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons. Belongs to the HrcA family. +Required for leukotriene biosynthesis by ALOX5 (5-lipoxygenase). Anchors ALOX5 to the membrane. Binds arachidonic acid, and could play an essential role in the transfer of arachidonic acid to ALOX5. Binds to MK-886, a compound that blocks the biosynthesis of leukotrienes (By similarity). Homotrimer. Interacts with LTC4S and ALOX5 (By similarity). The C-terminal part after residue 140 is mostly disordered. Belongs to the MAPEG family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) Binds 2 [4Fe-4S] clusters per subunit. NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I 23 kDa subunit family. +Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL16 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Plays a crucial role in crista junction formation and mitochondrial function (PubMed:25764979). Can promote cardiac lipotoxicity by enhancing mitochondrial respiration and fatty acid metabolism in cardiac myoblasts (PubMed:24743151). Promotes cholesterol efflux from macrophage cells. Detected in HDL, LDL and VLDL. Secreted by a microsomal triglyceride transfer protein (MTTP)-dependent mechanism, probably as a VLDL-associated protein that is subsequently transferred to HDL (PubMed:16956892). Component of the mitochondrial contact site and cristae organizing system (MICOS) complex, composed of at least MICOS10/MIC10, CHCHD3/MIC19, CHCHD6/MIC25, APOOL/MIC27, IMMT/MIC60, APOO/MIC23/MIC26 and MICOS13/MIC13. This complex was also known under the names MINOS or MitOS complex. he MICOS complex associates with mitochondrial outer membrane proteins SAMM50, MTX1 and MTX2 (together described as components of the mitochondrial outer membrane sorting assembly machinery (SAM) complex) and DNAJC11, mitochondrial inner membrane protein TMEM11 and with HSPA9 (PubMed:25764979, PubMed:25781180, PubMed:25997101). The MICOS and SAM complexes together with DNAJC11 are part of a large protein complex spanning both membranes termed the mitochondrial intermembrane space bridging (MIB) complex. Interacts with IMMT/MIC60 (PubMed:25764979, PubMed:25781180). Interacts with MICOS10/MIC10 and APOOL/MIC27 (PubMed:25764979). Exists in three distinct forms: a glycosylated and secreted form, an ER/Golgi-resident form and a non-glycosylated mitochondrial form. Expressed in all tissues examined. Up-regulated in diabetic heart. O-glycosylation; glycosaminoglycan of chondroitin-sulfate type. Belongs to the apolipoprotein O/MICOS complex subunit Mic27 family. +Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. Involved in late stages of cytokinesis. Plays a role in endosomal sorting/trafficking of EGF receptor (By similarity). Probable core component of the endosomal sorting required for transport complex III (ESCRT-III). ESCRT-III components are thought to multimerize to form a flat lattice on the perimeter membrane of the endosome. Several assembly forms of ESCRT-III may exist that interact and act sequentially (By similarity). Belongs to the SNF7 family. +Involved in DNA repair and RecF pathway recombination. Belongs to the RecO family. +Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate. 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = H(+) + 2 H2O + phosphate + pyridoxine 5'-phosphate Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. Homooctamer; tetramer of dimers. Belongs to the PNP synthase family. +Cell wall formation. NADP(+) + UDP-N-acetyl-alpha-D-muramate = H(+) + NADPH + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the MurB family. +carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family. +Belongs to the DEFL family. Lacks 1 of the 4 disulfide bonds, which are conserved features of the family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatC family. +Belongs to the bacterial ribosomal protein bL28 family. +Catalyzes the synthesis of beta-nicotinate D-ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP. 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H2O + nicotinate = ADP + diphosphate + nicotinate beta-D-ribonucleotide + phosphate Cofactor biosynthesis; NAD(+) biosynthesis; nicotinate D-ribonucleotide from nicotinate: step 1/1. Transiently phosphorylated on a His residue during the reaction cycle. Phosphorylation strongly increases the affinity for substrates and increases the rate of nicotinate D-ribonucleotide production. Dephosphorylation regenerates the low-affinity form of the enzyme, leading to product release. Belongs to the NAPRTase family. +Catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides. Release of any N-terminal amino acid, including proline, that is linked to proline, even from a dipeptide or tripeptide. Binds 2 manganese ions per subunit. Belongs to the peptidase M24B family. Extended N-terminus. Extended N-terminus. +Catalyzes the transfer of succinyl-CoA to arginine to produce N(2)-succinylarginine. L-arginine + succinyl-CoA = CoA + H(+) + N(2)-succinyl-L-arginine Amino-acid degradation; L-arginine degradation via AST pathway; L-glutamate and succinate from L-arginine: step 1/5. Belongs to the arginine N-succinyltransferase family. +Belongs to the UPF0309 family. +Protamines substitute for histones in the chromatin of sperm during the haploid phase of spermatogenesis. They compact sperm DNA into a highly condensed, stable and inactive complex. Testis. Belongs to the protamine P1 family. +E3 ubiquitin-protein ligase, which catalyzes ubiquitination of target proteins together with ubiquitin-conjugating enzyme E2 ube2l3. Acts as an atypical E3 ubiquitin-protein ligase by working together with cullin-RING ubiquitin ligase (CRL) complexes and initiating ubiquitination of CRL substrates: associates with CRL complexes and specifically mediates addition of the first ubiquitin on CRLs targets. The initial ubiquitin is then elongated. E3 ubiquitin-protein ligase activity is activated upon binding to neddylated cullin-RING ubiquitin ligase complexes. [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N(6)-ubiquitinyl-L-lysine. Autoinhibited by the ariadne domain, which masks the second RING-type zinc finger that contains the active site and inhibits the E3 activity. Inhibition is relieved upon binding to neddylated cullin-RING ubiquitin ligase complexes, which activate the E3 ligase activity of ARIH1. Protein modification; protein ubiquitination. Interacts (via the first RING-type zinc finger) with ube2l3. Associates with cullin-RING ubiquitin ligase (CRL) complexes containing neddylated cullin. Members of the RBR family are atypical E3 ligases. They interact with the E2 conjugating enzyme UBE2L3 and function like HECT-type E3 enzymes: they bind E2s via the first RING-type zinc finger, but require an obligate trans-thiolation step during the ubiquitin transfer, requiring a conserved active site Cys residue in the second RING-type zinc finger. The active site probably forms a thioester intermediate with ubiquitin taken from the active-site cysteine of the E2 before ultimately transferring it to a Lys residue on the substrate. The Ariadne domain inhibits activity by masking the second RING-type zinc finger that contains the active site. Belongs to the RBR family. Ariadne subfamily. +Acts as a chaperone. By heat shock. Acts as an early heat shock protein, induced within, and reaches a maximum by, 5 to 15 minutes of the start of heat stress. Levels decrease over time. On the 2D-gel the determined pI of this protein is: 4.7, its MW is: 70 kDa. Belongs to the heat shock protein 70 family. +Was identified as a high-confidence drug target. Belongs to the mycobacterial PPE family. +CIPK serine-threonine protein kinases interact with CBL proteins. Binding of a CBL protein to the regulatory NAF domain of CIPK protein lead to the activation of the kinase in a calcium-dependent manner. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts with CBL1/SCaBP5, CBL4/SOS3, ABI1 and ABI2. A number of isoforms are produced. According to EST sequences. Ubiquitous. Co-expressed with CBL1 in guard cells. Slightly repressed by salt stress. The activation loop within the kinase domain is the target of phosphorylation/activation by upstream protein kinases. The PPI motif mediates the interaction with the ABI (abscisic acid-insensitive) phosphatases (By similarity). Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. SNF1 subfamily. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Repressed under conditions of excess protein secretion capacity and derepressed when protein secretion becomes limiting. This is regulated by SecM. Belongs to the SecA family. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL30 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +Proton-conducting pore forming subunit of the membrane integral V0 complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. V-ATPase is a heteromultimeric enzyme composed of a peripheral catalytic V1 complex (main components: subunits A, B, C, D, E, and F) attached to an integral membrane V0 proton pore complex (main component: the proteolipid protein; which is present as a hexamer that forms the proton-conducting pore). Tonoplast. Belongs to the V-ATPase proteolipid subunit family. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG. Belongs to the NqrDE/RnfAE family. +Seems to be involved in transcriptional silencing in heterochromatin-like complexes. Recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression. May contribute to the association of the heterochromatin with the inner nuclear membrane through its interaction with lamin B receptor (LBR). Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins. Contributes to the conversion of local chromatin to a heterochromatin-like repressive state through H3 'Lys-9' trimethylation, mediates the recruitment of the methyltransferases SUV39H1 and/or SUV39H2 by the PER complex to the E-box elements of the circadian target genes such as PER2 itself or PER1. Mediates the recruitment of NIPBL to sites of DNA damage at double-strand breaks (DSBs) (PubMed:28167679). Binds directly to CHAF1A. Interacts with histone H3 methylated at 'Lys-9' (PubMed:11242053). Part of the E2F6.com-1 complex in G0 phase composed of E2F6, MGA, MAX, TFDP1, CBX3, BAT8, EUHMTASE1, RING1, RNF2, MBLR, L3MBTL2 and YAF2. Interacts with INCENP, TRIM28/TIF1B, KMT5B, KMT5C and SP100 (PubMed:10330177, PubMed:12004135, PubMed:9636146). Interacts with TIF1A (By similarity). Interacts with MIS12 and DSN1 (PubMed:15502821). Can interact directly with CBX5 via the chromoshadow domain (PubMed:9169472). Interacts with POGZ (PubMed:20850016, PubMed:20562864). Interacts with CHAMP1 (PubMed:20850016). The large PER complex involved in the histone methylation is composed of at least PER2, CBX3, TRIM28, SUV39H1 and/or SUV39H2; CBX3 mediates the formation of the complex. Interacts with INCENP (PubMed:9864353, PubMed:21346195). Interacts with NIPBL (via PxVxL motif) (PubMed:28167679). Interacts with LRIF1 (via PxVxL motif) (PubMed:23542155). Interacts with TTLL12 (PubMed:23251473). Interacts with ZNF263; recruited to the SIX3 promoter along with other proteins involved in chromatin modification and transcriptional corepression where it contributes to transcriptional repression (PubMed:32051553). Associates with euchromatin and is largely excluded from constitutive heterochromatin. May be associated with microtubules and mitotic poles during mitosis (Potential). Phosphorylated by PIM1. Phosphorylated during interphase and possibly hyper-phosphorylated during mitosis. Was previously reported to interact with ASXL1. However, this publication has been retracted. +Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions. H2O + XTP = diphosphate + H(+) + XMP dITP + H2O = dIMP + diphosphate + H(+) H2O + ITP = diphosphate + H(+) + IMP Binds 1 Mg(2+) ion per subunit. Homodimer. Belongs to the HAM1 NTPase family. +Plays a role in mediating bacterial evasion from the host autophagic pathway. Secreted via the bsa type III secretion system. Belongs to the BopA/IcsB family. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +The peptide sequences have not been found in the complete proteome. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (HmuV), two transmembrane proteins (HmuU) and a solute-binding protein (HmuT). Belongs to the ABC transporter superfamily. Heme (hemin) importer (TC 3.A.1.14.5) family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 4L family. +Multifunctional regulator of fatty acid metabolism. Homodimer. +mRNA cap-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. In the eIF-3 complex, eif3d specifically recognizes and binds the 7-methylguanosine cap of a subset of mRNAs. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The RNA gate region regulates mRNA cap recognition to prevent promiscuous mRNA-binding before assembly of eif3d into the full eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the eIF-3 subunit D family. +Involved in resistance to arsenate. Catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)]. The resulting arsenite is then extruded from the cell via the aquaglyceroporin AqpS. Does not display antimonate reductase activity. [glutaredoxin]-dithiol + arsenate + glutathione + H(+) = arsenite + glutathionyl-S-S-[glutaredoxin] + H2O Disruption mutant shows selective sensitivity to arsenate. Does not affect sensitivity to antimonate [Sb(V)]. Belongs to the ArsC family. +Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine Purine metabolism; AMP biosynthesis via salvage pathway; AMP from adenine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. +Catalyzes the reversible oxidation of malate to oxaloacetate. (S)-malate + NAD(+) = H(+) + NADH + oxaloacetate Belongs to the LDH/MDH superfamily. MDH type 3 family. +Belongs to the FliE family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the proton channel; it may play a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase A chain family. +Could be involved in late stage of protein degradation. Cleavage of Pro-|-Phe and Ala-|-Ala bonds. Binds 1 zinc ion. Present with 8910 molecules/cell in log phase SD medium. Belongs to the peptidase M3 family. +ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly) Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. +Major capsid protein that self-associates to form 240 hexon trimers, each in the shape of a hexagon, building most of the pseudo T=25 capsid. Assembled into trimeric units with the help of the chaperone shutoff protein. Transported by pre-protein VI to the nucleus where it associates with other structural proteins to form an empty capsid. Might be involved, through its interaction with host dyneins, in the intracellular microtubule-dependent transport of incoming viral capsid to the nucleus. Homotrimer. Interacts with the capsid vertex protein; this interaction binds the peripentonal hexons to the neighboring penton base. Interacts with the hexon-linking protein; this interaction tethers the hexons surrounding the penton to those situated in the central plate of the facet. Interacts with the hexon-interlacing protein; this interaction lashes the hexons together. Interacts with host dyneins DYNC1LI1 and DYNC1I2; this interaction might be involved in intracellular microtubule-dependent transport of incoming viral capsid. Interacts with the shutoff protein; this interaction allows folding and formation of hexons trimers. Interacts with pre-protein VI; this interaction probably allows nuclear import of hexon trimers and possibly pre-capsid assembly. Forms the capsid icosahedric shell. Present in 720 copies per virion, assembled in 240 trimers. Expressed in the late phase of the viral replicative cycle. All late proteins expressed from the major late promoter are produced by alternative splicing and alternative polyadenylation of the same gene giving rise to non-overlapping ORFs. A leader sequence is present in the N-terminus of all these mRNAs and is recognized by the viral shutoff protein to provide expression although conventional translation via ribosome scanning from the cap has been shut off in the host cell. Belongs to the adenoviridae hexon protein family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Belongs to the ODF3 family. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +Involved in the biosynthesis of nocamycin I and nocamycin II (PubMed:28818448). Catalyzes the methylation of nocamycin E to yield nocamycin I (PubMed:28818448). nocamycin E + S-adenosyl-L-methionine = nocamycin I + S-adenosyl-L-homocysteine Antibiotic biosynthesis. Mutant loses the capability to produce nocamycin I and nocamycin II. Mutant produces a new nocamycin intermediate, 21-demethyl-nocamycin I, which was designated as nocamycin E. Belongs to the methyltransferase superfamily. Extended N-terminus. +PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity). Modulates the uptake of MRP substrates into the vacuole; reduces metolachlor-GS (MOC-GS) and enhances 17-beta-estradiol 17-(beta-D-glucuronide) (E(2)17betaG) uptake. Regulates cell elongation and orientation. Functions as a positive regulator of PGP1-mediated auxin transport. Confers drug modulation of PGP1 efflux activity as interaction with NPA or flavonol quercetin prevents its physical and functional interaction with PGP1. Required for the proper localization of auxin-related ABCB transporters. Plays a role in brassinosteroid (BR) signaling pathway. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Interacts with calmodulin (CaM), MRP1, MRP2, MDR1/PGP1, MDR11/PGP19 and SHD/HSP90. Interacts with 1-naphthylphthalamic acid (NPA). Plants display helical rotation of several organs. Belongs to the FKBP-type PPIase family. +Histone methyltransferase that specifically monomethylates 'Lys-27' of histone H3 (H3K27me1). Has much higher activity on nucleosomes containing H3.1 than H3.3. Involved in the formation of constitutive heterochromatin and the silencing of heterochromatic elements. L-lysyl(27)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl(27)-[histone H3] + S-adenosyl-L-homocysteine Homodimer. Belongs to the class V-like SAM-binding methyltransferase superfamily. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. Plays a role in early development. In DNA damage response is required for cell survival after ionizing radiation. In vitro shown to be involved in the homologous recombination mechanism for the repair of double-strand breaks (DSBs). Its localization to DNA damage foci requires RNF8 and UBE2N. Recruits TP53BP1 to DNA damage foci and, at least in particular repair processes, effective DNA damage response appears to require the association with TP53BP1 phosphorylated by ATM at 'Ser-25'. Together with TP53BP1 regulates ATM association. Proposed to recruit PAGR1 to sites of DNA damage and the PAGR1:PAXIP1 complex is required for cell survival in response to DNA damage; the function is probably independent of MLL-containing histone methyltransferase (HMT) complexes. However, this function has been questioned (By similarity). Promotes ubiquitination of PCNA following UV irradiation and may regulate recruitment of polymerase eta and RAD51 to chromatin after DNA damage. Proposed to be involved in transcriptional regulation by linking MLL-containing histone methyltransferase (HMT) complexes to gene promoters by interacting with promoter-bound transcription factors such as PAX2. Associates with gene promoters that are known to be regulated by KMT2D/MLL2. During immunoglobulin class switching in activated B-cells is involved in trimethylation of histone H3 at 'Lys-4' and in transcription initiation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus; this function appears to involve the recruitment of MLL-containing HMT complexes. Conflictingly, its function in transcriptional regulation during immunoglobulin class switching is reported to be independent of the MLL2/MLL3 complex (By similarity). Interacts with the C-terminal transactivation domain of PAX2 (By similarity). Forms a constitutive complex with PAGR1 independently of the MLL2/MLL3 complex (By similarity). Interacts with TP53BP1 (when phosphorylated at the N-terminus by ATM) (PubMed:15456759, PubMed:17690115, PubMed:23727112). Interacts with HLTF (PubMed:19723507). Component of the KMT2 family MLL2/MLL3 complex (also named ASCOM complex), at least composed of the HMTs KMT2D and/or KMT2C, the common subunits ASH2L, RBBP5, WDR5 and DPY30, and the complex type-specific subunits PAXIP1/PTIP, PAGR1, NCOA6 and KDM6A; required for the association of PAGR1 with the MLL2/MLL3 complex (PubMed:17178841, PubMed:17500065, PubMed:17761849, PubMed:17925232). Interacts with NUPR1; this interaction prevents PAXIP1 inhibition of PAX2 transcription factor activity (PubMed:11940591). Localizes to DNA damage foci upon ionizing radiation. The BRCT 1 and 2 domains mediate the interaction with PAGR1A. The BRCT 5 and 6 domains mediate the association with the MLL2/MLL3 complex (By similarity). The BRCT 5 and 6 domains function as a single module and are necessary and sufficient for in vitro phospho-specific binding (substrates phosphorylated by the kinases ataxia telangiectasia-mutated (ATM), ataxia telangiectasia and RAD3-related (ATR) in response to gamma irradiation). In contrast, in vivo two pairs of BRCT domains (3-6) bind to phosphorylated TP53BP1 much more efficiently. The terminology of MLL proteins in mammalia is not consistent also concerning the terminology of MLL protein-containing complexes. The decribed MLL2/MLL3 complex is commonly described as MLL3/MLL4 complex in literature. Truncated N-terminus. Contaminating sequence. Intron retention. +RNA-binding protein implicated in the regulation of several post-transcriptional events. Involved in pre-mRNA alternative splicing, mRNA translation and stability. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of TNNT2 in embryonic, but not adult, skeletal muscle. Activates TNNT2 exon 5 inclusion by antagonizing the repressive effect of PTB. Acts as both an activator and repressor of a pair of coregulated exons: promotes inclusion of the smooth muscle (SM) exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs. Promotes inclusion of exonS 21 and exclusion of exon 5 of the NMDA receptor R1 pre-mRNA. Involved in the apoB RNA editing activity. Increases COX2 mRNA stability and inhibits COX2 mRNA translation in epithelial cells after radiation injury. Modulates the cellular apoptosis program by regulating COX2-mediated prostaglandin E2 (PGE2) expression. Binds to (CUG)n triplet repeats in the 3'-UTR of transcripts such as DMPK. Binds to the muscle-specific splicing enhancer (MSE) intronic sites flanking the TNNT2 alternative exon 5. Binds preferentially to UG-rich sequences, in particular UG repeat and UGUU motifs. Binds to apoB mRNA, specifically to AU-rich sequences located immediatly upstream of the edited cytidine. Binds AU-rich sequences in the 3'-UTR of COX2 mRNA. Binds to an intronic RNA element responsible for the silencing of exon 21 splicing. Binds to (CUG)n repeats (By similarity). May be a specific regulator of miRNA biogenesis. Binds to primary microRNA pri-MIR140 and, with CELF1, negatively regulates the processing to mature miRNA (By similarity). Interacts with A1CF. Accumulates in the cytoplasm after ionizing radiation. Colocalizes with APOBEC1 and A1CF. RNA-binding activity is detected in both nuclear and cytoplasmic compartments (By similarity). Belongs to the CELF/BRUNOL family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Catalytically inactive phosphatase (PubMed:7592916). Acts as a nuclear anchor for MAPK1/MAPK3 (ERK1/ERK2) (By similarity). Modulates cell-fate decisions and cell migration by spatiotemporal regulation of MAPK1/MAPK3 (ERK1/ERK2) (By similarity). By binding to the F-box of FBXW7, prevents the assembly of FBXW7 into the SCF E3 ubiquitin-protein ligase complex, and thereby inhibits degradation of its substrates (By similarity). Plays a role in spermatogenesis (PubMed:11842224). Interacts with MAPK1; independently of MAPK1 phosphorylation status (By similarity). Interacts with CARHSP1/Crhsp-24 (PubMed:11842224). Interacts (via FQQ motif) with FBXW7 (via F-box domain); the interaction is direct and prevents FBXW7 interaction with SKP1, a component of the SCF(FBXW7) complex (By similarity). Predominantly localizes to the nucleus. Widely expressed with highest levels in muscle, testis and brain (PubMed:7592916). In testis, expression starts 13-14 days after birth and is limited to the seminiferous tubule and to round and elongating spermatids (PubMed:11842224). Expression is low in condensing spermatids and pachytene spermatocytes, and absent in spermatogonia, spermatozoa and somatic Sertoli cells (PubMed:11842224). Males are infertile due to a disrupted spermatid development, resulting in a >1000-fold decrease in spermatozoa production. Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily. Contains a Gly residue instead of a conserved Cys residue at position 120 in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. The binding pocket is however sufficiently preserved to bind phosphorylated substrates, and may protect them from phosphatases. +Defense against chitin-containing fungal pathogens. Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins. By wounding. Belongs to the glycosyl hydrolase 19 family. Chitinase class I subfamily. +The actual biological function of YdiB remains unclear, nor is it known whether 3-dehydroshikimate or quinate represents the natural substrate. Catalyzes the reversible NAD-dependent reduction of both 3-dehydroshikimate (DHSA) and 3-dehydroquinate to yield shikimate (SA) and quinate, respectively. It can use both NAD or NADP for catalysis, however it has higher catalytic efficiency with NAD. L-quinate + NAD(+) = 3-dehydroquinate + H(+) + NADH L-quinate + NADP(+) = 3-dehydroquinate + H(+) + NADPH NADP(+) + shikimate = 3-dehydroshikimate + H(+) + NADPH NAD(+) + shikimate = 3-dehydroshikimate + H(+) + NADH Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 4/7. Homodimer. Belongs to the shikimate dehydrogenase family. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +H(+) + orotidine 5'-phosphate = CO2 + UMP Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. Belongs to the OMP decarboxylase family. +Class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and plasma cell membrane fusion, the heptad repeat (HR) regions assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and plasma cell membranes. Directs fusion of viral and cellular membranes leading to delivery of the nucleocapsid into the cytoplasm. This fusion is pH independent and occurs directly at the outer cell membrane. The trimer of F1-F2 (F protein) probably interacts with H at the virion surface. Upon HN binding to its cellular receptor, the hydrophobic fusion peptide is unmasked and interacts with the cellular membrane, inducing the fusion between cell and virion membranes. Later in infection, F proteins expressed at the plasma membrane of infected cells could mediate fusion with adjacent cells to form syncytia, a cytopathic effect that could lead to tissue necrosis (By similarity). Homotrimer of disulfide-linked F1-F2. The inactive precursor F0 is glycosylated and proteolytically cleaved into F1 and F2 to be functionally active. The cleavage is mediated by cellular proteases during the transport and maturation of the polypeptide (By similarity). Belongs to the paramyxoviruses fusion glycoprotein family. +Cleaves proteins, imported into the mitochondrion, to their mature size. While most mitochondrial precursor proteins are processed to the mature form in one step by mitochondrial processing peptidase (MPP), the sequential cleavage by MIP of an octapeptide after initial processing by MPP is a required step for a subgroup of nuclear-encoded precursor proteins destined for the matrix or the inner membrane (By similarity). Release of an N-terminal octapeptide as second stage of processing of some proteins imported into the mitochondrion. Binds 1 zinc ion. Belongs to the peptidase M3 family. +Exopeptidase that catalyzes the hydrolytic cleavage of multi-L-arginyl-poly-L-aspartic acid (cyanophycin; a water-insoluble reserve polymer) into aspartate-arginine dipeptides. [L-4-(L-arginin-2-N-yl)aspartate](n) + H2O = [L-4-(L-arginin-2-N-yl)aspartate](n-1) + L-4-(L-arginin-2-N-yl)aspartate Belongs to the peptidase S51 family. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group. Belongs to the acyl carrier protein (ACP) family. +D-arabinitol + NAD(+) = D-xylulose + H(+) + NADH Carbohydrate metabolism; D-arabinitol metabolism. Belongs to the mannitol dehydrogenase family. +Part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair. The complex may facilitate opening of the processed DNA ends to aid in the recruitment of HerA and NurA. Rad50 controls the balance between DNA end bridging and DNA resection via ATP-dependent structural rearrangements of the Rad50/Mre11 complex. Binds 1 zinc ion per homodimer. Homodimer. Forms a heterotetramer composed of two Mre11 subunits and two Rad50 subunits. The two conserved Cys that bind zinc constitute the zinc-hook, which separates the large intramolecular coiled coil regions. The 2 Cys residues coordinate one molecule of zinc with the help of the 2 Cys residues of the zinc-hook of another Rad50 molecule, thereby forming a V-shaped homodimer. Belongs to the SMC family. RAD50 subfamily. +Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions. H2O + XTP = diphosphate + H(+) + XMP dITP + H2O = dIMP + diphosphate + H(+) H2O + ITP = diphosphate + H(+) + IMP Binds 1 Mg(2+) ion per subunit. Homodimer. Belongs to the HAM1 NTPase family. +Belongs to the bacterial ribosomal protein bS21 family. +Receptor for a number of inflammatory CC-chemokines including CCL3/MIP-1-alpha, CCL4/MIP-1-beta and RANTES and subsequently transduces a signal by increasing the intracellular calcium ion level. May play a role in the control of granulocytic lineage proliferation or differentiation. Participates in T-lymphocyte migration to the infection site by acting as a chemotactic receptor. Interacts with PRAF2. Efficient ligand binding to CCL3/MIP-1alpha and CCL4/MIP-1beta requires sulfation, O-glycosylation and sialic acid modifications. Glycosylation on Ser-6 is required for efficient binding of CCL4. Interacts with GRK2. Interacts with ARRB1 and ARRB2. Interacts with CNIH4. Interacts with S100A4; this interaction stimulates T-lymphocyte chemotaxis. Sulfated on at least 2 of the N-terminal tyrosines. Sulfation is required for efficient binding of the chemokines, CCL3 and CCL4 (By similarity). Palmitoylation in the C-terminal is important for cell surface expression. Phosphorylation on serine residues in the C-terminal is stimulated by binding CC chemokines especially by APO-RANTES. O-glycosylated, but not N-glycosylated. Ser-6 appears to be the major site even if Ser-7 may be also O-glycosylated. Also sialylated glycans present which contribute to chemokine binding. Thr-16 and Ser-17 may also be glycosylated and, if so, with small moieties such as a T-antigen. Belongs to the G-protein coupled receptor 1 family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Belongs to the bacterial ribosomal protein bL36 family. +Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. The eIF-3 complex interacts with pix. Interacts with mxt (By similarity). Belongs to the eIF-3 subunit E family. +Activates the transcription of the soxS gene which itself controls the superoxide response regulon. SoxR contains a 2Fe-2S iron-sulfur cluster that may act as a redox sensor system that recognizes superoxide. The variable redox state of the Fe-S cluster is employed in vivo to modulate the transcriptional activity of SoxR in response to specific types of oxidative stress (By similarity). Homodimer. +Part of a complex that catalyzes the reversible cleavage of acetyl-CoA, allowing autotrophic growth from CO(2). Probably maintains the overall quaternary structure of the ACDS complex. Heterodimer of delta and gamma chains. The ACDS complex is made up of alpha, epsilon, beta, gamma and delta chains with a probable stoichiometry of (alpha(2)epsilon(2))(4)-beta(8)-(gamma(1)delta(1))(8). Belongs to the CdhD family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Belongs to the UPF0102 family. +Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed. Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides. Binds 2 divalent metal cations per subunit. Has a high-affinity and a low affinity metal-binding site. The true nature of the physiological cofactor is under debate. The enzyme is active with cobalt, zinc, manganese or divalent iron ions. Most likely, methionine aminopeptidases function as mononuclear Fe(2+)-metalloproteases under physiological conditions, and the catalytically relevant metal-binding site has been assigned to the histidine-containing high-affinity site. Monomer. Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily. +Part of the elfADCG-ycbUVF fimbrial operon, which promotes adhesion of bacteria to different abiotic surfaces. Could be required for the biogenesis of the ElfA fimbriae. Expression is negatively regulated by H-NS and subjected to cAMP receptor protein (CRP)-mediated catabolite repression. The operon is cryptic under classical laboratory conditions, but is functional when constitutively expressed. Belongs to the periplasmic pilus chaperone family. +Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP. H2O + P(1),P(4)-bis(5'-adenosyl) tetraphosphate = 2 ADP + 2 H(+) Belongs to the Ap4A hydrolase family. +Involved in the regulation of glutamine synthetase GlnA, a key enzyme in the process to assimilate ammonia. When cellular nitrogen levels are high, the C-terminal adenylyl transferase (AT) inactivates GlnA by covalent transfer of an adenylyl group from ATP to specific tyrosine residue of GlnA, thus reducing its activity. Conversely, when nitrogen levels are low, the N-terminal adenylyl removase (AR) activates GlnA by removing the adenylyl group by phosphorolysis, increasing its activity. The regulatory region of GlnE binds the signal transduction protein PII (GlnB) which indicates the nitrogen status of the cell. [glutamine synthetase]-O(4)-(5'-adenylyl)-L-tyrosine + phosphate = [glutamine synthetase]-L-tyrosine + ADP [glutamine synthetase]-L-tyrosine + ATP = [glutamine synthetase]-O(4)-(5'-adenylyl)-L-tyrosine + diphosphate Belongs to the GlnE family. +Belongs to the universal ribosomal protein uS9 family. +Catalyzes the ATP- as well as the pyrophosphate-dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK/P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P-Ser-HPr). [HPr protein]-L-serine + ATP = [HPr protein]-O-phospho-L-serine + ADP + H(+) [HPr protein]-O-phospho-L-serine + H(+) + phosphate = [HPr protein]-L-serine + diphosphate Homohexamer. The Walker A ATP-binding motif also binds Pi and PPi. Both phosphorylation and phosphorolysis are carried out by the same active site and suggest a common mechanism for both reactions. Belongs to the HPrK/P family. +Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins. Monomer. Stomach-specific. Lysozyme C is capable of both hydrolysis and transglycosylation; it shows also a slight esterase activity. It acts rapidly on both peptide-substituted and unsubstituted peptidoglycan, and slowly on chitin oligosaccharides. The ruminant gastric lysozymes, which digest symbiotic bacteria coming with cud from the rumen, are much more resistant to inactivation by pepsin than are other lysozymes. Belongs to the glycosyl hydrolase 22 family. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +Role in sperm cell division, maturation, or function. This receptor mediates its action by association with G proteins that activate a phosphatidylinositol-calcium second messenger system. Interacts with C6orf89. Belongs to the G-protein coupled receptor 1 family. +Possible transcriptional activator. Localized to the animal hemisphere of early cleavage stage embryos. Zygotic expression is restricted to the dorsal part of the epibranchial placodes of the head within a region located near the tip of the first, second and third visceral pouch. Expressed both maternally and zygotically. Maternal levels decrease rapidly during the early cleavage stages. Zygotic expression begins at neurulation. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +Positive regulator of germination and plant growth. Slower germination and root growth, delayed growth and flowering. +NADPH-dependent reductase which is a central component of the cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery. Transfers electrons from NADPH via its FAD and FMN prosthetic groups to the [2Fe-2S] cluster of dre2, another key component of the CIA machinery. In turn, this reduced cluster provides electrons for assembly of cytosolic iron-sulfur cluster proteins. Positively controls H(2)O(2)-induced cell death. NADPH + 2 oxidized [2Fe-2S]-[protein] = H(+) + NADP(+) + 2 reduced [2Fe-2S]-[protein] Interacts with dre2; as part of the cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery. Relocalizes to mitochondria after H(2)O(2) exposure. Belongs to the NADPH-dependent diflavin oxidoreductase NDOR1 family. In the N-terminal section; belongs to the flavodoxin family. In the C-terminal section; belongs to the flavoprotein pyridine nucleotide cytochrome reductase family. +Positive regulator of the expression of the gene (blaB) for beta-lactamase. Belongs to the LysR transcriptional regulatory family. +Promotes cell fusion during zygote formation. Localizes at the mating projection tip (shmoo). +May hydroxylate diterpenes. Expressed in roots. By UV irradiation. Belongs to the cytochrome P450 family. +May act as a GTPase-activating protein for Rab family protein(s). May play a role in the cell cycle and differentiation of various tissues. Involved in the trafficking and translocation of GLUT4-containing vesicles and insulin-stimulated glucose uptake into cells (By similarity). Interacts with APPL2 (via BAR domain); interaction is dependent of TBC1D1 phosphorylation at Ser-235; interaction diminishes the phosphorylation of TBC1D1 at Thr-596, resulting in inhibition of SLC2A4/GLUT4 translocation and glucose uptake. Insulin-stimulated phosphorylation by AKT family kinases stimulates SLC2A4/GLUT4 translocation. +V region of the variable domain of immunoglobulin light chains that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:20176268, PubMed:17576170). Immunoglobulins are composed of two identical heavy chains and two identical light chains; disulfide-linked. There are several alleles. The sequence shown is that of IMGT allele IGKV3-15*01. For an example of a full-length immunoglobulin kappa light chain see AC P0DOX7. Chimeric DNA corresponding to regions V and J of immunoglobulin kappa light chain. +DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-nicotinamide D-nucleotide. Belongs to the NAD-dependent DNA ligase family. LigA subfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. +Accepts electrons from ETF and reduces ubiquinone. a ubiquinone + reduced [electron-transfer flavoprotein] = a ubiquinol + H(+) + oxidized [electron-transfer flavoprotein] Binds 1 [4Fe-4S] cluster. Monomer. +Electrogenic proton/amino acid symporter with a high selectivity for the small side chains amino acids glycine, alanine and proline, where both L- and D-enantiomers are transported. Extension of the backbone length, as in beta-alanine and 4-aminobutanoate or methylation of the amino group, as in sarcosine and N,N-dimethylglycine, are also tolerated but decrease transport efficiency. A free carboxyl group is preferred. glycine(in) + H(+)(in) = glycine(out) + H(+)(out) H(+)(in) + L-alanine(in) = H(+)(out) + L-alanine(out) D-alanine(in) + H(+)(in) = D-alanine(out) + H(+)(out) H(+)(out) + L-proline(out) = H(+)(in) + L-proline(in) D-proline(out) + H(+)(out) = D-proline(in) + H(+)(in) 4-hydroxy-L-proline(in) + H(+)(in) = 4-hydroxy-L-proline(out) + H(+)(out) H(+)(in) + L-serine(in) = H(+)(out) + L-serine(out) D-serine(out) + H(+)(out) = D-serine(in) + H(+)(in) beta-alanine(in) + H(+)(in) = beta-alanine(out) + H(+)(out) 4-aminobutanoate(in) + H(+)(in) = 4-aminobutanoate(out) + H(+)(out) H(+)(in) + sarcosine(in) = H(+)(out) + sarcosine(out) H(+)(in) + N,N-dimethylglycine(in) = H(+)(out) + N,N-dimethylglycine(out) Inhibited by L- and D-pipecolic acid, nipecotic acid, isonipecotic acid, L- and D-cycloserine, and L-2-azetidine-carboxylate. Expressed in lung and spleen, and to a lower extent in brain, heart, kidney and skeletal muscle. Belongs to the amino acid/polyamine transporter 2 family. +PPIase that acts as a histone chaperone. Histone proline isomerase that increases the rate of cis-trans isomerization at prolines on the histone H3 N-terminal tail. Proline isomerization influences H3 methylation thereby regulating gene expression. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Inhibited by both FK506 and rapamycin. Binds to histones H3 and H4. Belongs to the FKBP-type PPIase family. FKBP3/4 subfamily. +Acts as a mitochondrial iron-sulfur (Fe-S) cluster assembly factor that facilitates [4Fe-4S] cluster insertion into a subset of mitochondrial proteins such as lipoyl synthase (LS) and succinate dehydrogenase (SDH) (PubMed:27532772). Required during the last step of iron-sulfur protein assembly when the iron-sulfur cluster is inserted into the target protein (PubMed:27532772). Probably acts together with the monothiol glutaredoxin GRX5, earlier than BOL3 and NFU1 in the [4Fe-4S] cluster insertion process (PubMed:27532773). Not required for [2Fe-2S] cluster insertion into mitochondrial proteins (PubMed:27532772). Interacts with GRX5. No visible phenotype (PubMed:27532773, PubMed:27532772). Cells lacking BOL1 and BOL3 display defects in a subset of mitochondrial [4Fe-4S] enzymes (PubMed:27532772). Present with 238 molecules/cell in log phase SD medium. Belongs to the BolA/IbaG family. +Forms an efflux pump with AaeA. Could function as a metabolic relief valve, allowing to eliminate certain compounds when they accumulate to high levels in the cell. Belongs to the aromatic acid exporter ArAE (TC 2.A.85) family. +a quinone + H(+) + NADH = a quinol + NAD(+) a quinone + H(+) + NADPH = a quinol + NADP(+) Binds 1 FMN per monomer. Belongs to the WrbA family. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +Voltage-dependent high-conductance channel with a slight cation-selectivity; selective for amino acids but excludes triosephosphates or uncharged sugars (By similarity). Non-essential amino acid-selective channel protein and translocation pore for NADPH:protochlorophyllide oxidoreductase A (PORA) and possibly PORB. Homodimer and oligomers in membrane. Detected in pollen and seeds. Present in leaves and cotyledons. Strongly expressed during the maturation phase in seeds and pollen grains, both desiccation-tolerant tissues. Regulated by ABI3 and ABI5. Belongs to the Tim17/Tim22/Tim23 family. Plastid outer envelope porin OEP16 (TC 1.B.30) subfamily. +Adds poly(A) tail to the 3' end of many RNAs, which usually targets these RNAs for decay. Plays a significant role in the global control of gene expression, through influencing the rate of transcript degradation, and in the general RNA quality control. ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. Extended N-terminus. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Catalyzes the reduction of the double bond of an array of alpha,beta-unsaturated aldehydes and ketones. It also reduces the nitro group of nitroester and nitroaromatic compounds. It could have a role in detoxification processes. A + H(+) + NADPH = AH2 + NADP(+) Homotetramer. Belongs to the NADH:flavin oxidoreductase/NADH oxidase family. NamA subfamily. +Capsid vertex-specific component that plays a role during viral DNA encapsidation, assuring correct genome cleavage and presumably stabilizing capsids that contain full-length viral genomes. Interacts (via C-terminus) with capsid vertex component 2/CVC2. Belongs to the herpesviridae CVC1 protein family. +Matrix protein p17 targets Gag and Gag-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex. Implicated in the release from host cell mediated by Vpu (By similarity). Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex. Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers (By similarity). p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1. Homotrimer. Interacts with gp41 (via C-terminus). Interacts with host TSG101 (By similarity). Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane (By similarity). Translation results in the formation of the Gag polyprotein most of the time. Ribosomal frameshifting at the gag-pol genes boundary occurs at low frequency and produces the Gag-Pol polyprotein. This strategy of translation probably allows the virus to modulate the quantity of each viral protein. Maintenance of a correct Gag to Gag-Pol ratio is essential for RNA dimerization and viral infectivity. Late-budding domains (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. p6-gag contains one L domain: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101 (By similarity). Capsid protein p24 is phosphorylated. Specific enzymatic cleavages by the viral protease yield mature proteins. The polyprotein is cleaved during and after budding, this process is termed maturation (By similarity). This is a macaque isolate. Produced by conventional translation. Belongs to the primate lentivirus group gag polyprotein family. +Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. Binds to the N-terminal domain of the chaperone ClpA. Belongs to the ClpS family. +RNA-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex. Belongs to the eIF-3 subunit B family. +Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA. acetyl-CoA + N(6)-carboxybiotinyl-L-lysyl-[protein] = malonyl-CoA + N(6)-biotinyl-L-lysyl-[protein] Binds 1 zinc ion per subunit. Lipid metabolism; malonyl-CoA biosynthesis; malonyl-CoA from acetyl-CoA: step 1/1. Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD). Belongs to the AccD/PCCB family. +Binds 2 magnesium or manganese ions per subunit. Belongs to the RimK family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +Contributes to the activation of female-specific DSX splicing in vivo by recognizing the RBP1 target sequences within the purine-rich polypyrimidine tract of the female-specific 3' splice site. Ubiquitous. Found at all developmental stages. Extensively phosphorylated on serine residues in the RS domain. Belongs to the splicing factor SR family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Belongs to the FAM163 family. +Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. Methylated by PrmC. Methylation increases the termination efficiency of RF1. Belongs to the prokaryotic/mitochondrial release factor family. +Belongs to the peptidase S1 family. +Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. Its motor activity is directed toward the microtubule's plus end. Composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it hydrolyzes ATP and binds microtubule), a central alpha-helical coiled coil domain that mediates the heavy chain dimerization; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. Belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Kinesin family. Kinesin subfamily. +1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 4/5. Belongs to the TrpC family. +Regulates actin polymerization by stimulating the actin-nucleating activity of the Arp2/3 complex. Involved in various processes, such as mitosis and cytokinesis, via its role in the regulation of actin polymerization. Together with CDC42, involved in the extension and maintenance of the formation of thin, actin-rich surface projections called filopodia. In addition to its role in the cytoplasm, also plays a role in the nucleus by regulating gene transcription, probably by promoting nuclear actin polymerization (By similarity). Binds to HSF1/HSTF1 and forms a complex on heat shock promoter elements (HSE) that negatively regulates HSP90 expression. Plays a role in dendrite spine morphogenesis (By similarity). Binds actin and the Arp2/3 complex. Interacts with CDC42 (By similarity). Interacts with FCHSD1. Interacts with FCHSD2 (By similarity). Binds to SH3 domains of GRB2. Interacts with the C-terminal SH3 domain of DNMBP (By similarity). Interacts with SNX9 (By similarity). Interacts with the WW domains of PRPF40A/FBP11 (By similarity). Interacts with PTK2/FAK1 (PubMed:14676198). Interacts with PACSIN1, PACSIN2 and PACSIN3 (By similarity). Interacts with NOSTRIN. Binds to TNK2. Interacts with SNX33. Interacts with NONO (via second RRM domain); the interaction is direct. Component of a multiprotein complex with NONO and SFPQ; associates with the complex via direct interaction with NONO (By similarity). Preferentially localized in the cytoplasm when phosphorylated and in the nucleus when unphosphorylated (By similarity). Exported from the nucleus by an nuclear export signal (NES)-dependent mechanism to the cytoplasm (By similarity). Phosphorylation at Ser-239, Tyr-253, Ser-480 and Ser-481 enhances actin polymerization activity. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Belongs to the SecA family. +May be involved in zinc transport out of the cell. Multimer. Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family. SLC30A subfamily. +Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH (S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4. Belongs to the DapB family. Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction. +P protein is probably the ATPase subunit of the terminase which directs cos cleavage. The Q, P and M proteins are needed to package DNA into proheads and for the conversion of proheads to capsids. To phage HP1 protein ORF16. +Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). Complex I is composed of at least 49 different subunits. Belongs to the complex I NDUFA13 subunit family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L24e. Belongs to the universal ribosomal protein uL3 family. +Associated with the fruiting bodies. Expressed only in fruiting dikaryons. Belongs to the CRISP family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Can hydrolyze phosphorylated Ser-, Thr- or Tyr-substrates in vitro. The natural substrate is unknown. H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Inhibited by cadmium, copper, zinc when added activity but with less efficiency. Optimum pH is 7.5-8.5. Optimum temperature is 30-37 degrees Celsius. Neither magnesium nor calcium stimulates activity. Belongs to the PPP phosphatase family. PP-1 subfamily. +Belongs to the herpesviridae US22 family. +N-acyltransferase required for nodulation. Acts in the production of a small, heat-stable compound (Nod) that stimulates mitosis in various plant protoplasts. Belongs to the NodA family. +May be a sulfotransferase involved in the transport of sulfate. Displays very low rhodanese activity. hydrogen cyanide + thiosulfate = 2 H(+) + sulfite + thiocyanate By sulfur deprivation. Contains two rhodanese domains with different primary structures but with near identical secondary structure conformations suggesting a common evolutionary origin. Only the C-terminal rhodanese domain contains the catalytic cysteine residue (By similarity). +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +Essential glycylase which modifies both tubulin and non-tubulin proteins, generating side chains of glycine on the gamma-carboxyl groups of specific glutamate residues of target proteins. Monoglycylates alpha-tubulin by adding a single glycine chain to generate monoglycine side chains, but is not involved in elongation step to generate polyglycine side chains on alpha-tubulin. Has the ability to both mono- and polyglycylate non-tubulin proteins such as up (Troponin T). Required for early steps of spermatogenesis. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity. Belongs to the universal ribosomal protein uS4 family. +Catalyzes the epimerization of dipeptides with L-Glu in the second position. Has epimerase activity with L-Gly-L-Glu, L-Ala-L-Glu, L-Ser-L-Glu, L-Pro-L-Glu, L-Val-L-Glu, L-Met-L-Glu, L-Thr-L-Glu and L-Phe-L-Glu (in vitro). Binds 1 Mg(2+) ion per subunit. Part of a large, functionally divergent protein family. Protein modeling and substrate docking was used to predict the substrate specificity, prior to biochemical analysis. Belongs to the mandelate racemase/muconate lactonizing enzyme family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS7 family. +Plays an important role in the organization of the cytoskeleton by regulating actin polymerization in two ways. Firstly, by binding to and sequestering actin monomers (G actin) inhibits actin polymerization. Secondly, by binding directly filamentous actin (F actin) promotes actin polymerization. Regulates the formation of cortical actin in oocytes conferring them enough rigidity to sustain the contractions during ovulation. Interacts (via repeats 1, 2 and 4) with G-actin in a 1:3 ratio. Interacts (via repeats 2 and 3) with F-actin. Localizes to the cell cortex and the cytoplasm in oocytes and at the inside edges of membrane cubicles surrounding germ cell nuclei. Co-localizes with actin at the cell-cell contact in two-cell stage embryo. At the comma stage, enriched in the developing nerve ring (at protein level). Ubiquitously expressed in larvae and adults with enrichment in the spermatheca, the intestinal tract and the posterior bulb of the pharynx (at protein level). Expressed in oocytes and in the gonad (at protein level). Expressed in embryo, larvae and adults (at protein level). The 4 repeats act cooperatively in the binding of G actin. Lethal at the L3/L4 larval stages or at the young adult stage. Mutants are shorter and stouter, and fail to produce a viable progeny. In oocytes, actin is diffused in the cytoplasm and F-actin accumulation at the cell cortex is reduced resulting in deformed oocytes in the spermatheca and the uterus. Belongs to the thymosin beta family. +A beta subtype methylase, recognizes the double-stranded sequence 5'-GCCNNNNNGGC-3', methylates C-2 on both strands, and protects the DNA from cleavage by the BglI endonuclease. a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = an N(4)-methyl-2'-deoxycytidine in DNA + H(+) + S-adenosyl-L-homocysteine Belongs to the N(4)/N(6)-methyltransferase family. +Endo-1,4-mannanase, a crucial enzyme for depolymerization of seed galactomannans and wood galactoglucomannans. Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans. Belongs to the glycosyl hydrolase 5 (cellulase A) family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Escorts unspliced or incompletely spliced viral pre-mRNAs (late transcripts) out of the nucleus of infected cells. These pre-mRNAs carry a recognition sequence called Rev responsive element (RRE) located in the env gene, that is not present in fully spliced viral mRNAs (early transcripts). This function is essential since most viral proteins are translated from unspliced or partially spliced pre-mRNAs which cannot exit the nucleus by the pathway used by fully processed cellular mRNAs. Rev itself is translated from a fully spliced mRNA that readily exits the nucleus. Rev's nuclear localization signal (NLS) binds directly to KPNB1/Importin beta-1 without previous binding to KPNA1/Importin alpha-1. KPNB1 binds to the GDP bound form of RAN (Ran-GDP) and targets Rev to the nucleus. In the nucleus, the conversion from Ran-GDP to Ran-GTP dissociates Rev from KPNB1 and allows Rev's binding to the RRE in viral pre-mRNAs. Rev multimerization on the RRE via cooperative assembly exposes its nuclear export signal (NES) to the surface. Rev can then form a complex with XPO1/CRM1 and Ran-GTP, leading to nuclear export of the complex. Conversion from Ran-GTP to Ran-GDP mediates dissociation of the Rev/RRE/XPO1/RAN complex, so that Rev can return to the nucleus for a subsequent round of export. Beside KPNB1, also seems to interact with TNPO1/Transportin-1, RANBP5/IPO5 and IPO7/RANBP7 for nuclear import. The nucleoporin-like HRB/RIP is an essential cofactor that probably indirectly interacts with Rev to release HIV RNAs from the perinuclear region to the cytoplasm. Homomultimer; when bound to the RRE. Multimeric assembly is essential for activity and may involve XPO1. Binds to human KPNB1, XPO1, TNPO1, RANBP5 and IPO7. Interacts with the viral Integrase. Interacts with human KHDRBS1. Interacts with human NAP1; this interaction decreases Rev multimerization and stimulates its activity. Interacts with human DEAD-box helicases DDX3 and DDX24; these interactions may serve for viral RNA export to the cytoplasm and packaging, respectively. Interacts with human PSIP1; this interaction may inhibit HIV-1 DNA integration by promoting dissociation of the Integrase-LEDGF/p75 complex. The presence of both nuclear import and nuclear export signals leads to continuous shuttling between the nucleus and cytoplasm. The RNA-binding motif binds to the RRE, a 240 bp stem-and-loop structure present in incompletely spliced viral pre-mRNAs. This region also contains the NLS which mediates nuclear localization via KPNB1 binding and, when the N-terminal sequence is present, nucleolar targeting. These overlapping functions prevent Rev bound to RRE from undesirable return to the nucleus. When Rev binds the RRE, the NLS becomes masked while the NES remains accessible. The leucine-rich NES mediates binding to human XPO1. Asymmetrically arginine dimethylated at one site by host PRMT6. Methylation impairs the RNA-binding activity and export of viral RNA from the nucleus to the cytoplasm. Phosphorylated by protein kinase CK2. Presence of, and maybe binding to the N-terminus of the regulatory beta subunit of CK2 is necessary for CK2-mediated Rev's phosphorylation. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Belongs to the HIV-1 REV protein family. +Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK (By similarity). Necessary for thermotolerance. Homohexamer. The oligomerization is ATP-dependent (By similarity). By heat shock. The Clp repeat (R) domain probably functions as a substrate-discriminating domain, recruiting aggregated proteins to the ClpB hexamer and/or stabilizing bound proteins. The NBD2 domain is responsible for oligomerization, whereas the NBD1 domain stabilizes the hexamer probably in an ATP-dependent manner. The movement of the coiled-coil domain is essential for ClpB ability to rescue proteins from an aggregated state, probably by pulling apart large aggregated proteins, which are bound between the coiled-coils motifs of adjacent ClpB subunits in the functional hexamer (By similarity). Also contributes to the overall thermotolerance of the bacterium. Belongs to the ClpA/ClpB family. +May act as a specific coactivator for the mammalian TEFs. Interacts with TEFs (By similarity). Interacts with IRF2BP2. Probable target of nonsense-mediated mRNA decay. Belongs to the vestigial family. Wrong choice of CDS. Extended N-terminus. +Belongs to the flavoredoxin family. +Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. Belongs to the NusB family. +One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA. Homotetramer, a dimer of dimers. One homotetramer interacts with 1 SecA dimer. Belongs to the SecB family. +Produces nitric oxide (NO) which is a messenger molecule with diverse functions throughout the body. In macrophages, NO mediates tumoricidal and bactericidal actions. Also has nitrosylase activity and mediates cysteine S-nitrosylation of cytoplasmic target proteins such PTGS2/COX2. As component of the iNOS-S100A8/9 transnitrosylase complex involved in the selective inflammatory stimulus-dependent S-nitrosylation of GAPDH implicated in regulation of the GAIT complex activity and probably multiple targets including ANXA5, EZR, MSN and VIM. Involved in inflammation, enhances the synthesis of pro-inflammatory mediators such as IL6 and IL8. H(+) + 2 L-arginine + 3 NADPH + 4 O2 = 4 H2O + 2 L-citrulline + 3 NADP(+) + 2 nitric oxide Binds 1 FAD. Binds 1 FMN. Tetrahydrobiopterin (BH4). May stabilize the dimeric form of the enzyme. Not stimulated by calcium/calmodulin. Homodimer. Interacts with SLC9A3R1. Interacts with GAPDH; induced by oxidatively-modified low-densitity lipoprotein (LDL(ox)). Interacts with S100A8 and S100A9 to form the iNOS-S100A8/9 transnitrosylase complex. Interacts with SPSB1, SPSB2 and SPSB4. Interacts with ELOC and CUL5 in the presence of SPSB1 or SPSB2 or SPSB4. Forms a complex with ASL, ASS1 and HSP90AA1; the complex regulates cell-autonomous L-arginine synthesis and citrulline recycling while channeling extracellular L-arginine to nitric oxide synthesis pathway. Localizes as discrete foci scattered throughout the cytosol and in the presence of SPSB1 and SPSB4, exhibits a more diffuse cytosolic localization. Detected in both stimulated and unstimulated immune cells and macrophages with little or no up-regulation following cellular stimulation with lipopolysaccharides (LPS) or concanavalin A (ConA). Little by LPS or ConA in spleen cells. Polyubiquitinated; mediated by SPSB1, SPSB2 and SPSB4, leading to proteasomal degradation. Belongs to the NOS family. +Part of the MIS12 complex which is required for normal chromosome alignment and segregation and kinetochore formation during mitosis. Component of the MIS12 complex composed of MIS12, DSN1, NSL1 and PMF1. Also interacts with KNL1, CBX3 and CBX5. Interacts with KNSTRN. Associated with the kinetochore. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. RnhC subfamily. +Belongs to the CinA family. +Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate Carbohydrate degradation; pentose phosphate pathway; D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step 1/1. Homodimer. Belongs to the ribose 5-phosphate isomerase family. +Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA. Heteromultimer composed of small subunits (RfcS) and large subunits (RfcL). Belongs to the activator 1 small subunits family. RfcL subfamily. +Belongs to the bacterial ribosomal protein bL27 family. +Probably involved in the osmoprotection via the biosynthesis of trehalose. Catalyzes the transfer of glucose from UDP-alpha-D-glucose (UDP-Glc) to D-glucose 6-phosphate (Glc-6-P) to form trehalose-6-phosphate. Acts with retention of the anomeric configuration of the UDP-sugar donor. D-glucose 6-phosphate + UDP-alpha-D-glucose = alpha,alpha-trehalose 6-phosphate + H(+) + UDP Glycan biosynthesis; trehalose biosynthesis. Homotetramer. Belongs to the glycosyltransferase 20 family. +Bifunctional serine/threonine kinase and phosphorylase involved in the regulation of the phosphoenolpyruvate synthase (PEPS) by catalyzing its phosphorylation/dephosphorylation. [pyruvate, water dikinase] + ADP = [pyruvate, water dikinase]-phosphate + AMP + H(+) [pyruvate, water dikinase]-phosphate + H(+) + phosphate = [pyruvate, water dikinase] + diphosphate Belongs to the pyruvate, phosphate/water dikinase regulatory protein family. PSRP subfamily. +Binds to 23S rRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL14 family. +Catalyzes the strictly specific dephosphorylation of 2'-deoxyribonucleoside 5'-monophosphates. a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-deoxyribonucleoside + phosphate Homodimer. Belongs to the 5DNU family. +Plays a role in the definition of cell polarity via the planar cell polarity (PCP) cascade. Required for ciliogenesis by controlling the organization of the apical actin cytoskeleton and the positioning of the basal bodies at the apical cell surface, which in turn is essential for the normal orientation of elongating ciliary microtubules. Proposed to function as core component of a functional module called CPLANE (ciliogenesis and planar polarity effectors) involved in recruitment of peripheral IFT-A proteins to basal bodies (PubMed:27158779). Controls the localization of both rhoa and disheveled in multi-ciliated cells. Has an indirect effect on hedgehog signaling. Interacts with fuz and wdpcp; fuz, intu and wdpcp probably form the core CPLANE (ciliogenesis and planar polarity effectors) complex. Enriched at the apical surface in ciliated cells. Localizes to the cell membrane in non-ciliated cells. Expressed in the neural plate during neural tube closure with subsequent strong expression in the ventral neural tube and in facial mesenchyme. Belongs to the inturned family. +Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). Binds 1 Mg(2+) ion per subunit. Belongs to the RuvC family. +E2 component of the 2-oxoglutarate dehydrogenase (OGDH) complex which catalyzes the second step in the conversion of 2-oxoglutarate to succinyl-CoA and CO(2). (R)-N(6)-dihydrolipoyl-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + succinyl-CoA = (R)-N(6)-(S(8)-succinyldihydrolipoyl)-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + CoA Binds 1 lipoyl cofactor covalently. Amino-acid degradation; L-lysine degradation via saccharopine pathway; glutaryl-CoA from L-lysine: step 6/6. Forms a 24-polypeptide structural core with octahedral symmetry. Part of the 2-oxoglutarate dehydrogenase (OGDH) complex composed of E1 (2-oxoglutarate dehydrogenase), E2 (dihydrolipoamide succinyltransferase) and E3 (dihydrolipoamide dehydrogenase); the complex contains multiple copies of the three enzymatic components (E1, E2 and E3). Belongs to the 2-oxoacid dehydrogenase family. +Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12. [sulfur carrier]-SH + AH2 + L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 2 S-adenosyl-L-methionine = 3-methylsulfanyl-L-aspartate(89)-[ribosomal protein uS12]-hydrogen + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Belongs to the methylthiotransferase family. RimO subfamily. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Probably functions as a manganese efflux pump. Belongs to the MntP (TC 9.B.29) family. +Belongs to the UPF0213 family. +Involved in the anomeric conversion of L-rhamnose. alpha-L-rhamnose = beta-L-rhamnose Carbohydrate metabolism; L-rhamnose metabolism. Homodimer. Belongs to the rhamnose mutarotase family. +Nuclear corepressor for KRAB domain-containing zinc finger proteins (KRAB-ZFPs) (PubMed:20164836, PubMed:22110054, PubMed:25247314, PubMed:27658112). Mediates gene silencing by recruiting CHD3, a subunit of the nucleosome remodeling and deacetylation (NuRD) complex, and SETDB1 (which specifically methylates histone H3 at 'Lys-9' (H3K9me)) to the promoter regions of KRAB target genes. Enhances transcriptional repression by coordinating the increase in H3K9me, the decrease in histone H3 'Lys-9 and 'Lys-14' acetylation (H3K9ac and H3K14ac, respectively) and the disposition of HP1 proteins to silence gene expression. Recruitment of SETDB1 induces heterochromatinization. May play a role as a coactivator for CEBPB and NR3C1 in the transcriptional activation of ORM1. Also a corepressor for ERBB4. Inhibits E2F1 activity by stimulating E2F1-HDAC1 complex formation and inhibiting E2F1 acetylation. May serve as a partial backup to prevent E2F1-mediated apoptosis in the absence of RB1. Important regulator of CDKN1A/p21(CIP1). Has E3 SUMO-protein ligase activity toward itself via its PHD-type zinc finger. Specifically sumoylates IRF7, thereby inhibiting its transactivation activity. Ubiquitinates p53/TP53 leading to its proteosomal degradation; the function is enhanced by MAGEC2 and MAGEA2, and possibly MAGEA3 and MAGEA6. Mediates the nuclear localization of KOX1, ZNF268 and ZNF300 transcription factors. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells. Required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:20164836). In ESCs, in collaboration with SETDB1, is also required for H3K9me3 and silencing of endogenous and introduced retroviruses in a DNA-methylation independent-pathway (PubMed:20164836). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing. The SETDB1-TRIM28-ZNF274 complex may play a role in recruiting ATRX to the 3'-exons of zinc-finger coding genes with atypical chromatin signatures to establish or maintain/protect H3K9me3 at these transcriptionally active regions (By similarity). Acts as a corepressor for ZFP568 (PubMed:22110054, PubMed:27658112). S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein sumoylation. Oligomer; the RBCC domain homotrimerizes and interacts with one molecule of KRAB to form the KRAB-KAP1 corepressor complex. Interacts with SETX (By similarity). Binding to a KRAB domain is an absolute requirement for silencing gene expression. Interacts with a number of KRAB-ZFP proteins including ZNF10, ZFP53, ZFP68, ZNF382 and ZNF256. Interacts with NCOR1, NR3C1 and CHD3. Interacts with CEBPB (via the RING-type and PHD-type zinc fingers). Interacts with CBX5 (via the PxVxL motif); the interaction occurs in interphase nuclei and competes for binding POGZ (PubMed:10562550, PubMed:10330177, PubMed:25247314). Interacts with POGZ; the interaction competes for interaction with CBX5. Interacts with SETDB1; the interaction is enhanced by KAP1 sumoylation, stimulates SETDB1 histone methyltransferase activity and gene silencing. Interacts (via the PHD-type zinc finger) with UBE2I; the interaction is required for sumoylation and repressor activity. Component of the TRIM28/KAP1-ERBB4-MDM2 complex involved in connecting growth factor and DNA damage responses. Interacts directly with ERBB4; the interaction represses ERBB4-mediated transcription activity. Interacts with MDM2; the interaction contributes to p53/TP53 inactivation. Component of the TRIM28/KAP1-MDM2-p53/TP53; involved in regulating p53/TP53 stabilization and activity. Interacts (via the leucine zipper alpha helical coiled-coil) with E2F1 (central region); the interaction inhibits E2F1 acetylation and transcriptional activity. Interacts with PPP1CA; the interaction dephosphorylates TRIM28 at Ser-824 and forms a complex at the p21 promoter site. Interacts with PPP1CB; the interaction is weak but is increased on dephosphorylation at Ser-824. Interacts with CEBPB and NR3C1. Interacts with CBX5 (via the PxVxL motif); the interaction occurs in interphase nuclei and competes for binding POGZ. Component of a ternary complex that includes TRIM28, a HP1 protein (CBX1, CBX3 OR CBX5), a KRAB domain-containing protein, and DNA. Interacts with SMARCAD1. Interacts with, and sumoylates IRF7. Interacts with MAGEC2. Part of a complex composed of TRIM28, HDAC1, HDAC2 and EHMT2. Interacts (via the RBCC domain) with KOX1 (via the KRAB domain), ZNF268 (via the KRAB domain) and ZNF300 (via the KRAB domain); the interactions increase KOX1, ZNF268 and ZNF300 nuclear localization activities. Interacts with AICDA. The large PER complex involved in the histone methylation is composed of at least PER2, CBX3, TRIM28, SUV39H1 and/or SUV39H2; CBX3 mediates the formation of the complex. Interacts with NR4A3; the interactions potentiates NR4A3 activity on NurRE promoter (PubMed:19321449). Interacts (unphosphorylated or phosphorylated form) with ZBTB1 (via BTB domain) (By similarity). Probably part of a corepressor complex containing ZNF304, TRIM28, SETDB1 and DNMT1. Interacts with ATRX. Forms a complex with ATRX, SETDB1 and ZNF274 (By similarity). Interacts with ZFP568; the interaction mediates ZFP568 transcriptional repression activity (PubMed:22110054, PubMed:27658112). Interacts with RRP1B (By similarity). Interacts with CRY1 (PubMed:27123980). Interacts with ZNF263; recruited to the SIX3 promoter along with other proteins involved in chromatin modification and transcriptional corepression where it contributes to transcriptional repression (By similarity). Interacts with CYREN (via XLF motif) (PubMed:30017584). Interacts with TRIM17; this interaction prevents TRIM28 activity (By similarity). Interacts with ZNF746 (By similarity). Associated with centromeric heterochromatin during cell differentiation through CBX1. The HP1 box is both necessary and sufficient for HP1 binding. The PHD-type zinc finger enhances CEBPB transcriptional activity. The PHD-type zinc finger, the HP1 box and the bromo domain, function together to assemble the machinery required for repression of KRAB domain-containing proteins. Acts as an intramolecular SUMO E3 ligase for autosumoylation of bromodomain. The RING-finger-B Box-coiled-coil/tripartite motif (RBCC/TRIM motif) is required for interaction with the KRAB domain of KRAB-zinc finger proteins. Binds four zinc ions per molecule. The RING finger and the N-terminal of the leucine zipper alpha helical coiled-coil region of RBCC are required for oligomerization. Contains one Pro-Xaa-Val-Xaa-Leu (PxVxL) motif, which is required for interaction with chromoshadow domains. This motif requires additional residues -7, -6, +4 and +5 of the central Val which contact the chromoshadow domain. ATM-induced phosphorylation on Ser-824 represses sumoylation leading to the de-repression of expression of a subset of genes involved in cell cycle control and apoptosis in response to genotoxic stress. Dephosphorylation by the phosphatases, PPP1CA and PP1CB forms, allows sumoylation and expression of TRIM28 target genes. Sumoylation/desumoylation events regulate TRIM28-mediated transcriptional repression. Sumoylation is required for interaction with CHD3 and SETDB1 and the corepressor activity. Represses and is repressed by Ser-824 phosphorylation. Enhances the TRIM28 corepressor activity, inhibiting transcriptional activity of a number of genes including GADD45A and CDKN1A/p21. Lys-554, Lys-779 and Lys-804 are the major sites of sumoylation. In response to Dox-induced DNA damage, enhanced phosphorylation on Ser-824 prevents sumoylation and allows de-repression of CDKN1A/p21. Auto-ubiquitinated; enhanced by MAGEA2 and MAGEC2. Citrullinated by PADI4. ADP-ribosylated by SIRT6, promoting TRIM28/KAP1 interaction with CBX5, thereby contributing to the packaging of LINE-1 retrotransposon elements into transcriptionally repressive heterochromatin. Embryonic lethal with arrest at stage E5.5. Gastrulation fails and expression of the critical mesoderm differentiation factor T/brachyury is lost. Belongs to the TRIM/RBCC family. +Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Homodimer. Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +Part of the ATP-driven transport system AdcABC for zinc. Belongs to the bacterial solute-binding protein 9 family. +Belongs to the bacterial ribosomal protein bL27 family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Involved in the export of PMA1, possibly through the monitoring or assisting of PMA1 folding and acquisition of competence to enter vesicles. Belongs to the SOP4 family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import. Cofactor biosynthesis; adenosylcobalamin biosynthesis. Forms an energy-coupling factor (ECF) transporter complex composed of an ATP-binding protein (A component, CbiO), a transmembrane protein (T component, CbiQ) and 2 possible substrate-capture proteins (S components, CbiM and CbiN) of unknown stoichimetry. Belongs to the CbiN family. +Envelope glycoprotein necessary for proper maturation of gM and modulation of its membrane fusion activity. Also plays a critical role in virion morphogenesis. Interacts (via N-terminus) with gM (via N-terminus). The gM-gN heterodimer forms the gCII complex. When coexpressed with gM, localizes in the host trans-Golgi network. Belongs to the herpesviridae glycoprotein N family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA. Belongs to the universal ribosomal protein uS15 family. +Catalyzes carboxymethyl transfer from carboxy-S-adenosyl-L-methionine (Cx-SAM) to 5-hydroxyuridine (ho5U) to form 5-carboxymethoxyuridine (cmo5U) at position 34 in tRNAs. 5-hydroxyuridine(34) in tRNA + carboxy-S-adenosyl-L-methionine = 5-carboxymethoxyuridine(34) in tRNA + H(+) + S-adenosyl-L-homocysteine Homotetramer. Belongs to the class I-like SAM-binding methyltransferase superfamily. CmoB family. +Belongs to the HflD family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln), leading to the formation of s(2)U34, the first step of tRNA-mnm(5)s(2)U34 synthesis. Sulfur is provided by IscS, via a sulfur-relay system. Binds ATP and its substrate tRNAs. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Interacts with TusE. Belongs to the MnmA/TRMU family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. Minor subunit located with subunit a in the membrane (By similarity). F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. Belongs to the ATPase protein 8 family. +Belongs to the TMEM144 family. +RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit. Belongs to the RnpA family. +ATP + CMP = ADP + CDP ATP + dCMP = ADP + dCDP Belongs to the cytidylate kinase family. Type 1 subfamily. +Efficient DNA binding requires dimerization with another bHLH protein. N-MYC2 proto-oncogene protein is overexpressed in liver tumors. N-MYC2 is totally silent in normal liver and is probably a retroposon. WHV virus activates N-MYC2 by integration. +Calcium-binding protein that interacts with rotavirus cell receptors once the initial attachment by VP4 has been achieved (By similarity). Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors (PubMed:12941907). Following entry into the host cell, low intracellular or intravesicular Ca(2+) concentration probably causes the calcium-stabilized VP7 trimers to dissociate from the virion. This step is probably necessary for the membrane-disrupting entry step and the release of VP4, which is locked onto the virion by VP7 (By similarity). Homotrimer; disulfide-linked. 2 Ca(2+) ions bound at each subunit interface in the trimer hold the trimer together. Interacts with the intermediate capsid protein VP6 (By similarity). Interacts with the outer capsid protein VP5* (By similarity). Interacts with host integrin heterodimer ITGAX/ITGB2 (PubMed:12941907). Interacts with host integrin heterodimer ITGA5/ITGB3 (PubMed:12941907). The outer layer contains 780 copies of VP7, grouped as 260 trimers. Immature double-layered particles assembled in the cytoplasm bud across the membrane of the endoplasmic reticulum, acquiring during this process a transient lipid membrane that is modified with the ER resident viral glycoproteins NSP4 and VP7; these enveloped particles also contain VP4. As the particles move towards the interior of the ER cisternae, the transient lipid membrane and the non-structural protein NSP4 are lost, while the virus surface proteins VP4 and VP7 rearrange to form the outermost virus protein layer, yielding mature infectious triple-layered particles. N-glycosylated. The N-terminus is blocked possibly by pyroglutamic acid. Some rotavirus strains are neuraminidase-sensitive and require sialic acid to attach to the cell surface. Some rotavirus strains are integrin-dependent. Some rotavirus strains depend on ganglioside for their entry into the host cell. Hsp70 also seems to be involved in the entry of some strains. In group A rotaviruses, VP7 defines the G serotype. Produced by alternative initiation at Met-30 of isoform 1. Belongs to the rotavirus VP7 family. +Catalyzes the hydrolysis of N(4)-acetylcytidine (ac4C). H2O + N(4)-acetylcytidine = acetate + cytidine + H(+) H2O + N(4)-acetyl-2'-deoxycytidine = 2'-deoxycytidine + acetate + H(+) H2O + N(4)-acetylcytosine = acetate + cytosine + H(+) Belongs to the N(4)-acetylcytidine amidohydrolase family. +Belongs to the DEFL family. The predicted gene has been split into 3 genes: At4g14270, At4g14272 and At4g14276. The predicted gene has been split into 3 genes: At4g14270, At4g14272 and At4g14276. +Belongs to the UPF0051 (ycf24) family. +May play a role in embryogenesis. Belongs to the PPR family. PCMP-H subfamily. +Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine Homodimer. Belongs to the RNA methyltransferase RlmH family. +Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner. GTP + H2O = GDP + H(+) + phosphate Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily. +Excises ethenocytosine and uracil, which can arise by alkylation or deamination of cytosine, respectively, from the corresponding mispairs with guanine in ds-DNA. It is capable of hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of the DNA and the mispaired base. The complementary strand guanine functions in substrate recognition. Required for DNA damage lesion repair in stationary-phase cells. Specifically hydrolyzes mismatched double-stranded DNA and polynucleotides, releasing free uracil. Binds DNA as a monomer. Belongs to the uracil-DNA glycosylase (UDG) superfamily. TDG/mug family. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a(1), b(1), b'(1) and c(9-12). Belongs to the ATPase alpha/beta chains family. +an acyl-CoA + sn-glycerol 3-phosphate = a 1-acyl-sn-glycero-3-phosphate + CoA Phospholipid metabolism; CDP-diacylglycerol biosynthesis; CDP-diacylglycerol from sn-glycerol 3-phosphate: step 1/3. The HXXXXD motif is essential for acyltransferase activity and may constitute the binding site for the phosphate moiety of the glycerol-3-phosphate. Belongs to the GPAT/DAPAT family. +Probable hydrophobic ligand-binding protein; may play a role in the transport of hydrophobic ligands like tocopherol, squalene and phospholipids. +Calcium-binding protein that interacts with rotavirus cell receptors once the initial attachment by VP4 has been achieved. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. Following entry into the host cell, low intracellular or intravesicular Ca(2+) concentration probably causes the calcium-stabilized VP7 trimers to dissociate from the virion. This step is probably necessary for the membrane-disrupting entry step and the release of VP4, which is locked onto the virion by VP7. Homotrimer; disulfide-linked. 2 Ca(2+) ions bound at each subunit interface in the trimer hold the trimer together. Interacts with the intermediate capsid protein VP6. Interacts with the outer capsid protein VP5*. The outer layer contains 780 copies of VP7, grouped as 260 trimers. Immature double-layered particles assembled in the cytoplasm bud across the membrane of the endoplasmic reticulum, acquiring during this process a transient lipid membrane that is modified with the ER resident viral glycoproteins NSP4 and VP7; these enveloped particles also contain VP4. As the particles move towards the interior of the ER cisternae, the transient lipid membrane and the non-structural protein NSP4 are lost, while the virus surface proteins VP4 and VP7 rearrange to form the outermost virus protein layer, yielding mature infectious triple-layered particles. N-glycosylated. The N-terminus is blocked possibly by pyroglutamic acid. Some rotavirus strains are neuraminidase-sensitive and require sialic acid to attach to the cell surface. Some rotavirus strains are integrin-dependent. Some rotavirus strains depend on ganglioside for their entry into the host cell. Hsp70 also seems to be involved in the entry of some strains. In group A rotaviruses, VP7 defines the G serotype. Belongs to the rotavirus VP7 family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Homotetramer. Belongs to the NDK family. +Removes acidic, neutral and basic amino acids as well as proline from the C-terminal position. Digests preferentially peptides containing a hydrophobic residue in P1' position, as well as arginine, lysine or phenylalanine in P1 position of ester substrate. Catalyzes also peptide synthesis. Inhibited by DFP. Optimum pH is 4. Unstable above pH 8. Monomer. Contains both N- and O-linked sugar chains. The N-linked oligosaccharides are unique structures of Man(10)GlcNAc(2) and Man(11)GlcNAc(2). Deglycosylation does neither affect catalytic activity, pH, thermal stability, or resistance to proteolysis of the enzyme. Belongs to the peptidase S10 family. +Lectin that functions as pattern recognizing receptor (PRR) specific for beta-1,3-linked and beta-1,6-linked glucans, which constitute cell wall constituents from pathogenic bacteria and fungi. Necessary for the TLR2-mediated inflammatory response and activation of NF-kappa-B: upon beta-glucan binding, recruits SYK via its ITAM motif and promotes a signaling cascade that activates some CARD domain-BCL10-MALT1 (CBM) signalosomes, leading to the activation of NF-kappa-B and MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) pathways which stimulate expression of genes encoding pro-inflammatory cytokines and chemokines. Enhances cytokine production in macrophages and dendritic cells. Mediates production of reactive oxygen species in the cell. Mediates phagocytosis of C.albicans conidia. Binds T-cells in a way that does not involve their surface glycans and plays a role in T-cell activation. Stimulates T-cell proliferation. Induces phosphorylation of SCIMP after binding beta-glucans. Homodimer. Interacts with SYK; participates in leukocyte activation in presence of fungal pathogens. Detected in dendritic cells, in paracortical and medullary regions of lymph nodes, and in spleen red pulp and white pulp. Phosphorylated on tyrosine residues in response to beta-glucan binding. +Trimeric GP1,2 complexes form the virion surface spikes and mediate the viral entry processes, with GP1 acting as the receptor-binding subunit and GP2 as the membrane fusion subunit. At later times of infection, down-regulates the expression of various host cell surface molecules that are essential for immune surveillance and cell adhesion. Down-modulates several integrins including ITGA1, ITGA2, ITGA3, ITGA4, ITGA5, ITGA6, ITGAV and ITGB1. This decrease in cell adhesion molecules may lead to cell detachment, contributing to the disruption of blood vessel integrity and hemorrhages developed during infection (cytotoxicity). Interacts with host TLR4 and thereby stimulates the differentiation and activation of monocytes leading to bystander death of T-lymphocytes. Down-regulates as well the function of host natural killer cells. Counteracts the antiviral effect of host BST2/tetherin that restricts release of progeny virions from infected cells. However, cooperates with VP40 and host BST2 to activate canonical NF-kappa-B pathway in a manner dependent on neddylation. Functions as a decoy for anti-GP1,2 antibodies thereby contributing to viral immune evasion. Interacts and activates host macrophages and dendritic cells inducing up-regulation of cytokine transcription. This effect is mediated throught activation of host TLR4. Responsible for binding to the receptor(s) on target cells. Interacts with CD209/DC-SIGN and CLEC4M/DC-SIGNR which act as cofactors for virus entry into dendritic cells (DCs) and endothelial cells (By similarity). Binding to the macrophage specific lectin CLEC10A also seems to enhance virus infectivity (By similarity). Interaction with FOLR1/folate receptor alpha may be a cofactor for virus entry in some cell types, although results are contradictory (By similarity). Members of the Tyro3 receptor tyrosine kinase family also seem to be cell entry factors in filovirus infection (By similarity). Once attached, the virions are internalized through clathrin-dependent endocytosis and/or macropinocytosis. After internalization of the virus into the endosomes of the host cell, proteolysis of GP1 by two cysteine proteases, CTSB/cathepsin B and CTSL/cathepsin L removes the glycan cap and allows GP1 binding to the host entry receptor NPC1. NPC1-binding, Ca(2+) and acidic pH induce a conformational change of GP2, which unmasks its fusion peptide and permit membranes fusion (By similarity). Acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in GP2, releasing the fusion hydrophobic peptide. Homotrimer; each monomer consists of a GP1 and a GP2 subunit linked by disulfide bonds. The resulting peplomers (GP1,2) protrude from the virus surface as spikes. Interacts with host integrin alpha-V/ITGAV. Interacts with host CLEC10A. Binds also to host CD209 and CLEC4M/DC-SIGN(R). Interacts with host FOLR1. Interacts with BST2; this interaction inhibits the antiviral effect of BST2 and this allows viral release from infected cells. Interacts with host FCN1; this interaction enhances viral entry. Interacts with host TLR4; this interaction induces T-lymphocyte death. Interacts with host entry receptor NPC1. GP1 and GP2delta are part of GP1,2delta soluble complexes released by ectodomain shedding. In the cell, localizes to the plasma membrane lipid rafts, which probably represent the assembly and budding site. GP1 is not anchored to the viral envelope, but forms a disulfid-linked complex with the extravirion surface GP2. In the cell, both GP1 and GP2 localize to the plasma membrane lipid rafts, which probably represent the assembly and budding site. GP1 can also be shed after proteolytic processing. GP2-delta bound to GP1 (GP1,2-delta) is produced by proteolytic cleavage of GP1,2 by host ADAM17 and shed by the virus. The mucin-like region seems to be involved in the cytotoxic function. This region is also involved in binding to human CLEC10A (By similarity). The coiled coil regions play a role in oligomerization and fusion activity. The signal peptide region modulates GP's high mannose glycosylation, thereby determining the efficiency of the interactions with DC-SIGN(R). N-glycosylated. O-glycosylated in the mucin-like region. Palmitoylation of GP2 is not required for its function. Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into GP1 and GP2 by host cell furin in the trans Golgi, and maybe by other host proteases, to yield the mature GP1 and GP2 proteins. The cleavage site corresponds to the furin optimal cleavage sequence [KR]-X-[KR]-R. This cleavage does not seem to be required for function. After the internalization of the virus into cell endosomes, GP1 C-terminus is removed by the endosomal proteases cathepsin B, cathepsin L, or both, leaving a 19-kDa N-terminal fragment which is further digested by cathepsin B. Proteolytic processing of GP1,2 by host ADAM17 can remove the transmembrane anchor of GP2 and leads to shedding of complexes consisting in GP1 and truncated GP2 (GP1,2delta) (By similarity). Partially edited. RNA editing at this position consists of an insertion of one adenine nucleotide. The sequence displayed here is the full-length transmembrane glycoprotein, derived from the edited RNA. The unedited RNA gives rise to the small secreted glycoprotein (AC P60173). Filoviruses entry requires functional lipid rafts at the host cell surface. Essential for infectivity, as it is the sole viral protein expressed at the virion surface. Belongs to the filoviruses glycoprotein family. +Vacuolar cation/proton exchanger (CAX). Translocates Ca(2+) and other metal ions into vacuoles using the proton gradient formed by H(+)-ATPase and H(+)-pyrophosphatase (By similarity). Tonoplast. Belongs to the Ca(2+):cation antiporter (CaCA) (TC 2.A.19) family. Cation/proton exchanger (CAX) subfamily. +Belongs to the sulfotransferase 1 family. +Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression. Purine metabolism; purine nucleotide biosynthesis [regulation]. Homodimer. Consists of two structural and functional domains: an N-terminal DNA-binding domain, approximately the first 60 residues, and a larger C-terminal domain, approximately 280 residues, which imparts the function of corepressor binding and oligomerization. +Essential counter-regulatory carboxypeptidase of the renin-angiotensin hormone system that is a critical regulator of blood volume, systemic vascular resistance, and thus cardiovascular homeostasis. Converts angiotensin I to angiotensin 1-9, a nine-amino acid peptide with anti-hypertrophic effects in cardiomyocytes, and angiotensin II to angiotensin 1-7, which then acts as a beneficial vasodilator and anti-proliferation agent, counterbalancing the actions of the vasoconstrictor angiotensin II. Also removes the C-terminal residue from three other vasoactive peptides, neurotensin, kinetensin, and des-Arg bradykinin, but is not active on bradykinin. Also cleaves other biological peptides, such as apelins, casomorphins and dynorphin A. Plays an important role in amino acid transport by acting as binding partner of amino acid transporter SLC6A19 in intestine, regulating trafficking, expression on the cell surface, and its catalytic activity. angiotensin II + H2O = angiotensin-(1-7) + L-phenylalanine angiotensin I + H2O = angiotensin-(1-9) + L-leucine bradykinin(1-8) + H2O = bradykinin(1-7) + L-phenylalanine H2O + neurotensin = L-leucine + neurotensin-(1-12) H2O + kinetensin = kinetensin-(1-8) + L-leucine dynorphin A-(1-13) + H2O = dynorphin A-(1-12) + L-lysine apelin-13 + H2O = apelin-12 + L-phenylalanine [Pyr1]apelin-13 + H2O = [Pyr1]apelin-12 + L-phenylalanine apelin-17 + H2O = apelin-16 + L-phenylalanine Binds 1 zinc ion per subunit. Binds 1 Cl(-) ion per subunit. Homodimer. Interacts with the catalytically active form of TMPRSS2 (By similarity). Interacts with SLC6A19; this interaction is essential for expression and function of SLC6A19 in intestine (By similarity). Interacts with ITGA5:ITGB1 (By similarity). Probably interacts (via endocytic sorting signal motif) with AP2M1; the interaction is inhibited by phosphorylation of Tyr-780 (By similarity). Interacts (via PDZ-binding motif) with SLC9A3R1 (via PDZ domains); the interaction may enhance ACE2 membrane residence (By similarity). Detected in both cell membrane and cytoplasm in neurons. The cytoplasmic tail contains several linear motifs such as LIR, PDZ-binding, PTB and endocytic sorting signal motifs that would allow interaction with proteins that mediate endocytic trafficking and autophagy. Proteolytic cleavage by ADAM17 generates a secreted form. Also cleaved by serine proteases: TMPRSS2, TMPRSS11D and HPN/TMPRSS1 (By similarity). Phosphorylated. Phosphorylation at Tyr-780 probably inhibits interaction with AP2M1 and enables interactions with proteins containing SH2 domains. Belongs to the peptidase M2 family. +May play an important role in the synaptic function of specific neuronal systems. Associates with proteins involved in vesicle docking and membrane fusion. Complexed with macromolecular elements of the nerve terminal. Isoforms differ by the usage of two alternative homologous exons which code for positions 55 to 94 and differ only in 11 positions out of 40. Expressed in several regions throughout the adult brain, including the mesencephalon. Belongs to the SNAP-25 family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Cytochrome P450 monooxygenase; part of the gene cluster that mediates the biosynthesis of a family of the mycotoxins cytochalasins E and K (PubMed:21983160). The hybrid PKS-NRPS synthetase ccsA and the enoyl reductase ccsC are responsible for fusion of phenylalanine with an octaketide backbone and subsequent release of the stable tetramic acid precursor (PubMed:21983160, PubMed:27551732). The polyketide synthase module (PKS) of the PKS-NRPS ccsA is responsible for the synthesis of the octaketide backbone (PubMed:21983160). The downstream nonribosomal peptide synthetase (NRPS) amidates the carboxyl end of the octaketide with a phenylalanine (PubMed:21983160). A reductase-like domain (R) at the C-terminus catalyzes the reductive release of the polyketide-amino acid intermediate (PubMed:21983160). Because ccsA lacks a designated enoylreductase (ER) domain, the required activity is provided the enoyl reductase ccsC (PubMed:21983160, PubMed:27551732). Upon formation of the 11-membered carbocycle-fused perhydroisoindolone intermediate, a number of oxidative steps are required to afford the final cytochalasin E and K, including two hydroxylations at C17 and C18, one alcohol oxidation at C17, one epoxidation at C6 and C7 and two Baeyer-Villiger oxidations (PubMed:21983160). The oxidative modification at C17, C18 and the C6-C7 epoxidation are likely to be catalyzed by the two cytochrome P450 oxygenases ccsD and ccsG (PubMed:21983160). CcsD may be responsible for the epoxidation of the C6-C7 double bond (PubMed:21983160). CcsG may be responsible for the successive oxidative modifications at C17 and C18 (PubMed:21983160). The double Baeyer-Villiger oxidations of ketocytochalasin to precytochalasin and cytochalasin Z(16) are among the final steps leading to cytochalasin E and K and are catalyzed by ccsB (PubMed:21983160, PubMed:24838010). The first oxygen insertion step follows that of the classic BVMO mechanism, generating the ester precytochalasin (PubMed:24838010). Release of precytochalasin into an aqueous environment can generate the shunt product iso-precytochalasin through spontaneous isomerization (PubMed:24838010). Alternatively, precytochalasin can undergo further oxidation by ccsB to yield the in-line carbonate-containing cytochalasin Z(16) (PubMed:24838010). Cytochalasin Z(16) is a precursor to cytochalasin E and cytochalasin K, whereas iso-precytochalasin is a precursor to cytochalasin Z(17) and rosellichalasin (PubMed:21983160, PubMed:24838010). The hydrolyase ccsE may catalyze hydrolysis of epoxide bond in cytochalasin E to afford cytochalasin K (PubMed:21983160). The function of ccsF has not been assigned but it may play a role in post-PKS-NRPS biosynthetic step, resistance or transport of cytochalasins and related PKS-NRPS products (PubMed:21983160). Mycotoxin biosynthesis. Belongs to the cytochrome P450 family. +Important regulator of cell cycle progression. Inhibits the kinase activity of CDK2 bound to cyclin A, but has little inhibitory activity on CDK2 bound to SPDYA. Involved in G1 arrest. Potent inhibitor of cyclin E- and cyclin A-CDK2 complexes. Forms a complex with cyclin type D-CDK4 complexes and is involved in the assembly, stability, and modulation of CCND1-CDK4 complex activation. Acts either as an inhibitor or an activator of cyclin type D-CDK4 complexes depending on its phosphorylation state and/or stoichometry. Forms a ternary complex composed of CCNE1, CDK2 and CDKN1B. Interacts directly with CCNE1; the interaction is inhibited by CDK2-dependent phosphorylation on Thr-187. Interacts with COPS5, subunit of the COP9 signalosome complex; the interaction leads to CDKN1B degradation. Interacts with NUP50; the interaction leads to nuclear import and degradation of phosphorylated CDKN1B. Interacts with CCND1 and SNX6 (By similarity). Interacts (Thr-198-phosphorylated form) with 14-3-3 proteins, binds strongly YWHAQ, weakly YWHAE and YWHAH, but not YWHAB nor YWHAZ; the interaction with YWHAQ results in translocation to the cytoplasm. Interacts with AKT1 and LYN; the interactions lead to cytoplasmic mislocation, phosphorylation of CDKN1B and inhibition of cell cycle arrest. Forms a ternary complex with CCNA2 and CDK2; CDKN1B inhibits the kinase activity of CDK2 through conformational rearrangements. Interacts (unphosphorylated form) with CDK2. Forms a complex with CDK2 and SPDYA, but does not directly interact with SPDYA. Forms a ternary complex composed of cyclin D, CDK4 and CDKN1B. Interacts (phosphorylated on Tyr-88 and Tyr-89) with CDK4; the interaction is required for cyclin D and CDK4 complex assembly, induces nuclear translocation and activates the CDK4 kinase activity. Interacts with GRB2. Interacts with PIM1. Identified in a complex with SKP1, SKP2 and CKS1B. Interacts with UHMK1; the interaction leads to cytoplasmic mislocation, phosphorylation of CDKN1B and inhibition of cell cycle arrest. Interacts also with CDK1. Dephosphorylated on Thr-187 by PPM1H, leading to CDKN1B stability (By similarity). Nuclear and cytoplasmic in quiescent cells. AKT- or RSK-mediated phosphorylation on Thr-198, binds 14-3-3, translocates to the cytoplasm and promotes cell cycle progression. Mitogen-activated UHMK1 phosphorylation on Ser-10 also results in translocation to the cytoplasm and cell cycle progression. Phosphorylation on Ser-10 facilitates nuclear export. Translocates to the nucleus on phosphorylation of Tyr-88 and Tyr-89 (By similarity). Colocalizes at the endosome with SNX6; this leads to lysosomal degradation (By similarity). A peptide sequence containing only AA 28-79 retains substantial Kip1 cyclin A/CDK2 inhibitory activity. Phosphorylated; phosphorylation occurs on serine, threonine and tyrosine residues. Phosphorylation on Ser-10 is the major site of phosphorylation in resting cells, takes place at the G(0)-G(1) phase and leads to protein stability. Phosphorylation on other sites is greatly enhanced by mitogens, growth factors, cMYC and in certain cancer cell lines. The phosphorylated form found in the cytoplasm is inactivate. Phosphorylation on Thr-198 is required for interaction with 14-3-3 proteins. Phosphorylation on Thr-187, by CDK1 and CDK2 leads to protein ubiquitination and proteasomal degradation. Tyrosine phosphorylation promotes this process. Phosphorylation by PKB/AKT1 can be suppressed by LY294002, an inhibitor of the catalytic subunit of PI3K. Phosphorylation on Tyr-88 and Tyr-89 has no effect on binding CDK2, but is required for binding CDK4. Dephosphorylated on tyrosine residues by G-CSF (By similarity). Dephosphorylated on Thr-187 by PPM1H, leading to CDKN1B stability (By similarity). Ubiquitinated; in the cytoplasm by the KPC complex (composed of RNF123/KPC1 and UBAC1/KPC2) and, in the nucleus, by SCF(SKP2). The latter requires prior phosphorylation on Thr-187. Ubiquitinated; by a TRIM21-containing SCF(SKP2)-like complex; leads to its degradation (By similarity). Subject to degradation in the lysosome. Interaction with SNX6 promotes lysosomal degradation (By similarity). Belongs to the CDI family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +May play a role in muscle cell metabolism. Belongs to the cytochrome b5 family. +Belongs to the major facilitator superfamily. +May interact with the nuclear pore complex. Belongs to the AIM4 family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreA releases sequences of 2 to 3 nucleotides. Belongs to the GreA/GreB family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. Minor subunit located with subunit a in the membrane (By similarity). F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. Component of an ATP synthase complex composed of ATP5PB, ATP5MC1, ATP5F1E, ATP5PD, ATP5ME, ATP5PF, ATP5MF, MT-ATP6, MT-ATP8, ATP5F1A, ATP5F1B, ATP5F1D, ATP5F1C, ATP5PO, ATP5MG, ATP5MK and ATP5MJ (By similarity). Interacts with PRICKLE3 (By similarity). Belongs to the ATPase protein 8 family. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +Molecular chaperone. Has ATPase activity. Homodimer. Belongs to the heat shock protein 90 family. +Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is transferred onto alpha-ketoisovalerate to form ketopantoate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = (6S)-5,6,7,8-tetrahydrofolate + 2-dehydropantoate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantoate from 3-methyl-2-oxobutanoate: step 1/2. Homodecamer; pentamer of dimers. Belongs to the PanB family. +Belongs to the UPF0391 family. +Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4-phosphonooxybutanoate to phosphohydroxythreonine. 2-oxoglutarate + O-phospho-L-serine = 3-phosphooxypyruvate + L-glutamate 2-oxoglutarate + 4-(phosphooxy)-L-threonine = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate Binds 1 pyridoxal phosphate per subunit. Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 2/3. Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 3/5. Homodimer. Expressed at high levels in the brain, liver, kidney and pancreas, and very weakly expressed in the thymus, prostate, testis and colon. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family. SerC subfamily. +Plays a crucial role in the maintenance of the structure of mitochondrial cristae and the proper assembly of the mitochondrial respiratory chain complexes. Required for the assembly of TOMM40 into the TOM complex. Associates with the mitochondrial contact site and cristae organizing system (MICOS) complex, composed of at least MICOS10/MIC10, CHCHD3/MIC19, CHCHD6/MIC25, APOOL/MIC27, IMMT/MIC60, APOO/MIC23/MIC26 and QIL1/MIC13. This complex was also known under the names MINOS or MitOS complex (By similarity). The MICOS complex associates with mitochondrial outer membrane proteins SAMM50, MTX1 and MTX2 (together described as components of the mitochondrial outer membrane sorting assembly machinery (SAM) complex) and DNAJC11, mitochondrial inner membrane protein TMEM11 and with HSPA9 (By similarity). The MICOS and SAM complexes together with DNAJC11 are part of a large protein complex spanning both membranes termed the mitochondrial intermembrane space bridging (MIB) complex (By similarity). Interacts with IMMT/MIC60 (By similarity). Interacts with CHCHD3/MIC19 (PubMed:21081504). Interacts with ARMC1 (By similarity). (Microbial infection) Interacts with parasite T.gondii RH strain MAF1b1; the interaction is probably indirect and results in the disruption of the MIB complex and the formation of SPOTs (structures positive for outer mitochondrial membrane (OMM)), a cellular response to OMM stress, which leads to the constitutive shedding of OMM vesicles. Its C-terminal part seems to contain many membrane-spanning sided beta-sheets, that have the potential to adopt a transmembrane beta-barrel type structure. Belongs to the SAM50/omp85 family. +Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine Purine metabolism; AMP biosynthesis via salvage pathway; AMP from adenine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. +Partially edited. Target of Adar. Belongs to the band 7/mec-2 family. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +The light-harvesting complex (LHC) functions as a light receptor, it captures and delivers excitation energy to photosystems with which it is closely associated. Binds at least 14 chlorophylls (8 Chl-a and 6 Chl-b) and carotenoids such as lutein and neoxanthin. The LHC complex consists of chlorophyll a-b binding proteins. The N-terminus of the protein extends into the stroma where it is involved with adhesion of granal membranes and post-translational modifications; both are believed to mediate the distribution of excitation energy between photosystems I and II. Photoregulated by reversible phosphorylation of its threonine residues. Belongs to the light-harvesting chlorophyll a/b-binding (LHC) protein family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Contaminating sequence. +Component of the chromosomal passenger complex (CPC), a complex that acts as a key regulator of mitosis. The CPC complex has essential functions at the centromere in ensuring correct chromosome alignment and segregation and is required for chromatin-induced microtubule stabilization and spindle assembly. Does not appear to exhibit anti-apoptotic activity. Plays a role in increasing blood vessel size during development (By similarity). Component of the CPC at least composed of survivin/birc5, incenp, cdca8/borealin and/or cdca9/dasra-A, and aurkb/aurora-B. Interacts directly with incenp (via N-terminus). Interacts with rxra; the interaction is stronger in the absence of 9-cis retinoic acids (By similarity). Localizes on chromosome arms and inner centromeres from prophase through metaphase and then transferring to the spindle midzone and midbody from anaphase through cytokinesis. The BIR2 domain is required for vascular development. Ubiquitination is required for centrosome-targeting. Belongs to the IAP family. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. +Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA. S-adenosyl-L-methionine + uridine(1939) in 23S rRNA = 5-methyluridine(1939) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. Extended N-terminus. +Part of the Tol-Pal system, which plays a role in outer membrane invagination during cell division and is important for maintaining outer membrane integrity. The Tol-Pal system is composed of five core proteins: the inner membrane proteins TolA, TolQ and TolR, the periplasmic protein TolB and the outer membrane protein Pal. They form a network linking the inner and outer membranes and the peptidoglycan layer. Belongs to the TolB family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Belongs to the SecA family. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 1 subfamily. +Catalyzes the deamination of dCTP to dUTP. dCTP + H(+) + H2O = dUTP + NH4(+) Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 1/2. Homotrimer. Belongs to the dCTP deaminase family. +Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8. Belongs to the universal ribosomal protein uL14 family. +Subunit of an amiloride-sensitive cation channel (degenerin channel complex) permeable for sodium, potassium, lithium and N-methylglucamine, and required for mechanosensory transduction (touch sensitivity) (PubMed:8655580, PubMed:12478294). Negatively regulates the turning step of male mating behavior (PubMed:17611271). Component of a non-voltage-gated amiloride-sensitive cation channel complex (also called the degenerin channel complex) composed of at least the mec-2, mec-4, mec-6 and mec-10 subunits; the complex mediates mechanotransduction in touch cells (PubMed:12478294). Interacts with mec-2, mec-6 and mec-10 (PubMed:12478294). Co-localizes with mec-6 in touch neuron axons. Expressed in AVM, ALM, PVM and PLM touch neurons. Mutations in mec-4 results in the degeneration of a small set of neurons which typically swell to several times their normal diameter before they disappear, presumably due to lysis. Belongs to the amiloride-sensitive sodium channel (TC 1.A.6) family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). Interacts with PHB2; the interaction decreases in absence of SPHK2 (By similarity). Interacts with AFG1L (By similarity). Interacts with ABCB7; this interaction allows the regulation of cellular iron homeostasis and cellular reactive oxygen species (ROS) levels in cardiomyocytes (By similarity). Belongs to the cytochrome c oxidase IV family. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F3 binds specifically to RB1 in a cell-cycle dependent manner. Inhibits adipogenesis, probably through the repression of CEBPA binding to its target gene promoters (By similarity). Component of the DRTF1/E2F transcription factor complex. Binds cooperatively with TFDP1/Dp-1 to E2F sites. Interacts with retinoblastoma protein RB1 and related proteins (such as RBL1) that inhibit the E2F transactivation domain. Binds EAPP. Belongs to the E2F/DP family. +This protein specifically catalyzes the removal of signal peptides from prolipoproteins. Release of signal peptides from bacterial membrane prolipoproteins. Hydrolyzes -Xaa-Yaa-Zaa-|-(S,diacylglyceryl)Cys-, in which Xaa is hydrophobic (preferably Leu), and Yaa (Ala or Ser) and Zaa (Gly or Ala) have small, neutral side chains. Protein modification; lipoprotein biosynthesis (signal peptide cleavage). Belongs to the peptidase A8 family. +Plays a positive role in plant adaptation to phosphate starvation (PubMed:18315545). Inhibits PHR1 DNA-binding activity in a Pi-dependent manner (PubMed:25271326). Interacts with PHR1 in a highly Pi-dependent manner (PubMed:25271326). Up-regulated under phosphate starvation. No effect on Pi accumulation, due to the redundancy with SPX2. Spx1 and spx2 double mutants have an increased root-to-shoot growth ratio and a reduced rot hair size when grown in Pi-sufficient conditions. +Belongs to the bacterial ribosomal protein bS16 family. +Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction. acetate + ATP = acetyl phosphate + ADP Mg(2+). Can also accept Mn(2+). Metabolic intermediate biosynthesis; acetyl-CoA biosynthesis; acetyl-CoA from acetate: step 1/2. Homodimer. Belongs to the acetokinase family. +Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel. Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL. Belongs to the GroES chaperonin family. +Destroys radicals which are normally produced within the cells and which are toxic to biological systems. 2 H(+) + 2 superoxide = H2O2 + O2 Binds 1 copper ion per subunit. Binds 1 zinc ion per subunit. Homotetramer. Belongs to the Cu-Zn superoxide dismutase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and probably 6 low-molecular weight proteins. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport (By similarity). Tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane. Interacts with ESYT1 and ESYT2. Localizes to endoplasmic reticulum-plasma membrane contact sites (EPCS) (PubMed:29469807, PubMed:30220461). Recruited to the cell membrane via the third C2 domain. Widely expressed with high level in cerebellum and skin. Anchored to the endoplasmic reticulum membrane by a transmembrane hairpin structure; both N-terminus and C-terminus are cytoplasmic. The C2 domains mediate lipid and calcium binding. The N-terminal C2 domain binds calcium ions and is important for calcium-dependent lipid binding and interaction with membranes. Two calcium ions are bound at a high-affinity site and a third calcium ion is bound with lower affinity. May bind up to four calcium ions. In contrast, the second C2 domain apparently does not bind calcium (By similarity). The third C2 domain mediates interaction with membranes enriched in phosphatidylinositol 4,5-bisphosphate and is required for location at the cell membrane (PubMed:23791178). The SMP-LTD domain is a barrel-like domain that binds glycerophospholipids in its interior (By similarity). Belongs to the extended synaptotagmin family. +Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate. ATP + formate + N(1)-(5-phospho-beta-D-ribosyl)glycinamide = ADP + H(+) + N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate Purine metabolism; IMP biosynthesis via de novo pathway; N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (formate route): step 1/1. Homodimer. Belongs to the PurK/PurT family. +In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins. Interacts with hair keratins. Belongs to the PMG family. +Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome (By similarity). Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily. +Responsible for spore hydrophobicity and protection. Expressed during conidiation. No expression in vegetative or sporulating aerial hyphae. By C and N starvation, and by light. Four disulfide bonds may be present. Belongs to the cerato-ulmin hydrophobin family. +Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. 2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde 3-phosphate Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Reduces arsenate [As(V)] to arsenite [As(III)]. Weakly induced by arsenite, antimonite and arsenate. Deletion of the arsADRC operon results in increased sensitivity to arsenite and antimonite but not arsenate. As expression is low no effect on arsenate resistance has been found. Belongs to the low molecular weight phosphotyrosine protein phosphatase family. +Involved in chlorophyll biosynthesis. Catalyzes the insertion of magnesium ion into protoporphyrin IX to yield Mg-protoporphyrin IX. The reaction takes place in two steps, with an ATP-dependent activation followed by an ATP-dependent chelation step. ATP + H2O + Mg(2+) + protoporphyrin IX = ADP + 3 H(+) + Mg-protoporphyrin IX + phosphate Porphyrin-containing compound metabolism; chlorophyll biosynthesis. The magnesium chelatase complex is a heterotrimer consisting of subunits CHLI, CHLD, AND CHLH. Homozygous KO plants are chlorotic lethal. Belongs to the Mg-chelatase subunits D/I family. +Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Binds 1 potassium ion per subunit. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. +Required for spliced RNA export out of the nucleus (PubMed:23149939). May play a role in spliceosome assembly. ATP + H2O = ADP + H(+) + phosphate Interacts with rsr-1/SRm160. RNAi-mediated knockdown prevents germ cells from entering meiosis and results in the accumulation of unspliced mRNAs in the cytoplasm. Belongs to the DEAD box helicase family. DECD subfamily. +Extracellular fibrinogen-binding protein that plays an important role in virulence. By interacting with the alpha chain of fibrinogen and its derivative fibrin, enhances a non-functional interaction between fibrinogen and platelets and is responsible for repression of fibrinogen-dependent platelet aggregation. In addition, assembles a fibrinogen protective shield around the bacteria which results in impaired phagocytic clearance by the host. Mechanistically, interacts with host complement C3b deposited on the surface of the bacterium via its C-terminal and then recruits fibrinogen via its N-terminal. Interacts with host fibrinogen alpha chain/FGA. Interacts with host complement protein C3. +Indispensable for the control of thyroid structure and metabolism. Heterodimer of a common alpha chain and a unique beta chain which confers biological specificity to thyrotropin, lutropin, follitropin and gonadotropin. Belongs to the glycoprotein hormones subunit beta family. +Has antimicrobial activity against Gram-positive bacterium S.aureus (MIC=3.79 uM), Gram-negative bacterium E.coli (MIC=7.81 uM) and yeasts C.krusei (MIC=26.3 uM) and C.neoformans (MIC=13.2 uM). Has hemolytic activity against rabbit erythrocytes. Forms pores in lipid bilayers in vitro; pore formation is reduced when cholesterol is present in the bilayers. Expressed by the venom gland. Belongs to the cationic peptide 04 (cupiennin) family. 05 subfamily. +Receptor for abscisic acid (ABA) required for ABA-mediated responses such as stomatal closure and germination inhibition. Inhibits the activity of group-A protein phosphatases type 2C (PP2Cs) when activated by ABA (By similarity). Suppresses the phosphatase activity of TOPP1 in a dose-dependent manner in vitro (PubMed:26943172). Homodimer. Binds ABA on one subunit only. Interacts with PP2Cs. Binds to CARs protein in an ABA-independent manner, both at the plasma membrane and in the nucleus (By similarity). Interacts with I-2 and TOPP1 (PubMed:26943172). Localizes at the plasma membrane in the presence of a CAR protein. Upon interaction with ABA, the 'latch' and 'gate' loops change in conformation leading to a tight dimerization and the creation a surface that enables the receptor to dock into and inhibit the PP2C active site. Belongs to the PYR/PYL/RCAR abscisic acid intracellular receptor family. +Belongs to the universal ribosomal protein uS2 family. +Binds 1 zinc ion per subunit. Belongs to the peptidase M48B family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Belongs to the imidazoleglycerol-phosphate dehydratase family. +Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain (By similarity). Dimer of alpha and beta chains. A typical microtubule is a hollow water-filled tube with an outer diameter of 25 nm and an inner diameter of 15 nM. Alpha-beta heterodimers associate head-to-tail to form protofilaments running lengthwise along the microtubule wall with the beta-tubulin subunit facing the microtubule plus end conferring a structural polarity. Microtubules usually have 13 protofilaments but different protofilament numbers can be found in some organisms and specialized cells. The highly acidic C-terminal region may bind cations such as calcium. The MREI motif is common among all beta-tubulin isoforms and may be critical for tubulin autoregulation. Some glutamate residues at the C-terminus are polyglycylated, resulting in polyglycine chains on the gamma-carboxyl group. Glycylation is mainly limited to tubulin incorporated into axonemes (cilia and flagella) whereas glutamylation is prevalent in neuronal cells, centrioles, axonemes, and the mitotic spindle. Both modifications can coexist on the same protein on adjacent residues, and lowering polyglycylation levels increases polyglutamylation, and reciprocally. Cilia and flagella glycylation is required for their stability and maintenance. Flagella glycylation controls sperm motility. Some glutamate residues at the C-terminus are polyglutamylated, resulting in polyglutamate chains on the gamma-carboxyl group (By similarity). Polyglutamylation plays a key role in microtubule severing by spastin (SPAST). SPAST preferentially recognizes and acts on microtubules decorated with short polyglutamate tails: severing activity by SPAST increases as the number of glutamates per tubulin rises from one to eight, but decreases beyond this glutamylation threshold (By similarity). Glutamylation is also involved in cilia motility (By similarity). Belongs to the tubulin family. +diphosphate + H2O = H(+) + 2 phosphate Binds 2 manganese ions per subunit. Belongs to the PPase class C family. +Functions as component of the transcription regulatory histone acetylation (HAT) complex SAGA. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction and promoter selectivity, interaction with transcription activators, and chromatin modification through histone acetylation and deubiquitination. SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). Sgf11 is involved in transcriptional regulation of a subset of SAGA-regulated genes and is required for histone H2B deubiquitination (By similarity). Component of the SAGA complex. Belongs to the ataxin-7 family. +Hydroxylation at Pro-62 affects translation termination efficiency. There are two genes for S23 in S.pombe. Belongs to the universal ribosomal protein uS12 family. +4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Belongs to the cytochrome c oxidase subunit 3 family. +Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls. H2O + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-2,6-diaminoheptanedioate + succinate Binds 2 Zn(2+) or Co(2+) ions per subunit. Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route): step 3/3. Homodimer. Belongs to the peptidase M20A family. DapE subfamily. +Catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP. Can also catalyze, although with low efficiency, the phosphorylation of bicarbonate, leading to the formation of carboxyphosphate, an unstable intermediate found in the reactions catalyzed by carbamoyl-phosphate synthase and biotin carboxylase. Can also use acetate. ATP + hydrogencarbonate + NH4(+) = ADP + carbamoyl phosphate + H(+) + H2O Inhibited by adenosine(5')pentaphospho(5')adenosine (Ap5A), Ap6A and to a much lower extent by Ap4A. Metabolic intermediate metabolism; carbamoyl phosphate degradation; CO(2) and NH(3) from carbamoyl phosphate: step 1/1. Homodimer (predominantly) and homotetramer. By arginine. Belongs to the carbamate kinase family. +Capsid protein p27: Self-associates to form the irregular polyhedron core composed of hexamers and pentamers, that encapsulates the genomic RNA-nucleocapsid complex. Assembles as a tube in vitro. Spacer peptide: Plays a role in the oligomerization of the Gag polyprotein and in the stabilization of the immature particle. Essential layering element during tube assembly. Binds strongly to viral nucleic acids and promote their aggregation. Also destabilizes the nucleic acids duplexes via highly structured zinc-binding motifs. The aspartyl protease that mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell. Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions (PubMed:2555556). This recombination event is an essential step in the viral replication cycle. Has a strong preference for using the 3'-OH at the viral DNA end as a nucleophile. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Endonucleolytic cleavage to 5'-phosphomonoester. The RT polymerase active site binds 2 magnesium ions. Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding. Binds 8 Mg(2+) ions per integrase homotetramer. Active as a homodimer. Homodimer; further associates as a homooctamer. Heterodimer of alpha and beta subunits. Three forms of RT exist: alpha-alpha (alpha-Pol), beta-beta (beta-Pol), and alpha-beta, with the major form being the heterodimer. Both the polymerase and RNase H active sites are located in the alpha subunit of heterodimeric RT alpha-beta. Heterodimer of alpha and beta subunits. Three forms of RT exist: alpha-alpha (alpha-Pol), beta-beta (beta-Pol), and alpha-beta, with the major form being the heterodimer. Both the polymerase and RNase H active sites are located in the alpha subunit of heterodimeric RT alpha-beta. Translation results in the formation of the Gag polyprotein. Ribosomal frameshifting at the gag/pol genes boundary produces the Gag-Pol polyprotein. Late-budding domains (L domains) are short sequence motifs essential for viral particle release. They can occur individually or in close proximity within structural proteins. They interacts with sorting cellular proteins of the multivesicular body (MVB) pathway. Most of these proteins are class E vacuolar protein sorting factors belonging to ESCRT-I, ESCRT-II or ESCRT-III complexes. P2B contains two L domain: a PPXY motif which probably binds to the WW domains of HECT (homologous to E6-AP C-terminus) E3 ubiquitin ligases and a LYPX(n)L domain which is known to bind the Alix adaptator protein. The core domain contains the D-x(n)-D-x(35)-E motif, named for the phylogenetically conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein (By similarity). Contains a nuclear export signal in p10 and a nucleolar localization signal in nucleocapsid protein p12. Capsid protein p27: Proton-driven dimerization of the C-terminus facilitates capsid assembly. Specific enzymatic cleavages in vivo yield mature proteins. Capsid protein p27: The cleavage at the C-terminus is slowly trimmed by the viral protease, sometimes being cut internally thereby generating the short version of the capsid protein and a capsid protein C-terminally extended by 3 amino acids in a ratio of 2:1. Reverse transcriptase: Error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template switching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs. Produced by -1 ribosomal frameshifting. +Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate. 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 6/7. Monomer. Belongs to the EPSP synthase family. +Involved in pyrimidine catabolism. Catalyzes the deamination of 3-aminoacrylate to malonic semialdehyde, a reaction that can also occur spontaneously. RutC may facilitate the reaction and modulate the metabolic fitness, rather than catalyzing essential functions. (Z)-3-aminoacrylate + H(+) + H2O = 3-oxopropanoate + NH4(+) Homotrimer. Belongs to the RutC family. +Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Also functions as deacetylase for non-histone targets, such as NR1D2, RELA, SP1, SP3 and TSHZ3. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Deacetylates NR1D2 and abrogates the effect of KAT5-mediated relieving of NR1D2 transcription repression activity (By similarity). Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Involved in CIART-mediated transcriptional repression of the circadian transcriptional activator: CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex or CRY1 through histone deacetylation (By similarity). In addition to protein deacetylase activity, also has protein-lysine deacylase activity: acts as a protein decrotonylase by mediating decrotonylation ((2E)-butenoyl) of histones (By similarity). H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl-[histone] H2O + N(6)-acetyl-L-lysyl-[protein] = acetate + L-lysyl-[protein] H2O + N(6)-(2E)-butenoyl-L-lysyl-[protein] = (2E)-2-butenoate + L-lysyl-[protein] Part of the core histone deacetylase (HDAC) complex composed of HDAC1, HDAC2, RBBP4 and RBBP7. The core complex associates with MTA2, MBD2, MBD3, MTA1L1, CHD3 and CHD4 to form the nucleosome remodeling and histone deacetylation (NuRD) complex, or with SIN3, SAP18 and SAP30 to form the SIN3 HDAC complex. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. Component of a mSin3A corepressor complex that contains SIN3A, SAP130, SUDS3/SAP45, ARID4B/SAP180, HDAC1 and HDAC2. Found in a trimeric complex with APBB1 and TSHZ3; the interaction between HDAC1 and APBB1 is mediated by TSHZ3. Component of a RCOR/GFI/KDM1A/HDAC complex. Part of a complex composed of TRIM28, HDAC1, HDAC2 and EHMT2. Part of a complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2. The large PER complex involved in the histone deacetylation is composed of at least HDAC1, PER2, SFPQ and SIN3A. Associates with the 9-1-1 complex; interacts with HUS1. Found in a complex with DNMT3A and HDAC7. Interacts with the non-histone region of MACROH2A1. Interacts with TRIM28; the interaction recruits HDAC1 to E2F1 and inhibits its acetylation. Interacts with SP1; the interaction deacetylates SP1 and regulates its transcriptional activity. Interacts with SP3; the interaction deacetylates SP3 and regulates its transcriptional activity. In vitro, C(18) ceramides increase this interaction and the subsequent SP3 deacetylation and SP3-mediated repression of the TERT promoter. Interacts with TSHZ3 (via N-terminus); the interaction is direct. Interacts with APEX1; the interaction is not dependent on the acetylated status of APEX1. Interacts with C10orf90/FATS (via its N-terminal); the interaction prevents binding of HDAC1 to CDKN1A/p21 and facilitates the acetylation and stabilization of CDKN1A/p21. Interacts with CDKN1A/p21. Interacts with CDK5 complexed to CDK5R1 (p25). Interacts directly with GFI1 and GFI1B. Interacts with NR1D2 (via C-terminus). Interacts with TSC22D3 isoform 1; this interaction affects HDAC1 activity on MYOG promoter and thus inhibits MYOD1 transcriptional activity. Interacts with BAZ2A/TIP5, BANP, BCL6, BCOR, BHLHE40/DEC1, BRMS1, BRMS1L, CBFA2T3, CHFR, CIART, CRY1, DAXX, DDIT3/CHOP, DDX5, DNMT1, E4F1, EP300, HCFC1, HDAC9, INSM1, NFE4, NR4A2/NURR1, MIER1, KDM4A, KDM5B, KLF1, MINT, NRIP1, PCAF, PHB2, PRDM6, PRDM16, RB1, RERE, SAMSN1, SAP30L, SETDB1, SMAD3, SMARCA4/BRG1, SMYD2, SUV39H1, TGIF, TGIF2, TRAF6, UHRF1, UHRF2, ZMYND15, ZNF431 and ZNF541. Interacts with KDM5A; this interaction impairs histone deacetylation (By similarity). Interacts with DNTTIP1. Identified in a histone deacetylase complex that contains DNTTIP1, HDAC1 and MIDEAS; this complex assembles into a tetramer that contains four copies of each protein chain. Interacts with CCAR2. Interacts with PPHLN1. Found in a complex with YY1, SIN3A and GON4L. Interacts with CHD4. Found in a complex composed of at least SINHCAF, SIN3A, HDAC1, SAP30, RBBP4, OGT and TET1. Interacts with SIN3A. Interacts with DHX36; this interaction occurs in a RNA-dependent manner (By similarity). Interacts with ZBTB7A (By similarity). Interacts with SMAD4; positively regulated by ZBTB7A (By similarity). Interacts with PACS2 (By similarity). Forms a complex comprising APPL1, RUVBL2, APPL2, CTNNB1 and HDAC2 (By similarity). Interacts with ZNF638 (By similarity). Interacts with SPHK2 (By similarity). Interacts with ERCC6 (By similarity). Interacts with SMYD4 (via MYND-type zinc finger) (By similarity). Interacts with PWWP2A in a MTA1-dependent manner (By similarity). Interacts with PWWP2B (By similarity). Interacts with ZNF516 and BRCC3; these interactions are enhanced in the presence of PWWP2B (By similarity). Interacts with SANBR (via the BTB domain) (By similarity). Sumoylated on Lys-444 and Lys-476; which promotes enzymatic activity. Desumoylated by SENP1. Phosphorylation on Ser-421 and Ser-423 promotes enzymatic activity and interactions with NuRD and SIN3 complexes. Phosphorylated by CDK5. Ubiquitinated by CHFR and KCTD11, leading to its degradation by the proteasome. Belongs to the histone deacetylase family. HD type 1 subfamily. +This protein binds specifically to 23S rRNA. The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +Involved in calcium binding and microtubule stabilization. Belongs to the TCTP family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved. Distribution is 50-50. Not essential, the disruption mutant is super-sensitive to azide, export of some proteins is decreased and has a small colony growth phenotype on rich agar medium. It cannot replace secA1. Belongs to the SecA family. +Mu-conotoxins block voltage-gated sodium channels (Nav). Expressed by the venom duct. The cysteine framework is III (CC-C-C-CC). Classified in the M-4 branch, since 4 residues stand between the fourth and the fifth cysteine residues. Belongs to the conotoxin M superfamily. +Binds 1 zinc ion per subunit. Belongs to the peptidase M48B family. Extended N-terminus. +Necessary for normal cell division and for the maintenance of normal septation. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. +Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel. Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL. Belongs to the GroES chaperonin family. +Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II). Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + UDP-N-acetyl-alpha-D-glucosamine = beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + H(+) + UDP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 28 family. MurG subfamily. +Involved in membrane trafficking and vacuole development through membrane fusion at the vacuole. Required for membrane trafficking machinery and accumulation of flavonoids in the seed coat. Abnormal pale brown color of seed coat (testa) due to low flavonoid accumulation levels. Belongs to the CLEC16A/gop-1 family. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII' complex. PolIII' associates with the gamma complex (composed of gamma, delta, delta', psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex (By similarity). As has been shown for E.coli (strain K12) and suggested for Salmonella typhimurium, the gamma subunit (approximately resides 1-430) might be generated by ribosomal frameshifting, leading to 2 protein products from 1 gene. Belongs to the DnaX/STICHEL family. +Early transcription factor that plays a key role in somitogenesis, paraxial mesoderm development and regulation of stem cell pluripotency (PubMed:7597044, PubMed:8955271, PubMed:23395635, PubMed:32669716, PubMed:24038871). Essential for the mesenchymal to epithelial transition associated with somite formation (PubMed:7597044, PubMed:8955271, PubMed:24038871). Required for somite morphogenesis, thereby regulating patterning of the axial skeleton and skeletal muscles (PubMed:8955271). Required for proper localization of somite epithelium markers during the mesenchymal to epithelial transition (PubMed:24038871). Also plays a key role in regulation of stem cell pluripotency (PubMed:23395635, PubMed:32669716). Promotes pluripotency exit of embryonic stem cells (ESCs) by priming ESCs for differentiation (PubMed:23395635). Acts as a key regulator of self-renewal of hematopoietic stem cells (HSCs) by mediating HSCs quiescence and long-term self-renewal (PubMed:32669716). Together with MEOX2, regulates transcription in heart endothelial cells to regulate fatty acid transport across heart endothelial cells (PubMed:25561514). Acts by forming a heterodimer with another helix-loop-helix (bHLH) protein, such as TCF3/E12, that binds DNA on E-box motifs (5'-CANNTG-3') and activates transcription of target genes (PubMed:15226298, PubMed:23395635). Heterodimer; efficient DNA binding requires dimerization with another bHLH protein, such as TCF3/E12 (PubMed:15226298, PubMed:23395635). Interacts with MEOX2 (PubMed:25561514). Expressed in heart and skeletal muscle (PubMed:8041747, PubMed:7597044). Specifically expressed in a subpopulation of embryonic stem cells (ESCs), that are still undifferentiated but primed for ifferentiation (PubMed:23395635). Expressed in hematopoietic stem cells (HSCs) (PubMed:32669716). Expressed in the embryonic day 4.5 embryo (PubMed:23395635). Expressed in paraxial mesoderm and developing somites (PubMed:7729571). At 7.5 dpc, low expression is detected in a subdomain of the primitive mesoderm (PubMed:8041747). At 8.5 dpc, expressed at high levels throughout the uncompartmentalized epithelial somites and in the rostral paraxial mesoderm (PubMed:8041747). By 9.5 dpc, expression is confined to the somite and is most prominent in the myotome and dermatome (PubMed:8041747). At 10 dpc, expression in somite declines in the myotome but persists at high level in the dermatome (PubMed:8041747). At 10.5 dpc, expression is seen only in the somites in the caudal portion of the embryo (PubMed:8041747). Lethality within an hour of birth, possibly caused by rib defects that lead to respiratory distress (PubMed:8955271). At birth, neonates display obvious caudal agenesis with tails that are shortened and curled (PubMed:8955271). They also lack the normal cervical flexure of the vertebral column, and their hindlimbs are curved towards the midline (PubMed:8955271). Neonates also display low-set ears, a thickened neck and loose skin (PubMed:8955271). Defects are caused by impaired formation of somites: cells from the paraxial mesoderm are unable to form epithelia, preventing formation of somites (PubMed:8955271). In the absence of normal somites, the axial skeleton and skeletal muscle form but are improperly patterned (PubMed:8955271). Hematopoietic stem cells (HSCs) show a specific loss of quiescent stem cells (PubMed:32669716). +Belongs to the class V-like SAM-binding methyltransferase superfamily. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Homodimer. Belongs to the GrpE family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position. Transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain. Glycan biosynthesis; glycogen biosynthesis. Monomer. Belongs to the glycosyl hydrolase 13 family. GlgB subfamily. +Interacts with CLK1, CLK3 and CLK4. +Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). diphosphate + N-(5-phospho-beta-D-ribosyl)anthranilate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate Binds 2 magnesium ions per monomer. Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 2/5. Homodimer. Belongs to the anthranilate phosphoribosyltransferase family. +Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser) ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec) Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. Homodimer. The tRNA molecule binds across the dimer. Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily. +Belongs to the bacterial ribosomal protein bL27 family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Binds 1 heme group per subunit. Monomer. Belongs to the truncated hemoglobin family. Group I subfamily. +Receptor for CCL19 and chemerin/RARRES2. Does not appear to be a signaling receptor, but may have a role in modulating chemokine-triggered immune responses by capturing and internalizing CCL19 or by presenting RARRES2 ligand to CMKLR1, a functional signaling receptor. Plays a critical role for the development of Th2 responses (By similarity). Expressed in macrophages, astrocytes, in glial cells. Constitutively expressed by mast cells. Detected in bronchial epithelium in OVA-induced airway inflammation. Up-regulated during dendritic cell (DC) maturation. By bacterial lipopolysaccharide in astrocytes. Lacks the conserved DRYLAIV motif in the second intracellular loop that is required for signaling of functional chemokine receptors. No visible phenotype. Deficient-mice have normal numbers of mast cells in all tissues analyzed. Wild-type and deficient mice develop marked local inflammation when sensitized with a high dose of DNP-specific IgE, however deficient mice have significantly reduced IgE-dependent passive cutaneous anaphylaxis (PCA) reactions when lower sensitizing dose is used. Deficient-mice show normal recruitment of circulating DC into the lung, but a defective trafficking of antigen-loaded lung DC to mediastinal lymph nodes. This defect was associated to a reduction in lymph node cellularity and reduced priming of T-helper cell 2 response. It was initially reported that CCRL2 responds functionally to CCL2, CCL5, CCL7, and CCL8 via intracellular calcium mobilization and transwell chemotaxis although no evidence for a direct ligand-receptor interaction was provided in this report (PubMed:14999816). These results are now controversial and other studies failed to confirm CCRL2 recognition and transwell chemotaxis of these chemokines or a series of other CC- and CXC-chemokines using CCRL2-transfected cells (PubMed:18794339). Belongs to the G-protein coupled receptor 1 family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase C chain family. +Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3. Belongs to the universal ribosomal protein uS11 family. +ATP + H2O + xenobioticSide 1 = ADP + phosphate + xenobioticSide 2. Belongs to the ABC transporter superfamily. Drug exporter-2 (TC 3.A.1.117) family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Belongs to the RNase HII family. +Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm. Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own. Belongs to the FKBP-type PPIase family. Tig subfamily. +Component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins (By similarity). Belongs to the universal ribosomal protein uL13 family. +Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; fumarate reductase is used in anaerobic growth, and succinate dehydrogenase is used in aerobic growth. Anchors the catalytic components of the fumarate reductase complex to the cell inner membrane, binds quinones. Part of an enzyme complex containing four subunits: a flavoprotein (FrdA), an iron-sulfur protein (FrdB), and two hydrophobic anchor proteins (FrdC and FrdD). Belongs to the FrdC family. +Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate. D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+) Binds 2 divalent metal cations per subunit. Magnesium or manganese. Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. Homodimer. Belongs to the DHBP synthase family. +Homodimer. In response to low temperature. +Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. Binds 3 Zn(2+) ions. Belongs to the AP endonuclease 2 family. +Catalyzes the ATP- as well as the pyrophosphate-dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK/P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P-Ser-HPr). The two antagonistic activities of HprK/P are regulated by several intracellular metabolites, which change their concentration in response to the absence or presence of rapidly metabolisable carbon sources (glucose, fructose, etc.) in the growth medium. Therefore, by controlling the phosphorylation state of HPr, HPrK/P is a sensor enzyme that plays a major role in the regulation of carbon metabolism and sugar transport: it mediates carbon catabolite repression (CCR), and regulates PTS-catalyzed carbohydrate uptake and inducer exclusion. [HPr protein]-L-serine + ATP = [HPr protein]-O-phospho-L-serine + ADP + H(+) [HPr protein]-O-phospho-L-serine + H(+) + phosphate = [HPr protein]-L-serine + diphosphate Homohexamer. The Walker A ATP-binding motif also binds Pi and PPi. Both phosphorylation and phosphorolysis are carried out by the same active site and suggest a common mechanism for both reactions. Belongs to the HPrK/P family. +Ethanolamine-phosphate cytidylyltransferase which catalyzes the second step of phosphatidylethanolamine biosynthesis. Involved in the maintenance of plasma membrane and required for proper sporulation. CTP + H(+) + phosphoethanolamine = CDP-ethanolamine + diphosphate Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from ethanolamine: step 2/3. By isooctane. Present with 4700 molecules/cell in log phase SD medium. Belongs to the cytidylyltransferase family. +Belongs to the universal ribosomal protein uS4 family. +Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine + [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. Homodimer. Belongs to the radical SAM superfamily. Biotin synthase family. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG. Belongs to the RnfG family. +Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain. acetyl-CoA + alpha-D-glucosamine 1-phosphate = CoA + H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate H(+) + N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine Binds 1 Mg(2+) ion per subunit. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; N-acetyl-alpha-D-glucosamine 1-phosphate from alpha-D-glucosamine 6-phosphate (route II): step 2/2. Nucleotide-sugar biosynthesis; UDP-N-acetyl-alpha-D-glucosamine biosynthesis; UDP-N-acetyl-alpha-D-glucosamine from N-acetyl-alpha-D-glucosamine 1-phosphate: step 1/1. Bacterial outer membrane biogenesis; LPS lipid A biosynthesis. Homotrimer. In the N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family. In the C-terminal section; belongs to the transferase hexapeptide repeat family. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(1) domain and the central stalk which is part of the complex rotary element. The gamma subunit protrudes into the catalytic domain formed of alpha(3)beta(3). Rotation of the central stalk against the surrounding alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Component of an ATP synthase complex composed of ATP5PB, ATP5MC1, ATP5F1E, ATP5PD, ATP5ME, ATP5PF, ATP5MF, MT-ATP6, MT-ATP8, ATP5F1A, ATP5F1B, ATP5F1D, ATP5F1C, ATP5PO, ATP5MG, ATP5MK and ATP5MJ. Belongs to the ATPase gamma chain family. +RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs. Homohexamer. Belongs to the Hfq family. +Fructose-bisphosphatase hydrolyzing fructose-2,6-bisphosphate as well as fructose-1,6-bisphosphate (By similarity). Acts as a negative regulator of glycolysis by lowering intracellular levels of fructose-2,6-bisphosphate in a p53/TP53-dependent manner, resulting in the pentose phosphate pathway (PPP) activation and NADPH production. Contributes to the generation of reduced glutathione to cause a decrease in intracellular reactive oxygen species (ROS) content, correlating with its ability to protect cells from oxidative or metabolic stress-induced cell death. Plays a role in promoting protection against cell death during hypoxia by decreasing mitochondria ROS levels in a HK2-dependent manner through a mechanism that is independent of its fructose-bisphosphatase activity. In response to cardiac damage stress, mediates p53-induced inhibition of myocyte mitophagy through ROS levels reduction and the subsequent inactivation of BNIP3. Reduced mitophagy results in an enhanced apoptotic myocyte cell death, and exacerbates cardiac damage. Plays a role in adult intestinal regeneration; contributes to the growth, proliferation and survival of intestinal crypts following tissue ablation. Plays a neuroprotective role against ischemic brain damage by enhancing PPP flux and preserving mitochondria functions. Protects glioma cells from hypoxia- and ROS-induced cell death by inhibiting glycolysis and activating mitochondrial energy metabolism and oxygen consumption in a TKTL1-dependent and p53/TP53-independent manner. Plays a role in cancer cell survival by promoting DNA repair through activating PPP flux in a CDK5-ATM-dependent signaling pathway during hypoxia and/or genome stress-induced DNA damage responses. Involved in intestinal tumor progression. beta-D-fructose 2,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate Interacts with HK2; the interaction increases hexokinase HK2 activity in a hypoxia- and HIF1A-dependent manner, resulting in the regulation of mitochondrial membrane potential, thus increasing NADPH production and decreasing intracellular ROS levels. Translocated to the mitochondria during hypoxia in a HIF1A-dependent manner. Colocalizes with HK2 in the mitochondria during hypoxia. Translocated to the nucleus during hypoxia and/or genome stress-induced DNA damage responses in cancer cells. Translocation to the mitochondria is enhanced in ischemic cortex after reperfusion and/or during oxygen and glucose deprivation (OGD)/reoxygenation insult in primary neurons. Belongs to the phosphoglycerate mutase family. Not expected to have any kinase activity. +Belongs to the UPF0229 family. +Binds 16S rRNA, required for the assembly of 30S particles. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS14 family. +Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + UDP-N-acetyl-alpha-D-glucosamine = a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + holo-[ACP] Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 1/6. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxA subfamily. +This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL22 family. +Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 2A subfamily. +Catalyzes the catabolism of the allantoin degradation intermediate (S)-ureidoglycolate, generating urea and glyoxylate. Involved in the anaerobic utilization of allantoin as sole nitrogen source. Reinforces the induction of genes involved in the degradation of allantoin and glyoxylate by producing glyoxylate. (S)-ureidoglycolate = glyoxylate + urea Nitrogen metabolism; (S)-allantoin degradation. Homodimer. Belongs to the ureidoglycolate lyase family. +Belongs to the UPF0735 family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. +Glycosidase. Binds 1 NAD(+) per subunit. The NAD(+) cannot dissociate. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the Gfo/Idh/MocA family. Glycosyl hydrolase 109 subfamily. +Catalyzes the reduction of 1-pyrroline-5-carboxylate (PCA) to L-proline. L-proline + NADP(+) = 1-pyrroline-5-carboxylate + 2 H(+) + NADPH L-proline + NAD(+) = 1-pyrroline-5-carboxylate + 2 H(+) + NADH Amino-acid biosynthesis; L-proline biosynthesis; L-proline from L-glutamate 5-semialdehyde: step 1/1. Belongs to the pyrroline-5-carboxylate reductase family. +May participate in meiotic recombination, specifically in homologous strand assimilation, which is required for the resolution of meiotic double-strand breaks (PubMed:10488231, PubMed:23300481). Mediates interhomolog recombination during meiosis (PubMed:17785529). Double stacked ring-shaped homooctamer (By similarity). Interacts with BRCA2A and BRCA2B (PubMed:16415210). Expressed in mitotic and/or meiotic tissues. Expressed in roots, leaves and anthers and carpels of young fower buds. Cell cycle regulated, peaking at the S phase. It is also expressed at high levels in exponentially growing cells in suspension cultures. Strongly reduced fertility and seed numbers due to defects in male and female gametogenesis. Belongs to the RecA family. DMC1 subfamily. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +High-affinity potassium transporter. Belongs to the HAK/KUP transporter (TC 2.A.72.3) family. +Involved in the fragmentation of the mitochondrial network and its perinuclear clustering. Plays a minor role in the recruitment and association of the fission mediator dynamin-related protein 1 (DNM1L) to the mitochondrial surface and mitochondrial fission. Can induce cytochrome c release from the mitochondrion to the cytosol, ultimately leading to apoptosis. Also mediates peroxisomal fission. Interacts with DNM1L/DLP1 through the TPR region. Interacts with MARCHF5. Interacts with MIEF1. Interacts with PEX11A, PEX11B and PEX11G (PubMed:20826455). The C-terminus is required for mitochondrial or peroxisomal localization, while the N-terminus is necessary for mitochondrial or peroxisomal fission, localization and regulation of the interaction with DNM1L. Ubiquitinated by MARCHF5. Belongs to the FIS1 family. +Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). 2-oxoglutarate + H(+) + isochorismate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2 Binds 1 thiamine pyrophosphate per subunit. Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 2/7. Quinol/quinone metabolism; menaquinone biosynthesis. Homodimer. Was identified as a high-confidence drug target. Belongs to the TPP enzyme family. MenD subfamily. +Protein required for cold tolerance (PubMed:25725023). Plays a role in the regulation of phosphate uptake (PubMed:25725023). Belongs to the CTO1 family. +Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I. di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the glycosyltransferase 4 family. MraY subfamily. +Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. a (3R)-hydroxyacyl-[ACP] + UDP-N-acetyl-alpha-D-glucosamine = a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + holo-[ACP] Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 1/6. Homotrimer. Belongs to the transferase hexapeptide repeat family. LpxA subfamily. +Pancreatic hormone is synthesized in pancreatic islets of Langerhans and acts as a regulator of pancreatic and gastrointestinal functions. Belongs to the NPY family. +Component of the cap-binding complex (CBC), which binds cotranscriptionally to the 5'-cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing and RNA-mediated gene silencing (RNAi). The CBC complex is involved in miRNA-mediated RNA interference via its interaction with Ars2 and is required for primary microRNAs (miRNAs) processing. Also involved in innate immunity via the short interfering RNAs (siRNAs) processing machinery by restricting the viral RNA production. In the CBC complex, Cbp80 does not bind directly capped RNAs (m7GpppG-capped RNA) but is required to stabilize the movement of the N-terminal loop of Cbp20 and lock the CBC into a high affinity cap-binding state with the cap structure (By similarity). Component of the nuclear cap-binding complex (CBC), a heterodimer composed of Cbp80 and Cbp20 that interacts with m7GpppG-capped RNA. Belongs to the NCBP1 family. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Omega-conotoxins act at presynaptic membranes, they bind and block voltage-gated calcium channels (Cav) (By similarity). Has strong insecticidal properties at a dose of only 100 pmol/g of body weight (when injected into the haemocoel of the wax moth G. mellonella larvae). Provoques tremor and uncontrolled movements in insect larvae, that are typical symptoms caused by neurotoxins (PubMed:22728460). On fish G.niger, intraperitoneal injection of the toxin causes full extension of the fins, change in posture, breathing difficulties (at 30 and 100 pmol/g body weight) and death (at 100 pmol/g body weight) (PubMed:22728460). Expressed by the venom duct. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. The cysteine framework is VI/VII (C-C-CC-C-C). LD(50) is more than 100 pmol/g body weight (at 24 hours) when injected into the haemocoel of the wax moth G. mellonella larvae. +Belongs to the eukaryotic ribosomal protein eL32 family. +Belongs to the UPF0719 family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta chain family. +1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 4/9. Belongs to the HisA/HisF family. +Almost completely overlaps SAS3. Product of a dubious gene prediction unlikely to encode a functional protein. Because of that it is not part of the S.cerevisiae S288c complete/reference proteome set. +Belongs to the UPF0310 family. +Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)). 7-carboxy-7-deazaguanine + ATP + NH4(+) = 7-cyano-7-deazaguanine + ADP + H(+) + H2O + phosphate Binds 1 zinc ion per subunit. Purine metabolism; 7-cyano-7-deazaguanine biosynthesis. Belongs to the QueC family. +Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP) (By similarity). Confers resistance to bacitracin. Is also required for virulence. di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available. Belongs to the UppP family. +Catalyzes the reversible phosphorylation of UMP to UDP. ATP + UMP = ADP + UDP Inhibited by UTP. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; UDP from UMP (UMPK route): step 1/1. Homohexamer. Belongs to the UMP kinase family. +Belongs to the universal ribosomal protein uS2 family. +Involved in DNA repair and RecF pathway recombination. Belongs to the RecO family. +The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. Belongs to the RecF family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs). Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the peptidase S14 family. +ATPase subunit of a proteasome-like degradation complex; this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. Belongs to the ClpX chaperone family. HslU subfamily. +GATA-type transcription repressor that regulates iron- acquisition genes through specific binding the GATA sequence elements of target promoters in a zinc-dependent manner (PubMed:9790585, PubMed:10194352, PubMed:12484767). Iron acquisition regulation is critical for survival under both iron-limiting conditions (to acquire essential iron) and iron-replete conditions (to limit iron toxicity) (PubMed:10194352). Represses the synthesis of siderophores in high iron conditions (PubMed:9790585). The promoter contains a number of GATA sequences; however, expression occurs in a constitutive fashion and is not regulated by the concentration of iron available to the cells (PubMed:9790585). The conserved cystein-rich region (CRR) localized between the zinc fingers is also involved in DNA-binding and transcription repressor activity (PubMed:12484767). Both the N-terminal and C-terminal zinc fingers are involved in DNA-binding, although the C-terminal finger plays a more important role in the binding (PubMed:10194352). Derepresses siderophore biosynthesis in high iron concentrations (PubMed:9790585). +Catalyzes the oxidation of L-galactonate to D-tagaturonate. Required for growth on L-galactonate as the sole carbon source. In vitro, can also use L-gulonate. L-galactonate + NAD(+) = H(+) + keto-D-tagaturonate + NADH Binds 2 Zn(2+) ions per subunit. Inhibited by EDTA. kcat is 0.51 sec(-1) with L-galactonate. Optimum pH is 8.0. Highly up-regulated during growth on L-galactonate. Cells lacking this gene fail to grow on L-galactonate as sole carbon source. Belongs to the zinc-containing alcohol dehydrogenase family. Extended N-terminus. +Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily. +Plays a role in the inhibition of gene silencing by the host nucleoid-associated protein H-NS/hns. Disrupts higher-order H-NS-DNA complexes. +Required during biogenesis of c-type cytochromes (cytochrome c6 and cytochrome f) at the step of heme attachment. May interact with ccs1. Belongs to the CcmF/CycK/Ccl1/NrfE/CcsA family. +Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate. L-lysyl-[protein] + octanoyl-[ACP] = H(+) + holo-[ACP] + N(6)-octanoyl-L-lysyl-[protein] Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 1/2. In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Belongs to the LipB family. +Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation. The tmRNA-SmpB complex associates with stalled 70S ribosomes. Belongs to the SmpB family. +Putative transcription factor. Homo- and heterodimer with other ZFHD proteins. The homeodomain differs form the typical one by having namely 4 instead of 3 extra amino acids inserted in the loop between helix 1 and helix 2. +Catalyzes the exchange of L-arginine for agmatine. The arginine uptake by the bacterium in the macrophage may be a virulence factor against the host innate immune response (By similarity). Belongs to the amino acid-polyamine-organocation (APC) superfamily. Basic amino acid/polyamine antiporter (APA) (TC 2.A.3.2) family. +Homodimer and heterodimers. Belongs to the Casparian strip membrane proteins (CASP) family. +Plays a role in viral particle release. Presumably acts by facilitating the fission of the virion bud at the cell surface. May prevent the antiviral activity of murine APOBEC3. Glycosylated by host. Cleaved by host near the middle of the molecule, releasing the c-terminal half containing capsid and nucleoprotein domains op GAG. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Mitochondrial aminoacyl-tRNA synthetase that catalyzes the ATP-dependent ligation of histidine to the 3'-end of its cognate tRNA, via the formation of an aminoacyl-adenylate intermediate (His-AMP). ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity and assembly of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 1 family. +Belongs to the multi antimicrobial extrusion (MATE) (TC 2.A.66.1) family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of a catalytic core of 3 subunits and several supernumerary subunits. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII). Belongs to the cytochrome c oxidase subunit 3 family. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Catalyzes the ATP-dependent phosphorylation of N-acetyl-L-glutamate. ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamyl 5-phosphate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 2/4. Belongs to the acetylglutamate kinase family. ArgB subfamily. +One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Belongs to the universal ribosomal protein uL3 family. +Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA, also called 7,8-diammoniononanoate) to form a ureido ring. (7R,8S)-7,8-diammoniononanoate + ATP + CO2 = (4R,5S)-dethiobiotin + ADP + 3 H(+) + phosphate Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 1/2. Homodimer. Belongs to the dethiobiotin synthetase family. +Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine Purine metabolism; AMP biosynthesis via salvage pathway; AMP from adenine: step 1/1. Homodimer. Belongs to the purine/pyrimidine phosphoribosyltransferase family. +May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. Belongs to the RecR family. +Probable ion channel inhibitor. Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Belongs to the neurotoxin 14 (magi-1) family. 01 (HNTX-16) subfamily. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity and assembly of complex I. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 1 family. +Belongs to the UPF0756 family. +GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Homomer. Belongs to the GTP cyclohydrolase I family. +The SMN complex catalyzes the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome, and thereby plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP (Sm core). In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. To assemble core snRNPs, the SMN complex accepts the trapped 5Sm proteins from CLNS1A forming an intermediate. Binding of snRNA inside 5Sm triggers eviction of the SMN complex, thereby allowing binding of SNRPD3 and SNRPB to complete assembly of the core snRNP. May also play a role in the metabolism of small nucleolar ribonucleoprotein (snoRNPs) (By similarity). ATP + H2O = ADP + H(+) + phosphate a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate Part of the core SMN complex. Belongs to the DEAD box helicase family. DDX20 subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be a menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 2 family. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +Catalyzes the hydrolytic cleavage of the carbon-nitrogen bond in imidazolone-5-propanoate to yield N-formimidoyl-L-glutamate. It is the third step in the universal histidine degradation pathway. 4-imidazolone-5-propanoate + H2O = N-formimidoyl-L-glutamate Binds 1 zinc or iron ion per subunit. Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 3/3. Belongs to the metallo-dependent hydrolases superfamily. HutI family. +This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Binds 1 zinc ion per subunit. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. Zinc-binding uS14 subfamily. +Modulates RecA activity. Belongs to the RecX family. +The reactive center loop (RCL) extends out from the body of the protein and directs binding to the target protease. The protease cleaves the serpin at the reactive site within the RCL, establishing a covalent linkage between the serpin reactive site and the active site of the protease. The resulting inactive serpin-protease complex is highly stable (By similarity). Belongs to the serpin family. +IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The glutaminase domain produces the ammonia necessary for the cyclase domain to produce IGP and AICAR from PRFAR. The ammonia is channeled to the active site of the cyclase domain. 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + H(+) + L-glutamate H2O + L-glutamine = L-glutamate + NH4(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 5/9. In the C-terminal section; belongs to the HisA/HisF family. +Cationic host defense peptide that have antibacterial activity by breaking membranes. Is more effective on Gram-positive than on Gram-negative bacteria. Forms a helical membrane channel in the prey. Expressed by the venom gland. Belongs to the non-disulfide-bridged peptide (NDBP) superfamily. Short antimicrobial peptide (group 4) family. +Binds single-stranded DNA at the primosome assembly site (PAS). During primosome assembly it facilitates the complex formation between PriA and DnaT. Component of the preprimosomal complex composed of one monomer of PriC and DnaT, two monomers of PriA, two dimers of PriB and one hexamer of DnaB. Upon transient interaction with DnaG it forms the primosome. Belongs to the PriB family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways. Plays a key role in hematopoiesis. AMP + ATP = 2 ADP Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. AK2 subfamily. +Binds to the DNA sequence mediating pheromone induction (called the pheromone response element = PRE) which is found in the upstream control region of several a-, alpha- and haploid-specific genes. Involved in the mating process (By similarity). Phosphorylated by the STE7 and STE11 kinases. Belongs to the STE12 transcription factor family. +Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase delta chain family. +Transcriptional repressor that controls expression of the genes required for the catabolism of sialic acids (PubMed:9864311, PubMed:12897000, PubMed:23935044). Represses expression of the nanATEK-yhcH, nanCMS and yjhBC operons. Acts by binding directly to the Nan box, a region of approximately 30 bp covering the promoter region (PubMed:23935044). N-acetylneuraminic acid (Neu5Ac) inactivates NanR by converting NanR oligomers to monomers. Homodimer (PubMed:12897000, PubMed:23935044). Might also form higher-order oligomers (PubMed:23935044). Belongs to the NanR family. +Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP Belongs to the NDK family. +Glycosyltransferase that catalyzes the C-glucosylation of daidzein to puerarin (PubMed:28207970). Shows activity with the isoflavones daidzein and genistein, but has no activity towards flavonoids such as 2-hydroxynaringenin (PubMed:28207970). Can use UDP-glucose, but not UDP-galactose or UDP-glucuronic acid as sugar donor (PubMed:28207970). Does not require bivalent cations for activity (PubMed:28207970). Inhibited by Cu(2+) or Zn(2+). kcat is 0.35 sec(-1) with daidzein as substrate. kcat is 0.45 sec(-1) with genistein as substrate. Optimum pH is 8.0. Belongs to the UDP-glycosyltransferase family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. cytidine(1402) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(4)-methylcytidine(1402) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmH family. +Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses fumarate or nitrate as electron acceptor. a quinone + sn-glycerol 3-phosphate = a quinol + dihydroxyacetone phosphate Polyol metabolism; glycerol degradation via glycerol kinase pathway; glycerone phosphate from sn-glycerol 3-phosphate (anaerobic route): step 1/1. Composed of a catalytic GlpA/B dimer and of membrane bound GlpC. Belongs to the anaerobic G-3-P dehydrogenase subunit B family. +carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Heterooligomer of catalytic and regulatory chains. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family. +ATP + L-aspartate + NH4(+) = AMP + diphosphate + H(+) + L-asparagine Amino-acid biosynthesis; L-asparagine biosynthesis; L-asparagine from L-aspartate (ammonia route): step 1/1. Belongs to the class-II aminoacyl-tRNA synthetase family. AsnA subfamily. +General activator of RNA polymerase III transcription. Requires for transcription from all three types of polymerase III promoters. Requires for transcription of genes with internal promoter elements and with promoter elements upstream of the initiation site (By similarity). Component of TFIIIB complex. The TFIIIB complex has two activities, alpha and beta. The TFIIIB-alpha and TFIIIB-beta activities are required for transcription of genes with TFIIIC-bound internal promoters and PSE transcription factor-bound external promoters, respectively. The TFIIIB-alpha activity complex is composed of TBP, BDP1, and a complex containing both BRF2 and at least four stably associated proteins; YY1 facilitates the formation of TFIIIB-alpha activity complex. The TFIIIB-beta activity complex is composed of TBP, BDP1, and BRF1. Interacts with BRF1; this interaction diminishes during mitosis resulting in the release of BDP1 from chromosomal templates. Component of TFIIIC complex. The TFIIIC complex has two activities, C1 and C2. The TFIIIC2 activity complex is only required for transcription of the 'classical' pol III genes whereas the TFIIIC1 activity complex is required for transcription of all pol III genes. The TFIIIC1 activity complex is composed at least of BDP1. Interacts with ZBTB43 (By similarity). Expressed in the cochlea, particularly in the spiral ligament, the capillaries of the stria vascularis and the basilar membrane. Phosphorylated by CSNK2A1 during mitosis, resulting in its release from chromatin and suppression of polymerase III transcription. Contaminating sequence. Sequence of unknown origin in the N-terminal part. +The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. Binds 1 lipoyl cofactor covalently. The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvH family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. Probably participates in protein translocation into and across both the cytoplasmic and thylakoid membranes in cyanobacterial cells. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved. Belongs to the SecA family. +Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving both as a receptor for the preprotein-SecB complex and as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane. ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2. May bind 1 zinc ion per subunit. Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF-YajC and YidC. Distribution is 50-50. Belongs to the SecA family. +Catalyzes the formation of NAD(+) from nicotinamide mononucleotide (NMN) and ATP. Can also use the deamidated form; nicotinic acid mononucleotide (NaMN) as substrate. ATP + beta-nicotinamide D-ribonucleotide + H(+) = diphosphate + NAD(+) ATP + H(+) + nicotinate beta-D-ribonucleotide = deamido-NAD(+) + diphosphate Cofactor biosynthesis; NAD(+) biosynthesis; deamido-NAD(+) from nicotinate D-ribonucleotide: step 1/1. Cofactor biosynthesis; NAD(+) biosynthesis; NAD(+) from nicotinamide D-ribonucleotide: step 1/1. Belongs to the eukaryotic NMN adenylyltransferase family. Extended N-terminus. Extended N-terminus. +Catalytic subunit of the nitrate reductase complex NapAB. Receives electrons from NapB and catalyzes the reduction of nitrate to nitrite. 2 Fe(II)-[cytochrome] + 2 H(+) + nitrate = 2 Fe(III)-[cytochrome] + H2O + nitrite Binds 1 [4Fe-4S] cluster. Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit. Component of the nitrate reductase NapAB complex composed of NapA and NapB. Membrane-associated. Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/NapA/NarB subfamily. +a carboxylic ester + H2O = a carboxylate + an alcohol + H(+) Contains a C-terminal autotransporter domain that integrates into the outer membrane and enables the translocation of the catalytic N-terminal domain to the bacterial cell surface. Belongs to the 'GDSL' lipolytic enzyme family. +Belongs to the UPF0178 family. +Essential protein (PubMed:19956626). Polymerase that creates the 3'-poly(A) tail of mRNA's (PubMed:15297145). Also required for the endoribonucleolytic cleavage reaction at some polyadenylation sites. May acquire specificity through interaction with a cleavage and polyadenylation specificity factor (CPSF) at its C-terminus (By similarity). ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide Binds 2 magnesium ions. Also active with manganese. Monomer (By similarity). Forms a complex with cleavage and polyadenylation specificity factor (CPSF) subunits FIPS5 and CPSF30 (PubMed:18479511). Expressed in leaves (mostly in petioles and tips), cotyledon, roots (tips, vascular tissue of the radicle, and throughout the root tissue excluding the elongation zone), stems, and flowers (restricted to the stigma and the pollen in mature anthers) (PubMed:15297145, PubMed:19956626). Active in the primary and secondary root systems (PubMed:19956626). Lethal. Belongs to the poly(A) polymerase family. +Participates in transcription elongation, termination and antitermination. Belongs to the NusG family. +Catalyzes the reversible oxidation of malate to oxaloacetate. (S)-malate + NAD(+) = H(+) + NADH + oxaloacetate Belongs to the LDH/MDH superfamily. MDH type 3 family. +Arginine hydroxylase involved in the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I, MT-ND1) at early stages (PubMed:18940309, PubMed:27226634). Acts by mediating hydroxylation of 'Arg-111' of NDUFS7 (PubMed:27226634). May also have methyltransferase activity (Probable). Interacts with NDUFAF8, leading to stabilize NDUFAF5 (PubMed:27499296). Interacts with NDUFS7 (PubMed:27226634). Peripherally localized on the matrix face of the mitochondrial inner membrane. The disease is caused by variants affecting the gene represented in this entry. Belongs to the methyltransferase superfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 13 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 2 family. +Soluble frizzled-related proteins (sFRPS) function as modulators of Wnt signaling through direct interaction with Wnts. They have a role in regulating cell growth and differentiation in specific cell types. SFRP5 may be involved in determining the polarity of photoreceptor, and perhaps other, cells in the retina. Inhibits Wnt8 signaling, in vitro. Strongly expressed in the retinal pigment epithelium (RPE). Weak expression in retina, brain, heart, liver, kidney, testis and muscle. The FZ domain is involved in binding with Wnt ligands. Belongs to the secreted frizzled-related protein (sFRP) family. +Belongs to the UPF0270 family. +Interacts with RIMS1. Secretory granules. Specifically expressed in the bone marrow mast cells. Belongs to the small GTPase superfamily. Rab family. +Belongs to the eukaryotic ribosomal protein eL15 family. +Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = H(+) + L-glutamyl-tRNA(Glu) + NADPH Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 1/2. Homodimer. Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization. During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA. Belongs to the glutamyl-tRNA reductase family. +Specifically methylates the N7 position of a guanine in 16S rRNA. Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase. Belongs to the HypA/HybF family. HybF subfamily. +Probable sterol 3-beta-glucosyltransferase that is not involved in cytoplasm to vacuole transport (Cvt), pexophagy or nonselective autophagy (By similarity). a sterol + UDP-alpha-D-glucose = a sterol 3-beta-D-glucoside + H(+) + UDP Belongs to the glycosyltransferase 28 family. +May mediate the cholesterol and gangliosides transport from the plasma membrane to intracellular vesicles in an ATP hydrolysis dependent manner, thus playing a role in their internalization by endocytic retrograde transport and may also participate in the endocytosis of synaptic vesicle in cortical neurons. ATP + cholesterol(in) + H2O = ADP + cholesterol(out) + H(+) + phosphate Ubiquitously expressed. May be primarily expressed in kidney. Homozygous knockout mice for Abca13 are born normally and seem to have normal appearance and life span but show sensorimotor gating deficits. Belongs to the ABC transporter superfamily. +Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP). isopentenyl diphosphate = dimethylallyl diphosphate Binds 1 Mg(2+) ion per subunit. The magnesium ion binds only when substrate is bound. Binds 1 Mn(2+) ion per subunit. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1. Belongs to the IPP isomerase type 1 family. +General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The phosphoryl group from phosphoenolpyruvate (PEP) is transferred to the phosphoryl carrier protein HPr by enzyme I. Phospho-HPr then transfers it to the PTS EIIA domain. P-Ser-HPr interacts with the catabolite control protein A (CcpA), forming a complex that binds to DNA at the catabolite response elements cre, operator sites preceding a large number of catabolite-regulated genes. Thus, P-Ser-HPr is a corepressor in carbon catabolite repression (CCR), a mechanism that allows bacteria to coordinate and optimize the utilization of available carbon sources. P-Ser-HPr also plays a role in inducer exclusion, in which it probably interacts with several non-PTS permeases and inhibits their transport activity (By similarity). Phosphorylation on Ser-46 inhibits the phosphoryl transfer from enzyme I to HPr. Belongs to the HPr family. +Specifically methylates the guanosine in position 1516 of 16S rRNA. guanosine(1516) in 16S rRNA + S-adenosyl-L-methionine = H(+) + N(2)-methylguanosine(1516) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RsmJ family. +Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP). (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate Cofactor biosynthesis; molybdopterin biosynthesis. Homohexamer; trimer of dimers. Belongs to the MoaC family. +Could be involved in insertion of integral membrane proteins into the membrane. Belongs to the UPF0161 family. +Binds to F-actin and exhibits pH-sensitive F-actin depolymerizing activity (PubMed:6509022, PubMed:9078368). In conjunction with the subcortical maternal complex (SCMC), plays an essential role for zygotes to progress beyond the first embryonic cell divisions via regulation of actin dynamics (PubMed:9078368). Required for the centralization of the mitotic spindle and symmetric division of zygotes (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization in epithelial cells (By similarity). Required for the up-regulation of atypical chemokine receptor ACKR2 from endosomal compartment to cell membrane, increasing its efficiency in chemokine uptake and degradation (By similarity). Required for neural tube morphogenesis and neural crest cell migration (By similarity). Can bind G- and F-actin in a 1:1 ratio of cofilin to actin (PubMed:6509022, PubMed:9078368). It is a major component of intranuclear and cytoplasmic actin rods (PubMed:9078368). Interacts with the subcortical maternal complex (SCMC) via interaction with TLE6 and NLRP5 (By similarity). Interacts with C9orf72 (By similarity). Colocalizes with the actin cytoskeleton in membrane ruffles and lamellipodia. Detected at the cleavage furrow and contractile ring during cytokinesis. Almost completely in nucleus in cells exposed to heat shock or 10% dimethyl sulfoxide. Widely distributed in various tissues. Inactivated by phosphorylation on Ser-3 (PubMed:9078368). Phosphorylated on Ser-3 in resting cells (By similarity). Dephosphorylated by PDXP/chronophin; this restores its activity in promoting actin filament depolymerization. The phosphorylation of Ser-24 may prevent recognition of the nuclear localization signal (By similarity). Phosphorylated via a ARRB1-RAC1-LIMK1-PAK1 cascade upon active ligand stimulation of atypical chemokine receptor ACKR2 (By similarity). Belongs to the actin-binding proteins ADF family. +Forms the proximal part of the tail tube. Present in 12 copies in the virion. Belongs to the phi29likevirus proximal tail tube connector protein family. +Deubiquitinates monoubiquitinated probes (in vitro). When ubiquitinated, cleaves 'Lys-63'-linked and 'Lys-48'-linked poly-ubiquitin chains (in vitro), hence may act as a deubiquitinating enzyme. May increase macropinocytosis and suppress clathrin- and caveolae-mediated endocytosis. May enhance membrane dynamics and cell motility independently of its catalytic activity (By similarity). Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Interacts with beta-actin/ACTB. Ubiquitination increases localization the plasma membrane. In the cytosol, the unubiquitinated form may be associated with the cytoskeleton via ACTB-binding. Widely expressed (at protein level). Monoubiquitinated. Ubiquitination activates deubiquitination activity in vitro. +Cysteine protease that plays a key role in cytoplasm to vacuole transport (Cvt) and autophagy by mediating both proteolytic activation and delipidation of ATG8. Required for selective autophagic degradation of the nucleus (nucleophagy) as well as for mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. The protease activity is required for proteolytic activation of ATG8: cleaves the C-terminal amino acid of ATG8 to reveal a C-terminal glycine. ATG8 ubiquitin-like activity requires the exposure of the glycine at the C-terminus for its conjugation to phosphatidylethanolamine (PE) and its insertion to membranes, which is necessary for autophagy. The ATG8-PE conjugate mediates tethering between adjacent membranes and stimulates membrane hemifusion, leading to expansion of the autophagosomal membrane during autophagy. In addition to the protease activity, also catalyzes deconjugation of PE-conjugated forms of ATG8 during macroautophagy: ATG8 delipidation is required to release the protein from membranes, which facilitates multiple events during macroautophagy, and especially for efficient autophagosome biogenesis, the assembly of ATG9-containing tubulovesicular clusters into phagophores/autophagosomes, and for the disassembly of PAS-associated ATG components. ATG8 delipidation by ATG4 also recycles ATG8-PE generated on inappropriate membranes to maintain a reservoir of unlipidated ATG8 that is required for autophagosome formation at the PAS. [protein]-C-terminal L-amino acid-glycyl-phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine Belongs to the peptidase C54 family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +NDH-1 shuttles electrons from an unknown electron donor, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) Binds 2 [4Fe-4S] clusters per subunit. NDH-1 is composed of at least 11 different subunits. Belongs to the complex I 23 kDa subunit family. +Brain peptide responsible for activation of prothoracic glands to produce ecdysone in insects. Heterodimer of a B chain and an A chain linked by two disulfide bonds. Belongs to the insulin family. +Required for formate-dependent nitrite reduction. Not required for the biosynthesis of any of the c-type cytochromes nor for the secretion of the periplasmic cytochromes. +Appears to play a crucial role in the insertion of secretory and membrane polypeptides into the ER. It is required for assembly of membrane and secretory proteins. Found to be tightly associated with membrane-bound ribosomes, either directly or through adaptor proteins (By similarity). Heterotrimeric complex composed of SEC61-alpha, SEC61-beta and SEC61-gamma. Belongs to the SecY/SEC61-alpha family. +Involved in iron-sulfur cluster biogenesis. Binds a 4Fe-4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe/S proteins. Could also act as a scaffold/chaperone for damaged Fe/S proteins. Binds 1 [4Fe-4S] cluster per subunit. The cluster is presumably bound at the interface of two monomers. Homodimer. Belongs to the NfuA family. +Regulates chromatin compaction in spermatid nuclei and is essential for male fertility. Functions in parallel with other chromatin-condensing proteins such as ProtA, ProtB and Mst77F. Expressed in mature sperm chromatin. Expressed in larva and adult male. Expression in the sperm nucleus begins between the early and late canoe stages before the protamines appear. Highly expressed from early spermatocyte to late spermatid and persists in mature sperm. The C-terminal part (169-201) is essential for male fertility and correct chromatin compaction in mature sperm. RNAi-mediated knockdown in late spermatogonia to early spermatocytes affects spermiogenesis and results in reduced male fertility. Sperm nuclei are long and needle-shaped due to the elongation of their chromatin region. No effect on the replacement of histones by protamines in the chromatin of sperm during the haploid phase of spermatogenesis. Belongs to the UPF0771 family. Extended N-terminus. Extended N-terminus. +AKT3 is one of 3 closely related serine/threonine-protein kinases (AKT1, AKT2 and AKT3) called the AKT kinase, and which regulate many processes including metabolism, proliferation, cell survival, growth and angiogenesis. This is mediated through serine and/or threonine phosphorylation of a range of downstream substrates. Over 100 substrate candidates have been reported so far, but for most of them, no isoform specificity has been reported. AKT3 is the least studied AKT isoform. It plays an important role in brain development and is crucial for the viability of malignant glioma cells. AKT3 isoform may also be the key molecule in up-regulation and down-regulation of MMP13 via IL13. Required for the coordination of mitochondrial biogenesis with growth factor-induced increases in cellular energy demands. Down-regulation by RNA interference reduces the expression of the phosphorylated form of BAD, resulting in the induction of caspase-dependent apoptosis. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Two specific sites, one in the kinase domain (Thr-305) and the other in the C-terminal regulatory region (Ser-472), need to be phosphorylated for its full activation (By similarity). IGF-1 leads to the activation of AKT3, which may play a role in regulating cell survival. Interacts (via PH domain) with TCL1A; this enhances AKT3 phosphorylation and activation. Interacts with TRAF6. Interacts with KCTD20 (By similarity). Interacts with BTBD10 (By similarity). Membrane-associated after cell stimulation leading to its translocation. In adult tissues, it is highly expressed in brain, lung and kidney, but weakly in heart, testis and liver. In fetal tissues, it is highly expressed in heart, liver and brain and not at all in kidney. Binding of the PH domain to the phosphatidylinositol 3-kinase alpha (PI(3)K) results in its targeting to the plasma membrane. Phosphorylation on Thr-305 and Ser-472 is required for full activity. Ubiquitinated. When fully phosphorylated and translocated into the nucleus, undergoes 'Lys-48'-polyubiquitination catalyzed by TTC3, leading to its degradation by the proteasome. O-GlcNAcylation at Thr-302 and Thr-309 inhibits activating phosphorylation at Thr-305 via disrupting the interaction between AKT and PDK1. AKT3 is a key modulator of several tumors like melanoma, glioma and ovarian cancer. Active AKT3 increases progressively during melanoma tumor progression with highest levels present in advanced-stage metastatic melanomas. Promotes melanoma tumorigenesis by decreasing apoptosis. Plays a key role in the genesis of ovarian cancers through modulation of G2/M phase transition. With AKT2, plays a pivotal role in the biology of glioblastoma. The disease is caused by variants affecting the gene represented in this entry. Belongs to the protein kinase superfamily. AGC Ser/Thr protein kinase family. RAC subfamily. In light of strong homologies in the primary amino acid sequence, the 3 AKT kinases were long surmised to play redundant and overlapping roles. More recent studies has brought into question the redundancy within AKT kinase isoforms and instead pointed to isoform specific functions in different cellular events and diseases. AKT1 is more specifically involved in cellular survival pathways, by inhibiting apoptotic processes; whereas AKT2 is more specific for the insulin receptor signaling pathway. Moreover, while AKT1 and AKT2 are often implicated in many aspects of cellular transformation, the 2 isoforms act in a complementary opposing manner. The role of AKT3 is less clear, though it appears to be predominantly expressed in brain. +Catalyzes the transfer of 4-deoxy-4-formamido-L-arabinose from UDP to undecaprenyl phosphate. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides. Plays an important role in pathogenesis by providing resistance to antimicrobial peptides within macrophages or at other anatomic sites encountered during infection. di-trans,octa-cis-undecaprenyl phosphate + UDP-4-deoxy-4-formamido-beta-L-arabinose = 4-deoxy-4-formamido-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + UDP Glycolipid biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate biosynthesis; 4-amino-4-deoxy-alpha-L-arabinose undecaprenyl phosphate from UDP-4-deoxy-4-formamido-beta-L-arabinose and undecaprenyl phosphate: step 1/2. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. Induced by BasR. Belongs to the glycosyltransferase 2 family. +Probably participates in efficiency of electron transfer from plastocyanin to P700 (or cytochrome c553 in algae and cyanobacteria). This plastocyanin-docking protein contributes to the specific association of plastocyanin to PSI. Belongs to the PsaF family. +Retroviral proteases have roles in the processing of the primary translation products and the maturation of the viral particle. Endogenous Pro proteins may have kept, lost or modified their original function during evolution (By similarity). Processing at the authentic HIV-1 PR recognition site and release of the mature p17 matrix and the p24 capsid protein, as a result of the cleavage of the -SQNY-|-PIVQ- cleavage site. Active as a homodimer. This protein is synthesized as Gag-Pro and Gag-Pro-Pol polyprotein. These polyproteins are thought, by similarity with type-B retroviruses, to be generated by -1 frameshifts occurring at the Gag-Pro and Pro-Pol genes boundaries. Autoproteolytically processed at the N-terminus. Expected C-terminal autoprocessing not detected. The sequence shown is that of the processed Pro protein (By similarity). Belongs to the peptidase A2 family. HERV class-II K(HML-2) subfamily. +NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. a quinone + 5 H(+)(in) + NADH = a quinol + 4 H(+)(out) + NAD(+) NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex. Belongs to the complex I subunit 2 family. +Catalyzes the excretion of spermidine. Forms a complex with MdtJ. Belongs to the drug/metabolite transporter (DMT) superfamily. Small multidrug resistance (SMR) (TC 2.A.7.1) family. MdtI subfamily. +Heterochromatin-binding protein that preferentially occupies long transposons and specifically recognizes the histone H3 'Lys-9' methylation (H3K9me) marks, with a stronger affinity for dimethylated H3K9 (H3K9me2) (PubMed:30382101, PubMed:30425322). Required for transcriptional silencing, non-CG DNA methylation (e.g. CHG and CHH regions), and H3K9 dimethylation (H3K9me2) at some loci (PubMed:30382101, PubMed:30425322). Mediates heterochromatin phase separation and chromocenter formation (PubMed:30425322). Enriched in heterochromatin, concentrated in centromeric and pericentromeric regions. Expressed ubiquitously during vegetative stage, in meristems (e.g. root tips and shoot apical meristem), and in ovules and young seeds during reproductive stage. The tandem Agenet domains (AGDs) mediate the specific recognition of the histone 3 lysine 9 dimethylation (H3K9me2) mark. Abnormal transcription up-regulation of some transposable elements (TEs) and of hypermethylated loci (including MU1, GP1, SN1 and ERT7) (PubMed:30382101, PubMed:30425322). Hypomethylated DNA CHG and CHH regions (PubMed:30382101, PubMed:30425322). Reduced H3K9me2 levels (PubMed:30382101). Increased ratio of decondensed nuclei (PubMed:30425322). +Usually encoded in the trnK tRNA gene intron. Probably assists in splicing its own and other chloroplast group II introns. Belongs to the intron maturase 2 family. MatK subfamily. +Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate Binds 1 zinc ion per subunit. Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetE route): step 1/1. Belongs to the vitamin-B12 independent methionine synthase family. +Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6-phosphate and D-lactate. H2O + N-acetyl-D-muramate 6-phosphate = (R)-lactate + N-acetyl-D-glucosamine 6-phosphate Amino-sugar metabolism; N-acetylmuramate degradation. Homodimer. A lyase-type mechanism (elimination/hydration) is suggested for the cleavage of the lactyl ether bond of MurNAc 6-phosphate, with the formation of an alpha,beta-unsaturated aldehyde intermediate with (E)-stereochemistry, followed by the syn addition of water to give product. Belongs to the GCKR-like family. MurNAc-6-P etherase subfamily. +Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1E gives rise to R-type calcium currents. R-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by nickel. They are however insensitive to dihydropyridines (DHP). Calcium channels containing alpha-1E subunit could be involved in the modulation of firing patterns of neurons which is important for information processing. Interacts with EFHC1. Voltage-dependent calcium channels are multisubunit complexes, consisting of alpha-1, alpha-2, beta and delta subunits in a 1:1:1:1 ratio. The channel activity is directed by the pore-forming and voltage-sensitive alpha-1 subunit. In many cases, this subunit is sufficient to generate voltage-sensitive calcium channel activity. The auxiliary subunits beta and alpha-2/delta linked by a disulfide bridge regulate the channel activity. Abundant in the cerebral cortex, hippocampus, and corpus striatum. Each of the four internal repeats contains five hydrophobic transmembrane segments (S1, S2, S3, S5, S6) and one positively charged transmembrane segment (S4). S4 segments probably represent the voltage-sensor and are characterized by a series of positively charged amino acids at every third position. Belongs to the calcium channel alpha-1 subunit (TC 1.A.1.11) family. CACNA1E subfamily. +Regulatory subunit of the calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction. Essential for embryonic development (By similarity). Homodimer or heterodimer of a large (catalytic) and a small (regulatory) subunit. In presence of calcium, the heterodimer dissociates (By similarity). Translocates to the plasma membrane upon calcium binding. The contact of the 5th EF-hand domain from each monomer allows the formation of the homodimer and also appears to mediate the contact between the large catalytic subunit and small regulatory subunit for the formation of the heterodimer. EF-hand domains are paired. EF-hand 1 is paired with EF-hand 2 and EF-hand 3 is paired with EF-hand 4. The fifth EF-hand domain, left unpaired, does not bind the calcium but is responsible of the dimerization by EF-embrace. The first four EF-hand domains bind calcium, however it is not sure if the binding of EF-hand 4 to calcium is physiologically relevant. Calpain +H2O + L-glutamine = L-glutamate + NH4(+) Homotetramer. Belongs to the glutaminase family. +Important role in the capacity of milk to transport calcium phosphate. Mammary gland specific. Secreted in milk. Belongs to the alpha-casein family. +Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. Part of the 30S ribosomal subunit. Contacts proteins S3 and S10. Belongs to the universal ribosomal protein uS14 family. +Covalent carrier of the coenzyme of citrate lyase. Oligomer with a subunit composition of (alpha,beta,gamma)6. Belongs to the CitD family. +NDH-1 shuttles electrons from an unknown electron donor, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) Binds 1 [4Fe-4S] cluster. NDH-1 can be composed of about 15 different subunits; different subcomplexes with different compositions have been identified which probably have different functions. Belongs to the complex I 20 kDa subunit family. +Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. 2 H(+) + 2 superoxide = H2O2 + O2 Binds 1 Mn(2+) ion per subunit. Belongs to the iron/manganese superoxide dismutase family. +Proton-dependent permease that transports di- and tripeptides. Belongs to the major facilitator superfamily. Proton-dependent oligopeptide transporter (POT/PTR) (TC 2.A.17) family. DtpA subfamily. +Plays a central role in chromosome condensation, segregation and cell cycle progression. Functions as a homodimer, which is essential for chromosome partition. Involved in negative DNA supercoiling in vivo, and by this means organize and compact chromosomes. May achieve or facilitate chromosome segregation by condensation DNA from both sides of a centrally located replisome during cell division. Homodimerization via its hinge domain. Binds to DNA via its C-terminal region. Interacts, and probably forms a ternary complex, with MukE and MukF via its C-terminal region. The complex formation is stimulated by calcium or magnesium. Interacts with tubulin-related protein FtsZ. Restricted to the nucleoid region. The hinge domain, which separates the large intramolecular coiled coil regions, allows the homodimerization, forming a V-shaped homodimer. Belongs to the SMC family. MukB subfamily. +carbamoyl phosphate + L-aspartate = H(+) + N-carbamoyl-L-aspartate + phosphate Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 2/3. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family. +Gibberellin 20-oxidase; part of the gene cluster that mediates the biosynthesis of gibberellins (GAs), diterpenoids that may provide a selective advantage during infection of the preferred host plant, rice (PubMed:23825955, PubMed:9917370, PubMed:10347043, PubMed:12750377, PubMed:15925394). Gibberellins (GAs) are diterpenoids and are synthesized via the mevalonate pathway (PubMed:12750377). Biosynthesis of the major metabolite GA3 (gibberellic acid) from geranylgeranyl diphosphate (GGPP) requires 13 steps (PubMed:12750377). The GGPP produced by the geranylgeranyl diphosphate synthase GGS2 is converted to ent-kaurene via ent-copalyldiphosphate in a two-step cyclization reaction performed by the bifunctional ent-copalyl diphosphate synthase/ent-kaurene synthase enzyme (CPS/KS) (PubMed:9745028, PubMed:10803977, PubMed:12750377). Ent-Kaurene is metabolized to GAs by a series of oxidation reactions catalyzed by cytochrome P450 monooxygenases (PubMed:9917370, PubMed:12750377). Cytochrome P450 monooxygenase P450-4 is an ent-kaurene oxidase that catalyzes the three oxidation steps between ent-kaurene and ent-kaurenoic acid (PubMed:11472927). The highly multifunctional cytochrome P450 monooxygenase P450-1 then catalyzes four steps involving oxidation at two carbon atoms, in the main pathway from ent-kaurenoic acid to GA14 via GA12-aldehyde as well as producing kaurenolides and fujenoic acids as by-products (PubMed:11320210). The cytochrome P450 monooxygenase P450-2 then converts GA14 to GA4 by removal of C-20 (PubMed:11943776). GA4 is further converted to GA7 by the GA4 desaturase DES via 1,2-desaturation before cytochrome P450 monooxygenase P450-3, a 13-hydroxylase, hydroxylates GA7 to GA3, the final product of the GA-biosynthetic pathway (PubMed:12750377). Plant hormone biosynthesis; gibberellin biosynthesis. Expression is induced under gibberellin-producing conditions (PubMed:9917370). Expression is repressed by high amounts of nitrogen but is not affected by the presence of biosynthetically advanced GAs (PubMed:11943776). Leads to the loss of gibberellins production (PubMed:9917370). Accumulates GA14 but later intermediates of the pathway are not detected (PubMed:11943776). Belongs to the cytochrome P450 family. +This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. Belongs to the bacterial ribosomal protein bL19 family. +Belongs to the universal ribosomal protein uS11 family. +Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P). ATP + D-ribose 5-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + H(+) Binds 2 Mg(2+) ions per subunit. Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route I): step 1/1. Homohexamer. Belongs to the ribose-phosphate pyrophosphokinase family. Class I subfamily. +Major transport protein for glucocorticoids and progestins in the blood of almost all vertebrate species. Proteolytic cleavage leads to an important conformation change. This reduces the affinity for steroids (By similarity). Glycosylation in position Asn-259 is needed for steroid binding. Belongs to the serpin family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Belongs to the TACO1 family. +IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. Monomer. Belongs to the IF-3 family. +Belongs to the bacterial ribosomal protein bS16 family. +Mediates, with Gag polyprotein, the essential events in virion assembly, including binding the plasma membrane, making the protein-protein interactions necessary to create spherical particles, recruiting the viral Env proteins, and packaging the genomic RNA via direct interactions with the RNA packaging sequence. Targets the polyprotein to the plasma membrane. Forms the core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Encapsulates and protects viral dimeric unspliced genomic RNA (gRNA). Binds these RNAs through its zinc fingers. Acts as a nucleic acid chaperone which is involved in rearrangement of nucleic acid secondary structure during gRNA retrotranscription. Also facilitates template switch leading to recombination. The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell. RT is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA-Trp binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perfom a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perfom the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends. Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. Endonucleolytic cleavage to 5'-phosphomonoester. 3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. dUTP + H2O = diphosphate + dUMP + H(+) a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) The RT polymerase active site binds 2 magnesium ions. Homotetramer; further associates as a homohexadecamer. Specific enzymatic cleavages by the viral protease yield mature proteins. The reverse transcriptase is an error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template swiching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs. Produced by a -1 ribosomal frameshifting between gag and pol. Belongs to the retroviral Pol polyprotein family. +NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34. Homodimer. Heterotetramer of two MnmE and two MnmG subunits. Belongs to the MnmG family. +Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin. di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available. Belongs to the UppP family. +Belongs to the SixA phosphatase family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Transcription factor that binds specifically to the DRE (dual repressor element) and represses HTR1A gene transcription in neuronal cells. Belongs to the CC2D1 family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +The surface protein (SU) attaches the virus to the host cell by binding to its receptor. This interaction triggers the refolding of the transmembrane protein (TM) and is thought to activate its fusogenic potential by unmasking its fusion peptide. Fusion occurs at the host cell plasma membrane (By similarity). The transmembrane protein (TM) acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Membranes fusion leads to delivery of the nucleocapsid into the cytoplasm (By similarity). The mature envelope protein (Env) consists of a trimer of SU-TM heterodimers attached by noncovalent interactions or by a labile interchain disulfide bond. The surface protein is not anchored to the viral envelope, but associates with the extravirion surface through its binding to TM. Both proteins are thought to be concentrated at the site of budding and incorporated into the virions possibly by contacts between the cytoplasmic tail of Env and the N-terminus of Gag (By similarity). Specific enzymatic cleavages in vivo yield mature proteins. Envelope glycoproteins are synthesized as an inactive precursor that is N-glycosylated and processed likely by host cell furin or by a furin-like protease in the Golgi to yield the mature SU and TM proteins. The cleavage site between SU and TM requires the minimal sequence [KR]-X-[KR]-R (By similarity). +Binds to host cell surface receptor and mediates fusion between viral and cellular membranes. Envelope protein is synthesized in the endoplasmic reticulum in the form of heterodimer with protein prM. They play a role in virion budding in the ER, and the newly formed immature particle is covered with 60 spikes composed of heterodimer between precursor prM and envelope protein E. The virion is transported to the Golgi apparatus where the low pH causes dissociation of PrM-E heterodimers and formation of E homodimers. prM-E cleavage is ineficient, and many virions are only partially matured. These uncleaved prM would play a role in immune evasion. Homodimer; in the endoplasmic reticulum and Golgi. N-glycosylated. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. +Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL1 family. +Plays a role in viral particle release. Presumably acts by facilitating the fission of the virion bud at the cell surface. Glycosylated by host. Cleaved by host near the middle of the molecule, releasing the c-terminal half containing capsid and nucleoprotein domains op GAG. +Purine nucleoside enzyme that catalyzes the phosphorolysis of adenosine and inosine nucleosides, yielding D-ribose 1-phosphate and the respective free bases, adenine and hypoxanthine. Also catalyzes the phosphorolysis of S-methyl-5'-thioadenosine into adenine and S-methyl-5-thio-alpha-D-ribose 1-phosphate. Also has adenosine deaminase activity. adenosine + phosphate = adenine + alpha-D-ribose 1-phosphate phosphate + S-methyl-5'-thioadenosine = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate inosine + phosphate = alpha-D-ribose 1-phosphate + hypoxanthine adenosine + H(+) + H2O = inosine + NH4(+) Homodimer. Belongs to the purine nucleoside phosphorylase YfiH/LACC1 family. +Mediates Mg(2+) transport. Belongs to the membrane magnesium transporter (TC 1.A.67) family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +1-(5-phospho-beta-D-ribosyl)-ATP + H2O = 1-(5-phospho-beta-D-ribosyl)-5'-AMP + diphosphate + H(+) Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 2/9. Belongs to the PRA-PH family. +Molecular chaperone. Has ATPase activity. Homodimer. Belongs to the heat shock protein 90 family. +Provides the rickettsial cell with host ATP in exchange for rickettsial ADP. This is an obligate exchange system. This energy acquiring activity is an important component of rickettsial parasitism (By similarity). Belongs to the ADP/ATP translocase tlc family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit. Binds 1 zinc ion per subunit. Monomer. Associates with 30S ribosomal subunit, binds 16S rRNA. Belongs to the TRAFAC class YlqF/YawG GTPase family. RsgA subfamily. +Receptor for RTN4, OMG and MAG (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:18411262, PubMed:22923615). Functions as receptor for the sialylated gangliosides GT1b and GM1 (PubMed:18411262). Besides, functions as receptor for chondroitin sulfate proteoglycans (PubMed:22406547). Can also bind heparin (PubMed:22406547). Intracellular signaling cascades are triggered via the coreceptor NGFR (By similarity). Signaling mediates activation of Rho and downstream reorganization of the actin cytoskeleton (PubMed:22325200). Mediates axonal growth inhibition (By similarity). Mediates axonal growth inhibition and plays a role in regulating axon regeneration and neuronal plasticity in the adult central nervous system (PubMed:11201742, PubMed:12089450, PubMed:15504325, PubMed:22923615). Plays a role in postnatal brain development (PubMed:27339102). Required for normal axon migration across the brain midline and normal formation of the corpus callosum (PubMed:27339102). Protects motoneurons against apoptosis; protection against apoptosis is probably mediated via interaction with MAG (PubMed:26335717). Acts in conjunction with RTN4 and LINGO1 in regulating neuronal precursor cell motility during cortical development (PubMed:20093372). Like other family members, plays a role in restricting the number dendritic spines and the number of synapses that are formed during brain development (PubMed:22325200). Homodimer (PubMed:29095159). Interacts with MAG (PubMed:12089450). Interacts with RTN4 (PubMed:15504325). Interacts with NGFR(PubMed:22923615). Interacts with LINGO1(PubMed:22923615). Interacts with KIAA0319L (By similarity). Interacts with OLFM1; this inhibits interaction with LINGO1 and NGFR (PubMed:22923615). Interacts with OMG (By similarity). Detected along dendrites and axons, close to synapses, but clearly excluded from synapses. Detected in embryonic hippocampus neurons (PubMed:22325200). Detected in brain (at protein level) (PubMed:15504325, PubMed:22406547). Detected in neurons in the neocortex, in hippocampus, dorsal thalamus, cerebellum granule cell layer and the mitral cell layer in the olfactory bulb (PubMed:15647357). Detected in brain, dorsal root ganglion and heart. N-glycosylated (PubMed:29095159). O-glycosylated. Contains terminal sialic acid groups on its glycan chains (By similarity). Mice are born at the expected Mendelian rate, are viable and fertile (PubMed:15504325, PubMed:15647357). They display subtle changes in exploratory behavior, manifest deficits in spatial working memory performance, and show impaired ability to stay on a rotarod (PubMed:15504325 and PubMed:19052207). Compared to wild-type littermates, cultured hippocampus neurons from mutant mice display an increased number of excitatory synapses (PubMed:22325200). Effects on neurite outgrowth are controversial and may depend on the mouse strain, cell type, and the experimental conditions (PubMed:15504325, PubMed:15647357, PubMed:18411262, PubMed:19367338). Cultured neurons display impaired axon growth cone collapse in response to myelin, MAG and RTN4 (PubMed:15504325). Mutant cerebellar and dorsal root ganglion neurons show no decrease of the inhibition of neurite outgrowth by myelin or RTN4 (PubMed:15647357). Mutant cerebellar neurons display decreased inhibition of neurite outgrowth mediated by MAG and by cross-linking ganglioside GT1b (in vitro) (PubMed:18411262). Likewise, mutant sensory neurons show no decrease of the inhibition of neurite outgrowth by MAG (PubMed:19367338). Mutant mice have improved functional recovery and increased regeneration of rubrospinal and raphespinal fibers after spinal cord transection. Still, there is no regeneration of corticospinal fibers (PubMed:15504325, PubMed:15647357). Mice lacking both Rtn4r and Rtn4rl2 display no visible phenotype (PubMed:19367338). Sensory neurons from mice lacking both Rtn4r and Rtn4rl2 show moderately decreased inhibition of neurite outgrowth by MAG (PubMed:19367338). Mice with a triple gene disruption that lack Rtn4r, Rtn4rl1 and Rtn4rl2 have no visible phenotype, are healthy and viable (PubMed:22406547). Mice with a triple gene disruption that lack Rtn4r, Rtn4rl1 and Rtn4rl2 have normal brain size and grossly normal brain anatomy, but display disruption of medial brain structures, including an absence of the fasciola cinereum, corpus callosum agenesis and formation of bilateral Probst bundles indicative of the failure of callosally projecting neurons to extend across the midline (PubMed:27339102). Mice with a triple gene disruption of Rtn4r, Rtn4rl1 and Rtn4rl2 display impaired ability to stay on a rotarod and increased spontaneous locomotion (PubMed:27339102). These mice display an increased number of excitatory synapses in the apical dendritic regions of hippocampus neurons, an increase in the complexity of dendrite structure and increased total dendrite length (PubMed:22325200). One month after birth, mice with a triple gene disruption that lack Rtn4r, Rtn4rl1 and Rtn4rl2 show a significant reduction in the survival of motoneurons (PubMed:26335717). Compared to wild-type or single mutants, cerebellar granule cells from mice lacking Rtn4r, Rtn4rl1 and Rtn4rl2 show decreased myelin-mediated inhibition of neurite outgrowth, an inhibition that is strongly decreased on myelin deficient in Mag, Rtn4 and Omg (PubMed:22406547). Mice lacking both Rtn4r and Rtn4rl1 show increased axon regeneration after injury; the same effect is observed when Rtn4r, Rtn4rl1 and Rtn4rl2 are disrupted (PubMed:22406547). Combined disruption of Rtn4r, Rtn4rl1 and Ptprs further increases axon regeneration after injury (PubMed:22406547). Single gene disruption of Rtn4r, Rtn4rl1 and Rtn4rl2 and combined disruption of Rtn4r and Rtn4rl2 have no effect on axon regeneration (PubMed:22406547). Belongs to the Nogo receptor family. Nerve regrowth: nipped by a no-go - Issue 69 of April 2006 +Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA. Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule. Binds 2 Zn(2+) ions. Homodimer. Belongs to the RNase Z family. +Lipid transfer protein required for autophagosome completion and peroxisome degradation. Tethers the edge of the isolation membrane (IM) to the endoplasmic reticulum (ER) and mediates direct lipid transfer from ER to IM for IM expansion. Atg2 binds to the ER exit site (ERES), which is the membrane source for autophagosome formation, using basic residues in its N-terminal region (NR) and to the expanding edge of the IM through its C-terminal region. The latter binding is assisted by an atg18-PtdIns3P interaction. Atg2 then extracts phospholipids from the membrane source using its NR and transfers them to atg9 to the IM through its predicted beta-sheet-rich structure for membrane expansion. a 1,2-diacyl-sn-glycero-3-phosphocholine(in) = a 1,2-diacyl-sn-glycero-3-phosphocholine(out) a 1,2-diacyl-sn-glycero-3-phospho-L-serine(in) = a 1,2-diacyl-sn-glycero-3-phospho-L-serine(out) a 1,2-diacyl-sn-glycero-3-phosphoethanolamine(in) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine(out) Belongs to the ATG2 family. +Catalyzes the cleavage of 5-oxoproline to form L-glutamate coupled to the hydrolysis of ATP to ADP and inorganic phosphate. 5-oxo-L-proline + ATP + 2 H2O = ADP + H(+) + L-glutamate + phosphate Forms a complex composed of PxpA, PxpB and PxpC. Belongs to the LamB/PxpA family. +Catalyzes the ATP-dependent condensation of GlcN-Ins and L-cysteine to form L-Cys-GlcN-Ins. 1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside + ATP + L-cysteine = 1D-myo-inositol 2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranoside + AMP + diphosphate + H(+) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. MshC subfamily. +Plays an essential role virus particle assembly and budding. Promotes virus assembly and budding by interacting with host proteins of the multivesicular body pathway. The interaction with host E3 ubiquitin ligase SMURF2 facilitates virus budding (By similarity). The interaction with the nucleocapsid and the plasma membrane may also facilitate virus budding. Specific interactions with membrane-associated GP and VP24 during the budding process may also occur (By similarity). May play a role in genome replication (By similarity). Exists as a dimer until it reorganizes at the plasma membrane into multimeric form. Interacts with host TSG101. Interacts (via PPXY motif) with SMURF2 (via WW domains); the interaction positively regulates virus budding. In virion, localizes on the intravirional side of the membrane. In the host cell, it is found associated with virus-induced membrane proliferation foci and probably also in multivesicular bodies. These VP40-enriched membrane clusters are then redistributed to the plasma membrane where budding takes place. Late-budding domains (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. VP40 contains one L domain: a PPXY motif which potentially interacts with the WW domain 3 of NEDD4 E3 ubiquitin ligase and the three WW domains of SMURF2 E3 ubiquitin ligase. Most abundant protein in the virion. Belongs to the filoviridae matrix protein VP40 family. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +Essential protein (PubMed:19383897). Involved in the secondary cell wall (SCW) formation of vessel elements (e.g. protoxylem and metaxylem), thus promoting tracheary element (TE) differentiation (PubMed:19383897). Expressed preferentially in differentiating vessel elements in seedlings. Restricted to differentiating vessel elements of protoxylem and metaxylem. Constitutive loss of function results in seedling lethality (PubMed:19383897). In conditionnal loss of function, aberrant secondary cell wall (SCW) formation of root vessel elements; this phenotype is stronger in double mutant plants lacking both TED6 and TED7 (PubMed:19383897). +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P). S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 1/6. Belongs to the eIF-2B alpha/beta/delta subunits family. MtnA subfamily. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes. Belongs to the RbfA family. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +Cysteine protease that plays a key role in autophagy by mediating both proteolytic activation and delipidation of ATG8 family proteins (PubMed:21177865, PubMed:29458288, PubMed:30661429). The protease activity is required for proteolytic activation of ATG8 family proteins: cleaves the C-terminal amino acid of ATG8 proteins MAP1LC3 and GABARAPL2, to reveal a C-terminal glycine (PubMed:21177865). Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy (By similarity). In addition to the protease activity, also mediates delipidation of ATG8 family proteins (PubMed:29458288, PubMed:33909989). Catalyzes delipidation of PE-conjugated forms of ATG8 proteins during macroautophagy (PubMed:29458288, PubMed:33909989). Also involved in non-canonical autophagy, a parallel pathway involving conjugation of ATG8 proteins to single membranes at endolysosomal compartments, by catalyzing delipidation of ATG8 proteins conjugated to phosphatidylserine (PS) (PubMed:33909989). ATG4D plays a role in the autophagy-mediated neuronal homeostasis in the central nervous system (By similarity). Compared to other members of the family (ATG4A, ATG4B or ATG4C), constitutes the major protein for the delipidation activity, while it promotes weak proteolytic activation of ATG8 proteins (By similarity). Involved in phagophore growth during mitophagy independently of its protease activity and of ATG8 proteins: acts by regulating ATG9A trafficking to mitochondria and promoting phagophore-endoplasmic reticulum contacts during the lipid transfer phase of mitophagy (PubMed:33773106). Plays a role as an autophagy regulator that links mitochondrial dysfunction with apoptosis. The mitochondrial import of ATG4D during cellular stress and differentiation may play important roles in the regulation of mitochondrial physiology, ROS, mitophagy and cell viability. [protein]-C-terminal L-amino acid-glycyl-phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine [protein]-C-terminal L-amino acid-glycyl-phosphatidylserine + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phospho-L-serine Inhibited by N-ethylmaleimide. Imported into mitochondrial matrix after cleavage by CASP3 during oxidative stress and cell death. Widely expressed in testis. The cryptic mitochondrial transit peptide is revealed after cleavage by caspase upon oxidative stress and cell death (PubMed:22441018). It acts then as a functional transit peptide, and allows the import of the cleaved protein into the mitochondria (PubMed:22441018). Cleaved by CASP3 during apoptosis which leads to increased activity (PubMed:19549685, PubMed:22441018). The cleavage by CASP3 reveals a cryptic mitochondrial targeting sequence immediately downstream of their canonical caspase cleavage sites which leads to mitochondrial import of the protein (PubMed:19549685, PubMed:22441018). Belongs to the peptidase C54 family. A paper describing ATG4D tissue expression has been retracted, due to concerns of image duplication in some of the figures. +Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily. +Envelope protein part of the entry-fusion complex responsible for the virus membrane fusion with host cell membrane during virus entry. Also plays a role in cell-cell fusion (syncytium formation) (By similarity). Part of a stable entry-fusion complex (EFC) which is at least composed of proteins A16, A21, A28, G3, G9, H2, J5, and L5. Formation of the viral membrane is necessary for the assembly of the complex. Interacts with G9 (By similarity). Component of the mature virion (MV) membrane. The mature virion is located in the cytoplasm of infected cells and is probably released by cell lysis. Expressed in the late phase of the viral replicative cycle. Most cysteines are linked by disulfide bonds. They are created by the viral disulfide bond formation pathway, a poxvirus-specific redox pathway that operates on the cytoplasmic side of the MV membranes (By similarity). Belongs to the poxviridae A16/G9/J5 family. +Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell. Homopentamer. Belongs to the MscL family. +Catalyzes the hydrolysis of UDP-3-O-myristoyl-N-acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate, the committed step in lipid A biosynthesis. a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 2/6. Belongs to the LpxC family. +Belongs to the universal ribosomal protein uL16 family. +Participates in sensory organ patterning by antagonizing the neurogenic activity of the Achaete-scute complex (AS-C). It lacks a basic DNA-binding domain but is able to form heterodimers with other HLH proteins, thereby inhibiting DNA binding. May sequester proneural proteins in complexes inefficient for DNA interaction. EMC also affects vein differentiation. Inhibits the activity of AS-C proteins by forming an non-DNA binding heterodimer. Heterodimer with other HLH proteins. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala) a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H(+) Homodimer. A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids. Belongs to the DTD family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase epsilon chain family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. This function is generally fulfilled by the C-terminal part of HisG, which is missing in some bacteria such as this one. Belongs to the class-II aminoacyl-tRNA synthetase family. HisZ subfamily. +Constant region of T cell receptor (TR) alpha chain (PubMed:24600447). Alpha-beta T cell receptors are antigen specific receptors which are essential to the immune response and are present on the cell surface of T lymphocytes. Recognize peptide-major histocompatibility (MH) (pMH) complexes that are displayed by antigen presenting cells (APC), a prerequisite for efficient T cell adaptive immunity against pathogens (PubMed:25493333). Binding of alpha-beta TR to pMH complex initiates TR-CD3 clustering on the cell surface and intracellular activation of LCK that phosphorylates the ITAM motifs of CD3G, CD3D, CD3E and CD247 enabling the recruitment of ZAP70. In turn, ZAP70 phosphorylates LAT, which recruits numerous signaling molecules to form the LAT signalosome. The LAT signalosome propagates signal branching to three major signaling pathways, the calcium, the mitogen-activated protein kinase (MAPK) kinase and the nuclear factor NF-kappa-B (NF-kB) pathways, leading to the mobilization of transcription factors that are critical for gene expression and essential for T cell growth and differentiation (PubMed:23524462). The T cell repertoire is generated in the thymus, by V-(D)-J rearrangement. This repertoire is then shaped by intrathymic selection events to generate a peripheral T cell pool of self-MH restricted, non-autoaggressive T cells. Post-thymic interaction of alpha-beta TR with the pMH complexes shapes TR structural and functional avidity (PubMed:15040585). Alpha-beta TR is a heterodimer composed of an alpha and beta chain; disulfide-linked. The alpha-beta TR is associated with the transmembrane signaling CD3 coreceptor proteins to form the TR-CD3 (TcR or TCR). The assembly of alpha-beta TR heterodimers with CD3 occurs in the endoplasmic reticulum where a single alpha-beta TR heterodimer associates with one CD3D-CD3E heterodimer, one CD3G-CD3E heterodimer and one CD247 homodimer forming a stable octomeric structure. CD3D-CD3E and CD3G-CD3E heterodimers preferentially associate with TR alpha and TR beta chains, respectively. The association of the CD247 homodimer is the last step of TcR assembly in the endoplasmic reticulum and is required for transport to the cell surface. The connecting peptide (CP) domain contributes to the TR-CD3 assembly and signal transduction. The TM domain mediates the interaction with the CD3 subunits. There are several alleles. The sequence shown is that of IMGT allele TRAC*01. The disease is caused by variants affecting the gene represented in this entry. Chimeric mRNA corresponding to regions V, J and C of T cell receptor (TR) alpha chain. +Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H(+) + L-methionine Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiC family. +Catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 2/4. Belongs to the GPI family. +Ferredoxin are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. Although the function of this ferredoxin is unknown it is probable that it has a role as a cellular electron transfer protein. Involved in the in vivo assembly of the Fe-S clusters in a wide variety of iron-sulfur proteins. Binds 1 [2Fe-2S] cluster. Belongs to the adrenodoxin/putidaredoxin family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +Necessary for formate dehydrogenase activity. Belongs to the FdhE family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. One or more lysine residues are methylated. Belongs to the universal ribosomal protein uL11 family. +Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol, an intermediate step in ubiquinone biosynthesis. a 4-hydroxy-3-all-trans-polyprenylbenzoate + H(+) = a 2-all-trans-polyprenylphenol + CO2 Binds 1 prenylated FMN (prenyl-FMN) per subunit. Cofactor biosynthesis; ubiquinone biosynthesis. Homohexamer. Belongs to the UbiD family. +Required for the assembly of the ubiquinol-cytochrome c reductase complex (mitochondrial respiratory chain complex III or cytochrome b-c1 complex), mediating cytochrome b recruitment and probably stabilization within the complex. Thereby, plays an important role in ATP production by mitochondria. Cardiolipin-binding protein, it may also control the cardiolipin composition of mitochondria membranes and their morphology. Associates with the ubiquinol-cytochrome c reductase complex (mitochondrial respiratory chain complex III or cytochrome b-c1 complex). Probably cleaved by OMA1 under mitochondrial stress conditions. Belongs to the UQCC3 family. +Belongs to the UPF0473 family. +Component of the large ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Component of the large ribosomal subunit (PubMed:23636399, PubMed:32669547). Interacts with CRY1 (By similarity). Hydroxylated on His-216 by RIOX1. The modification is impaired by hypoxia. This protein can be partially incorporated into E.coli polysomes in vivo, indicating it can replace the endogenous protein. Belongs to the universal ribosomal protein uL2 family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 2 subfamily. +Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS15 family. +Involved in cell fusion during mating by stabilizing the plasma membrane fusion event. Belongs to the PRM1 family. +Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (By similarity). Protein biosynthesis; polypeptide chain elongation. Belongs to the elongation factor P family. +Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Complex I is composed of 45 different subunits. Belongs to the complex I NDUFA2 subunit family. +Transcription factor required for gene expression specific to photoreceptor cells. +Catalyzes the oxidative cleavage of heme at the alpha-methene bridge carbon, released as carbon monoxide (CO), to generate biliverdin IXalpha, while releasing the central heme iron chelate as ferrous iron (By similarity). Affords protection against programmed cell death and this cytoprotective effect relies on its ability to catabolize free heme and prevent it from sensitizing cells to undergo apoptosis (By similarity). Catalyzes the oxidative cleavage of heme at the alpha-methene bridge carbon, released as carbon monoxide (CO), to generate biliverdin IXalpha, while releasing the central heme iron chelate as ferrous iron. heme b + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = biliverdin IXalpha + CO + Fe(2+) + H(+) + 3 H2O + 3 oxidized [NADPH--hemoprotein reductase] A soluble form arises by proteolytic removal of the membrane anchor. Belongs to the heme oxygenase family. +Rod-core linker protein required for attachment of phycocyanin to allophycocyanin in cores of phycobilisomes. Linker polypeptides determine the state of aggregation and the location of the disk-shaped phycobiliprotein units within the phycobilisome and modulate their spectroscopic properties in order to mediate a directed and optimal energy transfer. The phycobilisome is a hemidiscoidal structure that is composed of two distinct substructures: a core complex and a number of rods radiating from the core. Belongs to the phycobilisome linker protein family. +Belongs to the UPF0758 family. +Binds RpoD and negatively regulates RpoD-mediated transcription activation by preventing the interaction between the primary sigma factor RpoD with the catalytic core of the RNA polymerase and with promoter DNA. May be involved in replacement of the RNA polymerase sigma subunit from RpoD to RpoS during the transition from exponential growth to the stationary phase. Interacts with RpoD. Belongs to the Rsd/AlgQ family. +Aminopeptidase that preferentially cleaves di- and tripeptides. Also has low epoxide hydrolase activity (in vitro). Can hydrolyze the epoxide leukotriene LTA(4) but it forms preferentially 5,6-dihydroxy-7,9,11,14-eicosatetraenoic acid rather than the cytokine leukotriene B(4) as the product compared to the homologous mammalian enzyme (in vitro). an epoxide + H2O = an ethanediol Binds 1 zinc ion per subunit. Belongs to the peptidase M1 family. Truncated N-terminus. +Acts as a chaperone. By stress conditions e.g. heat shock. Belongs to the heat shock protein 70 family. +Interacts with EP300 and acts as a repressor of MYOD-dependent transcription and muscle differentiation. Inhibits EP300 histone acetyltransferase activity. Acts as a repressor of TGFB/SMAD transcriptional responses. May act as a repressor of the TGFB/SMAD3-dependent signaling by selectively blocking formation of TGFB-induced SMAD3-SMAD4 complex (By similarity). Heterodimer with EID2B. Interacts with the C-terminus of EP300. Interacts with HDAC1 and HDAC2. Interacts with SMAD2, SMAD4 and with the MH2 domain of SMAD3 (By similarity). The N-terminal portion of EID2 is required for nuclear localization. +Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. (2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 4/5. Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface. Belongs to the enolase family. +Belongs to the SfsA family. +Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide. Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES. Belongs to the chaperonin (HSP60) family. +Involved in the trimming of pre-amylopectin chains. Accelerates the crystallization of nascent amylopectin molecules during starch synthesis. ISA1 and ISA2 work exclusively together as a multimeric holoenzyme. ISA1-ISA2 removes preferentially branches that are very close to other branches. Glycan biosynthesis; starch biosynthesis. Associates with ISA1 to form the heteromultimeric complex Iso1 required for amylopectin synthesis. Strong reduction of the starch level in leaves, but 50-fold increase of water-soluble polysaccharides. No alteration of the amylase-to-amylopectin ratio. Belongs to the glycosyl hydrolase 13 family. Amino acids thought to be required for catalysis are not conserved in ISA2, suggesting that it may not be an active debranching enzyme and acts via its interaction with ISA1. +Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. Binds 2 Zn(2+) ions per monomer. Homodimer. The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity. Belongs to the DnaJ family. +Dopamine receptor whose activity is mediated by G proteins which inhibit adenylyl cyclase. Promotes cell proliferation (By similarity). Interacts with CLIC6 (By similarity). Interacts with GRK4. Interacts with PALM. Interacts with FLNA (via filamin repeat 21); increases PKA-mediated phosphorylation of FLNA (By similarity). Phosphorylated by GRK4. Palmitoylated. Belongs to the G-protein coupled receptor 1 family. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine. L-leucyl-tRNA(Leu) + N-terminal L-lysyl-[protein] = H(+) + N-terminal L-leucyl-L-lysyl-[protein] + tRNA(Leu) L-leucyl-tRNA(Leu) + N-terminal L-arginyl-[protein] = H(+) + N-terminal L-leucyl-L-arginyl-[protein] + tRNA(Leu) an N-terminal L-alpha-aminoacyl-[protein] + L-phenylalanyl-tRNA(Phe) = an N-terminal L-phenylalanyl-L-alpha-aminoacyl-[protein] + tRNA(Phe) Belongs to the L/F-transferase family. +Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L-cysteine from sulfate. 3 H2O + hydrogen sulfide + 3 NADP(+) = 4 H(+) + 3 NADPH + sulfite Binds 1 siroheme per subunit. Binds 1 [4Fe-4S] cluster per subunit. Sulfur metabolism; hydrogen sulfide biosynthesis; hydrogen sulfide from sulfite (NADPH route): step 1/1. Alpha(8)-beta(8). The alpha component is a flavoprotein, the beta component is a hemoprotein. Belongs to the nitrite and sulfite reductase 4Fe-4S domain family. +Adds the first Dol-P-Man derived mannose in an alpha-1,3 linkage to Man(5)GlcNAc(2)-PP-Dol. a dolichyl beta-D-mannosyl phosphate + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphosphodolichol = a dolichyl phosphate + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphosphodolichol + H(+) Protein modification; protein glycosylation. Belongs to the ALG3 family. +Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; fumarate reductase is used in anaerobic growth, and succinate dehydrogenase is used in aerobic growth. Anchors the catalytic components of the fumarate reductase complex to the cell inner membrane, binds quinones. Part of an enzyme complex containing four subunits: a flavoprotein (FrdA), an iron-sulfur protein (FrdB), and two hydrophobic anchor proteins (FrdC and FrdD). Belongs to the FrdC family. +Participates in transcription elongation, termination and antitermination. Does not interact with Rho. Belongs to the NusG family. +Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion. Involved in chitin degradation. alpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + NH4(+) kcat is 97.5 sec(-1) with GlcN6P as substrate. kcat is 44.2 sec(-1) with Fru6P as substrate. kcat is 39.6 sec(-1) with ammonia as substrate. Optimum pH is 8.0-8.5. Optimum temperature is 95-100 degrees Celsius. Glycan degradation; chitin degradation. Homodimer. Expression is induced by diacetylchitobiose (GlcNAc2) but not by chitobiose or maltose. +This enzyme is required for electron transfer from NADP to cytochrome P450 in microsomes. It can also provide electron transfer to heme oxygenase and cytochrome B5. Involved in ergosterol biosynthesis. NADPH + 2 oxidized [cytochrome P450] = H(+) + NADP(+) + 2 reduced [cytochrome P450] Binds 1 FAD per monomer. Binds 1 FMN per monomer. Expression is induced in the presence of benzoic acid (PubMed:10852481, Ref.3). Expression regulation is particularly complex, involving regulatory promoter elements, differential promoter use and regulation at the post-transcriptional level (PubMed:10852481). Belongs to the NADPH--cytochrome P450 reductase family. In the N-terminal section; belongs to the flavodoxin family. In the C-terminal section; belongs to the flavoprotein pyridine nucleotide cytochrome reductase family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 2 family. +(R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Belongs to the prokaryotic pantothenate kinase family. +Belongs to the aldo/keto reductase family. +Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein. Monomer. Belongs to the LolB family. +Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-cysteinyl-[protein] Belongs to the MnmA/TRMU family. +Catalyzes the reversible phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha-D-ribose 1-phosphate a purine 2'-deoxy-D-ribonucleoside + phosphate = 2-deoxy-alpha-D-ribose 1-phosphate + a purine nucleobase Homohexamer; trimer of homodimers. Belongs to the PNP/UDP phosphorylase family. +Acts as a phosphoinositide 5- and phosphoinositide 6-phosphatase and regulates cellular levels of inositol pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) (PubMed:33257696). Also acts as a 2,3-bisphosphoglycerate 3-phosphatase, by mediating the dephosphorylation of 2,3-bisphosphoglycerate (2,3-BPG) to produce phospho-D-glycerate without formation of 3-phosphoglycerate. May play a role in bone development (endochondral ossification). May play a role in the transition of chondrocytes from proliferation to hypertrophy (By similarity). Through the regulation of intracellular inositol polyphosphates, may control intracellular cation homeostasis, including that of calcium and iron, hence affecting free cation availability required for neural cell signaling (PubMed:33257696). myo-inositol hexakisphosphate + H2O = myo-inositol pentakisphosphate (mixed isomers) + phosphate. (2R)-2,3-bisphosphoglycerate + H2O = (2R)-2-phosphoglycerate + phosphate Widely expressed with highest levels in kidney, liver, cerebellum and placenta. Disease susceptibility is associated with variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. Belongs to the histidine acid phosphatase family. MINPP1 subfamily. Extended N-terminus. +CTP-dependent diacylglycerol kinase that catalyzes the phosphorylation of diacylglycerol (DAG) to phosphatidate (PA). Controls phosphatidate levels at the nuclear envelope. Counteracts the activity of PA phosphatase ned1. May be involved in vesicle trafficking between the endoplasmic reticulum and the Golgi apparatus (By similarity). Involved in pre-tRNA splicing (PubMed:11955632). a 1,2-diacyl-sn-glycerol + CTP = a 1,2-diacyl-sn-glycero-3-phosphate + CDP + H(+) Belongs to the DGK1 family. +Required for insertion of 4Fe-4S clusters. Binds 1 iron-sulfur cluster per subunit. Homodimer. Belongs to the HesB/IscA family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 3 subfamily. +Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-aspartyl-tRNA(Asx) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. +Belongs to the UPF0397 family. +Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP (By similarity). Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. Belongs to the eukaryotic/archaeal RNase P protein component 2 family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Represses ulaG and the ulaABCDEF operon. +Belongs to the hssA/B family. +Catalyzes the transfer of an acetyl group from acetyl-CoA to tetrahydrodipicolinate. (S)-2,3,4,5-tetrahydrodipicolinate + acetyl-CoA + H2O = CoA + L-2-acetamido-6-oxoheptanedioate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (acetylase route): step 1/3. Belongs to the transferase hexapeptide repeat family. DapH subfamily. +Catalyzes the synthesis of GMP from XMP. ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate Purine metabolism; GMP biosynthesis; GMP from XMP (L-Gln route): step 1/1. Homodimer. +Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate Binds 1 [4Fe-4S] cluster per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 2/4. Heterodimer of LeuC and LeuD. Belongs to the aconitase/IPM isomerase family. LeuC type 1 subfamily. +Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation. Expressed at stage 4 in the ectoderm, at stage 6 in the anterior most neural plate, at stage 7 and 8 in the anterior neural fold and at stage 9-10 in the evaginating optic vesicles. At stage 14, highly expressed in developing retina and in infundibulum region. Belongs to the paired homeobox family. Bicoid subfamily. +Most prominent protein induced by estrogen in hypothalamus and most prominent protein induced by LH-RH in pituitary. +Component of the Integrator complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. Belongs to the multiprotein complex Integrator. Belongs to the Integrator subunit 6 family. +Catalyzes the formation of S-adenosylmethionine from methionine and ATP. ATP + H2O + L-methionine = diphosphate + phosphate + S-adenosyl-L-methionine Amino-acid biosynthesis; S-adenosyl-L-methionine biosynthesis; S-adenosyl-L-methionine from L-methionine: step 1/1. Belongs to the AdoMet synthase 2 family. +Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. The 26S proteasome is composed of a core protease, known as the 20S proteasome, capped at one or both ends by the 19S regulatory complex (RC). The RC is composed of at least 18 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and distal to the 20S proteolytic core, respectively (By similarity). Belongs to the proteasome subunit S3 family. +Chitin elicitor-binding protein involved in the perception of chitin oligosaccharide elicitor. Forms homooligomers. Interacts with CERK1 (By similarity). Binds to chitin oligosaccharide elicitor. +Pancreatic hormone is synthesized in pancreatic islets of Langerhans and acts as a regulator of pancreatic and gastrointestinal functions. Belongs to the NPY family. +Promotes absorption of the essential vitamin cobalamin (Cbl) in the ileum. After interaction with CUBN, the CBLIF-cobalamin complex is internalized via receptor-mediated endocytosis (By similarity). Interacts with CUBN (via CUB domains). Belongs to the eukaryotic cobalamin transport proteins family. +May function as a regulator of both motility- and head-associated functions such as capacitation and the acrosome reaction. May bind calcium in vitro (By similarity). Interacts with FSCB. Localizes to fibrous sheath including the surface of the longitudinal columns and ribs of the principal piece of sperm flagella. Expressed in spermatozoa. Phosphorylated on tyrosine residues during in vitro capacitation. Dephosphorylation affects its ability to bind calcium (By similarity). +Belongs to the UPF0060 family. +An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Monomer. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. +Odorant receptor which mediates acceptance or avoidance behavior, depending on its substrates. The odorant receptor repertoire encodes a large collection of odor stimuli that vary widely in identity, intensity, and duration. Forms a complex with Orco to form odorant-sensing units, providing sensitive and prolonged odorant signaling and calcium permeability. Involved in the behavioral responses to benzaldehyde and acetophenone. Interacts with Orco. Complexes exist early in the endomembrane system in olfactory sensory neurons (OSNs), coupling these complexes to the conserved ciliary trafficking pathway. Expressed in olfactory sensory neurons in the antenna. The atypical heteromeric and topological design of the odorant receptors appears to be an insect-specific solution for odor recognition, making the OR/Orco complex an attractive target for the development of highly selective insect repellents to disrupt olfactory-mediated host-seeking behaviors of insect disease vectors. Odor-evoked OR currents are independent of known G-protein-coupled second messenger pathways. Belongs to the insect chemoreceptor superfamily. Heteromeric odorant receptor channel (TC 1.A.69) family. Or49a subfamily. +May be involved in splicing. Belongs to the SQS1 family. +Catalytic component of the DNA-directed RNA polymerase (RNAP) that catalyzes the transcription in the cytoplasm of viral DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity). Forms the polymerase active center together with RPB2 (By similarity). Part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template (By similarity). a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Part of the viral DNA-directed RNA polymerase that consists of 8 polII-like subunits (RPB1, RPB2, RPB3, RPB5, RPB6, RPB7, RPB9, RPB10), a capping enzyme and a termination factor. Found in association with viral nucleoid. Expressed in the late phase of the viral replicative cycle. Lacks the typical C-terminal domain (CTD). Belongs to the RNA polymerase beta' chain family. +Binds together with S18 to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS6 family. +Belongs to the phospholipase D family. In contrast to other members of the family, it lacks the conserved active sites, suggesting that it has no phospholipase activity. Truncated C-terminus. +Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity. 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. Lacks the C-terminal regulatory region which is replaced by HisZ. Belongs to the ATP phosphoribosyltransferase family. Short subfamily. +Involved in nucleolar integrity and required for processing of the pre-rRNA for the 60S ribosome subunit. Belongs to the CGR1 family. +Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate Binds 1 divalent metal cation per subunit. Belongs to the SurE nucleotidase family. +Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate. 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 6/7. Monomer. Belongs to the EPSP synthase family. +Heme-dependent dioxygenase that catalyzes the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring and converts L-tryptophan to N-formyl-L-kynurenine. Catalyzes the oxidative cleavage of the indole moiety. L-tryptophan + O2 = N-formyl-L-kynurenine Binds 1 heme group per subunit. Amino-acid degradation; L-tryptophan degradation via kynurenine pathway; L-kynurenine from L-tryptophan: step 1/2. Homotetramer. Belongs to the tryptophan 2,3-dioxygenase family. +Has antibacterial activity. Belongs to the beta-defensin family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements. Belongs to the RNA polymerase alpha chain family. +Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. guanosine(527) in 16S rRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(527) in 16S rRNA + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family. +Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine. H(+) + L-aspartate = beta-alanine + CO2 Binds 1 pyruvoyl group covalently per subunit. Cofactor biosynthesis; (R)-pantothenate biosynthesis; beta-alanine from L-aspartate: step 1/1. Heterooctamer of four alpha and four beta subunits. Is synthesized initially as an inactive proenzyme, which is activated by self-cleavage at a specific serine bond to produce a beta-subunit with a hydroxyl group at its C-terminus and an alpha-subunit with a pyruvoyl group at its N-terminus. Belongs to the PanD family. +E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. +Probably involved in transport through the plasma membrane. Belongs to the CTL (choline transporter-like) family. +Required for maturation of urease via the functional incorporation of the urease nickel metallocenter. UreD, UreF and UreG form a complex that acts as a GTP-hydrolysis-dependent molecular chaperone, activating the urease apoprotein by helping to assemble the nickel containing metallocenter of UreC. The UreE protein probably delivers the nickel. Belongs to the UreF family. +Modulates RecA activity. Belongs to the RecX family. +Putative adhesion molecule that mediates sialic-acid dependent binding to red blood cells (PubMed:10856141, PubMed:10625619). Preferentially binds to alpha-2,3-linked sialic acid. Also binds to alpha-2,6-linked sialic acid. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface (PubMed:10625619). Recognizes simultaneously epitopes having a terminal N-acetylneuraminic acid (sialic acid) and an underlying 6-O-sulfated galactose. Preferentially binds to Gal-6-sulfated sialyl-Lewis X glycan epitopes (PubMed:27357658). Expressed specifically on red blood cells namely basophil, mast cells and eosinophils. Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. Belongs to the immunoglobulin superfamily. SIGLEC (sialic acid binding Ig-like lectin) family. Siglec-8 +Global transcriptional regulator that plays a key role in stress response and exerts either positive or negative regulation of genes. Acts by interacting with the C-terminal domain of the alpha subunit of the RNA polymerase (RNAP). This interaction can enhance binding of RNAP to the promoter region of target genes and stimulate their transcription, or block interaction of RNAP with activator. Interacts with the C-terminal domain of the alpha subunit of the RNAP. Belongs to the ArsC family. Spx subfamily. +Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins (By similarity). [protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family. +Involved in the biosynthesis of isoprenoids. Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP). isopentenyl diphosphate = dimethylallyl diphosphate Homooctamer. Dimer of tetramers. Belongs to the IPP isomerase type 2 family. +D-glyceraldehyde 3-phosphate + NADP(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADPH D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5. Homotetramer. Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. +The GPI-like anchor contains a phosphoceramide lipid group. The anchor position has not been determined. +Pectinesterase required for cell type-specific pectin degradation to separate microspores. [(1->4)-alpha-D-galacturonosyl methyl ester](n) + n H2O = [(1->4)-alpha-D-galacturonosyl](n) + n H(+) + n methanol Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-gluconate from pectin: step 1/5. Expressed in flower buds, siliques, developing guard cells, floral nectares, at the stigmatic surface, in the hypocotyl-root transition zone and the area of lateral root emergence. Not expressed in mature leaves. Expressed in anther tissues shortly after meiosis is completed and during the late developmental phases of siliques. The mature pollen grains are arranged in a tetrad. Belongs to the pectinesterase family. +Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. H2O + IMP + NAD(+) = H(+) + NADH + XMP Mycophenolic acid (MPA) is a non-competitive inhibitor that prevents formation of the closed enzyme conformation by binding to the same site as the amobile flap. In contrast, mizoribine monophosphate (MZP) is a competitive inhibitor that induces the closed conformation. MPA is a potent inhibitor of mammalian IMPDHs but a poor inhibitor of the bacterial enzymes. MZP is a more potent inhibitor of bacterial IMPDH. Potently inhibited by MPA. Purine metabolism; XMP biosynthesis via de novo pathway; XMP from IMP: step 1/1. Homotetramer. Expressed at equal levels in the yeast or hyphal form. Belongs to the IMPDH/GMPR family. +Natriuretic peptide that dose-dependently induces the rapid relaxation of rat aortic strips phenylephrine-precontracted. Acts by stimulating cGMP production in a dose-dependent manner (by probably activating NPR1 and/or NPR2). May also show potent hypotensive effects. Expressed by the venom gland. Does not inhibits platelet aggregation. Belongs to the natriuretic peptide family. +Belongs to the adenoviridae E1B 19 kDa protein family. +This protein binds to 23S rRNA in the presence of protein L20. Part of the 50S ribosomal subunit. Contacts protein L20. Belongs to the bacterial ribosomal protein bL21 family. +Displays esterase activity towards short chain fatty esters (acyl chain length of up to 8 carbons). Able to hydrolyze triacetylglycerol (triacetin) and tributyrylglycerol (tributyrin), but not trioleylglycerol (triolein) or cholesterol oleate. Negatively regulates MalT activity by antagonizing maltotriose binding. Inhibits MelA galactosidase activity. Homodimer. Interacts with MalT and MelA. Belongs to the 'GDXG' lipolytic enzyme family. +Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate Binds 1 Mg(2+) ion per subunit. Activated by phosphorylation. Belongs to the phosphohexose mutase family. +Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo-MPT) cofactor (Moco or molybdenum cofactor) to form Mo-molybdopterin guanine dinucleotide (Mo-MGD) cofactor. GTP + H(+) + Mo-molybdopterin = diphosphate + Mo-molybdopterin guanine dinucleotide Monomer. The N-terminal domain determines nucleotide recognition and specific binding, while the C-terminal domain determines the specific binding to the target protein. Belongs to the MobA family. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. Belongs to the radical SAM superfamily. Lipoyl synthase family. +As a component of the inner core of AMPAR complexes, modifies AMPA receptor (AMPAR) gating. Component of the inner core of AMPAR complexes. AMPAR complexes consist of an inner core made of 4 pore-forming GluA/GRIA proteins (GRIA1, GRIA2, GRIA3 and GRIA4) and 4 major auxiliary subunits arranged in a twofold symmetry. One of the two pairs of distinct binding sites is occupied either by CNIH2, CNIH3 or CACNG2, CACNG3. The other harbors CACNG2, CACNG3, CACNG4, CACNG8 or GSG1L. This inner core of AMPAR complexes is complemented by outer core constituents binding directly to the GluA/GRIA proteins at sites distinct from the interaction sites of the inner core constituents. Outer core constituents include at least PRRT1, PRRT2, CKAMP44/SHISA9, FRRS1L and NRN1. The proteins of the inner and outer core serve as a platform for other, more peripherally associated AMPAR constituents. Alone or in combination, these auxiliary subunits control the gating and pharmacology of the AMPAR complexes and profoundly impact their biogenesis and protein processing. Expressed in the brain, including hippocampus (at protein level). Belongs to the GSG1 family. +Binds 1 zinc ion per subunit. Belongs to the eukaryotic ribosomal protein eL43 family. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG. Belongs to the RnfG family. +In response to low temperature. Belongs to the peptidase C1 family. +Important role in the capacity of milk to transport calcium phosphate. Antioxidant peptide has 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity. Mammary gland specific. Secreted in milk. Causes an allergic reaction in human. Has six major and 3 minor IgE-binding regions and 5 major and 1 minor IgG-binding regions. Is a cause of cow's milk allergy (CMA). The B variant sequence is shown. Belongs to the alpha-casein family. Of buttons, digestion and glue - Issue 16 of November 2001 +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys) Binds 3 Mg(2+) ions per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis. Cannot utilize a phosphoryl donor other than ATP. (R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) Monovalent cations. Ammonium or potassium. Not regulated by feedback inhibition by CoA and its thioesters as described for many other pantothenate kinases. Not inhibited by N-pentylpantothenamide (N5-Pan), and this compound cannot act as a substrate either. Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Homodimer. Belongs to the type III pantothenate kinase family. +Snake venom serine protease that may act in the hemostasis system of the prey. Monomer. Expressed by the venom gland. Average mass. Belongs to the peptidase S1 family. Snake venom subfamily. +Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP). (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate Cofactor biosynthesis; molybdopterin biosynthesis. Homohexamer; trimer of dimers. Belongs to the MoaC family. +Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. Binds to the N-terminal domain of the chaperone ClpA. Belongs to the ClpS family. +Might be involved in translocating phthiocerol dimycocerosates (PDIM) from the cell membrane to the outer membrane; PDIM forms part of the cell wall. Forms a U-shaped beta-half-barrel with a large hydrophobic cavity which is large enough to hold a single phthiocerol dimycocerosate (PDIM) molecule. Modified by Lgt on Cys-27 with an S-linked diacylglycerol with a mixture of C16 and C19 fatty acids (palmitic and tuberculostearic acid), signal peptide is removed by LspA, modified by Lnt with an amide-linked mixture of C16 and C19 fatty acids. Belongs to the LppX/LprAFG lipoprotein family. +Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. AMP + ATP = 2 ADP Purine metabolism; AMP biosynthesis via salvage pathway; AMP from ADP: step 1/1. Monomer. Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis. Belongs to the adenylate kinase family. +PPIases accelerate the folding of proteins by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) Inhibited by both FK506 and rapamycin. Highly expressed in growing cells. Expression levels decrease during the first few hours of development. Belongs to the FKBP-type PPIase family. +Required for spermatogenesis and is involved in the suppression of retrotransposon transcription in male germ cells. Belongs to the UPF0224 (FAM112) family. +Belongs to the bacterial ribosomal protein bL36 family. +Tegument protein that plays different roles during the time course of infection (By similarity). Participates in both the accumulation of viral mRNAs and viral protein translation at late time of infection (By similarity). Modulates the RNase activity of the virion host shutoff protein UL41 probably to ensure necessary levels of key cellular mRNAs and proteins (By similarity). Plays a role in microtubule reorganization that occurs after viral infection by stabilizing microtubule network (By similarity). Plays a role in the inhibition of host innate immune system by targeting the CGAS enzymatic activity which is the principal cytosolic DNA sensor that detects invading viral DNA. Acts by mediating disruption of liquid-like droplets in which CGAS is activated, thereby preventing CGAS activity (By similarity). Interacts with gE (via C-terminus); this interaction is necessary for the recruitment of VP22 to the Golgi and its packaging into virions (By similarity). Interacts with gM (via C-terminus) (By similarity). Interacts with VP16; this interaction allows the formation of a tripartite complex composed of VP16, VP22 and UL41/VHS (By similarity). Interacts with the capsid-binding protein UL16 (By similarity). Interacts with host CGAS (By similarity). One of the most abundant tegument protein (about 2000 copies per virion). Localizes in the cytoplasm at 8 hours postinfection and in the nucleus at 16 hours postinfection. During virion morphogenesis, this protein probably accumulates at the trans-Golgi where secondary envelopment occurs. Highly phosphorylated in the host cell. Packaging is selective for underphosphorylated forms. Belongs to the alphaherpesvirinae VP22 tegument protein family. +Probably acts as a heme chaperone, transferring heme to an unknown acceptor. Binds one molecule of heme per monomer, possibly covalently (By similarity). Binds 1 [2Fe-2S] cluster. Although this protein has sequence motifs typically found in proteins binding the [4Fe-4S]-AdoMet radical-SAM cluster and S-adenosylmethionine, spectroscopic evidence suggests that a [2Fe-2S] cluster is present; S-adenosylmethionine was not detected. Has no detectable coproporphyrinogen-III oxidase activity (PubMed:20194361). Induced under microoxic conditions. Cells lacking this gene have no detectable phenotype. Might carry two S-adenosyl-L-methionine binding sites with only one binding to the iron-sulfur cluster. Belongs to the anaerobic coproporphyrinogen-III oxidase family. HemW subfamily. +Catalyzes the addition of N-acetylglucosamine (GlcNAc) in beta 1-6 linkage to the alpha-linked mannose of biantennary N-linked oligosaccharides (PubMed:8340368, PubMed:7615638). Catalyzes an important step in the biosynthesis of branched, complex-type N-glycans, such as those found on EGFR, TGFR (TGF-beta receptor) and CDH2 (By similarity). Via its role in the biosynthesis of complex N-glycans, plays an important role in the activation of cellular signaling pathways, reorganization of the actin cytoskeleton, cell-cell adhesion and cell migration (PubMed:7615638). MGAT5-dependent EGFR N-glycosylation enhances the interaction between EGFR and LGALS3 and thereby prevents rapid EGFR endocytosis and prolongs EGFR signaling. Required for efficient interaction between TGFB1 and its receptor. Enhances activation of intracellular signaling pathways by several types of growth factors, including FGF2, PDGF, IGF, TGFB1 and EGF. MGAT5-dependent CDH2 N-glycosylation inhibits CDH2-mediated homotypic cell-cell adhesion and contributes to the regulation of downstream signaling pathways. Promotes cell migration. Contributes to the regulation of the inflammatory response. MGAT5-dependent TCR N-glycosylation enhances the interaction between TCR and LGALS3, limits agonist-induced TCR clustering, and thereby dampens TCR-mediated responses to antigens. Required for normal leukocyte evasation and accumulation at sites of inflammation (By similarity). Inhibits attachment of monocytes to the vascular endothelium and subsequent monocyte diapedesis (By similarity). Promotes proliferation of umbilical vein endothelial cells and angiogenesis, at least in part by promoting the release of the growth factor FGF2 from the extracellular matrix. N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAcl-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = H(+) + N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAcl-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP Protein modification; protein glycosylation. Detected in kidney (at protein level). Detected in kidney. N-glycosylated. A secreted form is released from the membrane after cleavage by gamma-secretase. Belongs to the glycosyltransferase 18 family. +Involved in peptide bond synthesis. Alleviates ribosome stalling that occurs when 3 or more consecutive Pro residues or the sequence PPG is present in a protein, possibly by augmenting the peptidyl transferase activity of the ribosome. Modification of Lys-34 is required for alleviation. Protein biosynthesis; polypeptide chain elongation. Is beta-lysylated on the epsilon-amino group of Lys-34 by the combined action of EpmA and EpmB, and then hydroxylated on the C5 position of the same residue by EpmC. Lysylation is critical for the stimulatory effect of EF-P on peptide-bond formation. The lysylation moiety would extend toward the peptidyltransferase center and stabilize the terminal 3-CCA end of the tRNA. The hydroxylation of the C5 position on Lys-34 would allow additional potential stabilizing hydrogen-bond interactions with the P-tRNA. Belongs to the elongation factor P family. +RAB11A-binding protein that plays a role in neurite outgrowth. Interacts with RAB11A; this interaction recruits TBC1D12 to RAB11A-positive recycling endosomes. Knock-down promotes neurite outgrowth in a RAB11A-dependent manner. +Carrier of the growing fatty acid chain in fatty acid biosynthesis. Lipid metabolism; fatty acid biosynthesis. 4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by acpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group (By similarity). Belongs to the acyl carrier protein (ACP) family. +This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs. Belongs to the universal ribosomal protein uL18 family. +Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. Belongs to the GHMP kinase family. IspE subfamily. +One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome. Belongs to the universal ribosomal protein uL23 family. +GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+) Cofactor biosynthesis; 7,8-dihydroneopterin triphosphate biosynthesis; 7,8-dihydroneopterin triphosphate from GTP: step 1/1. Toroid-shaped homodecamer, composed of two pentamers of five dimers. Belongs to the GTP cyclohydrolase I family. +Transcriptional activator of the nitrous-oxide reductase gene NosZ. To P.denitrificans NirI. +Causes an allergic reaction in human. Causes grass pollen allergy. Binds to IgE. Belongs to the expansin family. Expansin B subfamily. +Catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 2/4. Belongs to the GPI family. +Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions. diphosphate + H2O = H(+) + 2 phosphate Homohexamer. Belongs to the PPase family. +By abscisic acid (ABA) and dehydration. Belongs to the LEA type 4 family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Contacts proteins S5 and S12. Belongs to the universal ribosomal protein uS8 family. +ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP. Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes. Belongs to the ClpX chaperone family. +Component of the small ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains about 33 different proteins and 1 molecule of RNA (18S). The 60S subunit contains about 49 different proteins and 3 molecules of RNA (25S, 5.8S and 5S). Belongs to the eukaryotic ribosomal protein eS1 family. +Peptide which can recruit, activate and subsequently lyse neutrophils, thus eliminating the main cellular defense against infection. Belongs to the phenol-soluble modulin alpha peptides family. +Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS. [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + a uridine in tRNA + ATP + H(+) + 2 reduced [2Fe-2S]-[ferredoxin] = [ThiI sulfur-carrier protein]-L-cysteine + a 4-thiouridine in tRNA + AMP + diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] [sulfur-carrier protein ThiS]-C-terminal Gly-Gly-AMP + AH2 + S-sulfanyl-L-cysteinyl-[cysteine desulfurase] = [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH + A + AMP + H(+) + L-cysteinyl-[cysteine desulfurase] Cofactor biosynthesis; thiamine diphosphate biosynthesis. Belongs to the ThiI family. +Cell membrane polyamine/proton symporter involved in the polyamine uptake in cells. Possesses high affinity for spermine and spermidine and lower affinity for putrescine. Transports paraquat, a polyamine analog, and thus confers sensitivity to this chemical which is used as a herbicide. Plasma membrane. Expressed in hypocotyls and petioles of cotyledons in 1- to 3-day-old seedlings. No visible phenotype under normal growth conditions, but mutant plants show increased tolerance to paraquat. Methyl viologen is the brand name of paraquat. Plants over-expressing RMV1 show hypersensitivity to paraquat (PubMed:22492932). Belongs to the amino acid-polyamine-organocation (APC) superfamily. Polyamine:cation symporter (PHS) (TC 2.A.3.12) family. +Receptor for adenosine. The activity of this receptor is mediated by G proteins which inhibits adenylyl cyclase. Phosphorylation on Thr-317 and Thr-318 may be crucial for rapid desensitization. Phosphorylation on Thr-317 may be necessary for phosphorylation on Thr-318 to occur. Belongs to the G-protein coupled receptor 1 family. +Non-reducing polyketide synthase; part of the gene cluster that mediates the biosynthesis of neosartoricin B, a prenylated anthracenone that probably exhibits T-cell antiproliferative activity, suggestive of a physiological role as an immunosuppressive agent (PubMed:23758576). The non-reducing polyketide synthase nscA probably synthesizes and cyclizes the decaketide backbone (By similarity). The hydrolase nscB then mediates the product release through hydrolysis followed by spontaneous decarboxylation (By similarity). The prenyltransferase nscD catalyzes the addition of the dimethylallyl group to the aromatic C5 (By similarity). The FAD-dependent monooxygenase nscC is then responsible for the stereospecific hydroxylation at C2 (By similarity). Neosartoricin B can be converted into two additional compounds neosartoricins C and D (By similarity). Neosartoricin C is a spirocyclic compound that is cyclized through the attack of C3 hydroxyl on C14, followed by dehydration (By similarity). On the other hand, neosartoricin D is a further cyclized compound in which attack of C2 on C14 in neosartoricin C results in the formation of the acetal-containing dioxabicyclo-octanone ring (By similarity). Both of these compounds are novel and possibly represent related metabolites of the gene cluster (By similarity). Binds 1 phosphopantetheine covalently. Secondary metabolite biosynthesis. Multidomain protein; including a starter unit:ACP transacylase (SAT) that selects the starter unit; a ketosynthase (KS) that catalyzes repeated decarboxylative condensation to elongate the polyketide backbone; a malonyl-CoA:ACP transacylase (MAT) that selects and transfers the extender unit malonyl-CoA; a product template (PT) domain that controls the immediate cyclization regioselectivity of the reactive polyketide backbone; and an acyl-carrier protein (ACP) that serves as the tether of the growing and completed polyketide via its phosphopantetheinyl arm (By similarity). +Plays an important role in the regulation of interdigestive gastrointestinal motility and indirectly causes rhythmic contraction of duodenal and colonic smooth muscle. Present in the gut mucosa with the exception of the gastric corpus. Also present in medulla oblongata, nucleus of the solitary tract, hypophysis, spinal cord, hypothalamus, and cerebellum but not in the cerebral cortex. Belongs to the motilin family. +Phosphodiesterase (PDE) that has higher activity toward cAMP than cGMP, as substrate. Plays a role in cell proliferation, is able to induce cell motility and acts as a negative regulator of NME1 (By similarity). diphosphate + H2O = H(+) + 2 phosphate Binds 2 manganese ions per subunit. Activated by magnesium ions and inhibited by manganese ions. Inhibited by dipyridamole, moderately sensitive to IBMX and inhibited by vinpocetine (By similarity). Homooligomer. Able to homodimerize via its C-terminal domain. Interacts with NME1. Interacts with GSK3; at focal adhesion complexes where paxillin and vinculin are colocalized. Belongs to the PPase class C family. Prune subfamily. +Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. (2S,6S)-2,6-diaminoheptanedioate = meso-2,6-diaminoheptanedioate Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1. Homodimer. Belongs to the diaminopimelate epimerase family. Truncated N-terminus. +May participate in the formation of a layer of cross-linked glycosylated fibrils at the viral surface thus giving it a hairy-like appearance. May be hydroxylated on lysine by the viral-encoded procollagen-lysine,2-oxoglutarate 5-dioxygenase. +Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins. Binds 1 zinc ion per subunit. Homohexamer. In the central section; belongs to the AAA ATPase family. In the C-terminal section; belongs to the peptidase M41 family. +CTP + H(+) + phosphoethanolamine = CDP-ethanolamine + diphosphate Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from ethanolamine: step 2/3. Expressed in late sporogonial stages. Belongs to the cytidylyltransferase family. +Involved in the biosynthesis of the osmoprotectant glycine betaine. Catalyzes the irreversible oxidation of betaine aldehyde to the corresponding acid. betaine aldehyde + H2O + NAD(+) = glycine betaine + 2 H(+) + NADH Binds 2 potassium ions per subunit. Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway; betaine from betaine aldehyde: step 1/1. Dimer of dimers. Belongs to the aldehyde dehydrogenase family. +Transcription factor acting redundantly with MYB21 and MYB24 to control stamen filament elongation in the late developed flowers. Repressed at the transcript levels by DELLA proteins. Expressed specifically in flowers. No visible phenotype. Myb21 and myb57 double mutant has an intermediate sterility phenotype and petals that grew to a final height parallel to the pistil. Myb24 and myb57 double mutant has petals that grew to a final height parallel to the pistil. Myb21, myb24 and myb57 triple mutant has a strongly reduced fertility and an arrested growth of the petals that never grew out of the sepals. +Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity). [thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-diphosphate Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding to separate specificity and activation sites on the large subunit. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction. Stimulated by ATP and inhibited by dATP binding to the activity site (By similarity). Genetic information processing; DNA replication. Heterodimer of a large and a small subunit. Belongs to the ribonucleoside diphosphate reductase large chain family. +(S)-malate + a quinone = a quinol + oxaloacetate Carbohydrate metabolism; tricarboxylic acid cycle; oxaloacetate from (S)-malate (quinone route): step 1/1. Belongs to the MQO family. +Catalyzes the hydrolysis of N(4)-acetylcytidine (ac4C). H2O + N(4)-acetylcytidine = acetate + cytidine + H(+) H2O + N(4)-acetyl-2'-deoxycytidine = 2'-deoxycytidine + acetate + H(+) H2O + N(4)-acetylcytosine = acetate + cytosine + H(+) Belongs to the N(4)-acetylcytidine amidohydrolase family. +GTP-binding protein involved in nucleocytoplasmic transport. Required for the import of protein into the nucleus and also for RNA export. Involved in chromatin condensation and control of cell cycle (By similarity). Found in a nuclear export complex with RanGTP, exportin and pre-miRNA (By similarity). Interacts with RANBP1A and RANBP1B (PubMed:9025305). Interacts with TRN1 (PubMed:14756317). Interacts with ATX1 (PubMed:17223078). Interacts with KPNB1 (PubMed:23582042). Binds to XPO1 (PubMed:10652141). Interacts with MOS14 (PubMed:21738492). Binds to NTF2B (PubMed:16428596). Regulated by light. Belongs to the small GTPase superfamily. Ran family. +Activates the ATG1 kinase in a nutritional condition dependent manner through the TOR pathway, leading to autophagy. Also involved in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt vesicle formation. Seems to play a role in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage during stationary phase (By similarity). Interacts with ATG1 to form the ATG1-ATG13 kinase complex. Belongs to the ATG13 family. Fungi subfamily. +Belongs to the UPF0260 family. +Polycomb group (PcG) protein. Catalytic component of the PR-DUB complex, a complex that specifically mediates deubiquitination of histone H2A monoubiquitinated at 'Lys-118' (H2AK118ub1). Does not deubiquitinate monoubiquitinated histone H2B. Required to maintain the transcriptionally repressive state of homeotic genes throughout development. The PR-DUB complex has weak or no activity toward 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Component of the PR-DUB complex, at least composed of calypso and Asx. Localizes to PcG response elements (PREs). Polycomb phenotype leading to lethality, probably due to misexpression of homeotic genes. Belongs to the peptidase C12 family. BAP1 subfamily. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has four main subunits: a(1), b(1), b'(1) and c(9-12). Belongs to the ATPase alpha/beta chains family. +Thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions (By similarity). SLIT1 and SLIT2 together seem to be essential for midline guidance in the forebrain by acting as repulsive signal preventing inappropriate midline crossing by axons projecting from the olfactory bulb. Interacts with ROBO1 and GREM1. Predominantly expressed in adult forebrain. Expressed in fetal brain, lung and kidney. +Essential for the assembly of the photosystem I (PSI) complex. May act as a chaperone-like factor to guide the assembly of the PSI subunits. Belongs to the Ycf3 family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units. Binds 1 Ca(2+) ion per subunit. Binds 1 Cl(-) ion per subunit. Monomer. At least 6 electrophoretic isozymes are known: Amy1, Amy2, Amy3, Amy4, Amy5 and Amy6. Strains KO123 expresses Amy1; J87 expresses Amy3; 1420#1, L16 and TN256 express Amy6. Belongs to the glycosyl hydrolase 13 family. +Has nucleotide phosphatase activity towards ATP, GTP, CTP, TTP and UTP. May hydrolyze nucleoside diphosphates with lower efficiency. a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + H(+) + phosphate Belongs to the THEP1 NTPase family. +Seems to act as an ATP-dependent zinc metallopeptidase. Binds 1 zinc ion per subunit. In the N-terminal section; belongs to the AAA ATPase family. In the C-terminal section; belongs to the peptidase M41 family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Belongs to the ATPase epsilon chain family. +Has a 11,12(11',12') 9-cis epoxycarotenoid cleavage activity. Catalyzes the first step of abscisic-acid biosynthesis from carotenoids. a 9-cis-epoxycarotenoid + O2 = 2-cis,4-trans-xanthoxin + a 12'-apo-carotenal 9-cis-violaxanthin + O2 = (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al + 2-cis,4-trans-xanthoxin 9'-cis-neoxanthin + O2 = (3S,5R,6R)-3,5-dihydroxy-6,7-didehydro-5,6-dihydro-12'-apo-beta-caroten-12'-al + 2-cis,4-trans-xanthoxin Binds 1 Fe(2+) ion per subunit. Down-regulated by submergence (PubMed:17205969). Induced by drought stress (PubMed:25735958). Down-regulated by glucose (PubMed:22859682). Belongs to the carotenoid oxygenase family. +Plays a functionally redundant role in shifting germ cell sexual differentiation in hermaprodites. Required for the development of somatic gonad structures and for progression from larval stage to adulthood. Extensively phosphorylated on serine residues in the RS domain. RNA-mediated interference (RNAi) of rsp-5 and rsp-6 result in fertile animals that exhibit excessive sperm and delayed oocyte production, and sterile animals that develop morphological abnormalities of somatic gonads. Rsp-2/rsp-6 RNAi caused severe abnormalities in somatic gonad structures and in some cases animals were arrested or dead at the larval stage. Belongs to the splicing factor SR family. +Belongs to the TACO1 family. +Belongs to the HesB/IscA family. +One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit. Binds 1 zinc ion per subunit. Monomer. Associates with 30S ribosomal subunit, binds 16S rRNA. Belongs to the TRAFAC class YlqF/YawG GTPase family. RsgA subfamily. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine. Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 1/9. Heteromultimer composed of HisG and HisZ subunits. This function is generally fulfilled by the C-terminal part of HisG, which is missing in some bacteria such as this one. Belongs to the class-II aminoacyl-tRNA synthetase family. HisZ subfamily. +Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives. [[Fe-S] cluster scaffold protein carrying a second [4Fe-4S](2+) cluster] + 4 H(+) + N(6)-octanoyl-L-lysyl-[protein] + 2 oxidized [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + 2 5'-deoxyadenosine + [[Fe-S] cluster scaffold protein] + 4 Fe(3+) + 2 hydrogen sulfide + 2 L-methionine + 2 reduced [2Fe-2S]-[ferredoxin] Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Protein modification; protein lipoylation via endogenous pathway; protein N(6)-(lipoyl)lysine from octanoyl-[acyl-carrier-protein]: step 2/2. Belongs to the radical SAM superfamily. Lipoyl synthase family. +Involved in deacetylation of histones, chromatin assembly and chromosome segregation. May act as a transcriptional oscillator, directing histone deacetylases to specific chromosomal domains. Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair (By similarity). Component of the NuA4 histone acetyltransferase complex. Belongs to the MRG family. +GTPase that plays an essential role in the late steps of ribosome biogenesis. Associates with the 50S ribosomal subunit. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. +Belongs to the EamA transporter family. +Possible metal-dependent hydrolase. Binds 1 zinc ion per subunit. Homodimer. Belongs to the metal hydrolase YfiT family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the anticodon-binding domain and the C-terminal extension. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily. +Involved in cell division and chromosome segregation. Belongs to the WhiA family. +Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase A chain family. +Catalyzes the oxidation of cytokinins, a family of N(6)-substituted adenine derivatives that are plant hormones, where the substituent is an isopentenyl group. A + H2O + N(6)-dimethylallyladenine = 3-methyl-2-butenal + adenine + AH2 Monomer. Belongs to the oxygen-dependent FAD-linked oxidoreductase family. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +2-oxoglutarate + L-histidinol phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 7/9. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily. +Potent voltage-gated sodium channel blocker (IC(50)=190 nM and 210 nM on human and rat Nav1.3/SCN3A respectively, 430 nM on human Nav1.7/SCN9A, 770 nM and 290 nM on human and rat Nav1.8/SCN10A respectively) (PubMed:24211312). Binds the voltage-sensor domain of the potassium channel KvAP (from Aeropyrum pernix) and weakly inhibits this channel (By similarity). Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. Monoisotopic mass. Shows only a very weak inhibition on human Nav1.5/SCN5A. The primary structure of the mature peptide is identical to that of VSTX3 from Grammostola rosea (AC P0C2P5). Belongs to the neurotoxin 10 (Hwtx-1) family. 61 (VSTX3) subfamily. +Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage. Belongs to the RecA family. +Membrane-anchoring subunit of succinate dehydrogenase (SDH) that is involved in system II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). SDH3 and SDH4 form the membrane dimer that anchors the catalytic dimer formed by SDH1 and SDH2 to the matrix surface of the mitochondrial inner membrane. Electrons originating from the catalytic dimer enter the membrane dimer for ubiquinone reduction. Carbohydrate metabolism; tricarboxylic acid cycle. Forms part of complex II containing four subunits: a flavoprotein (FP), an iron-sulfur protein (IP) and a cytochrome b composed of a large and a small subunit. Present with 7920 molecules/cell in log phase SD medium. Belongs to the CybS family. +Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis. ATP + beta-D-fructose 6-phosphate = ADP + beta-D-fructose 1,6-bisphosphate + H(+) Allosterically activated by ADP and other diphosphonucleosides, and allosterically inhibited by phosphoenolpyruvate. Optimum pH is 7.2-7.8. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose: step 3/4. Homotetramer. Belongs to the phosphofructokinase type A (PFKA) family. ATP-dependent PFK group I subfamily. Prokaryotic clade 'B1' sub-subfamily. +Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs. a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O Belongs to the thioester dehydratase family. FabZ subfamily. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group. (2E,6E)-farnesyl diphosphate + H2O + heme b = diphosphate + Fe(II)-heme o Porphyrin-containing compound metabolism; heme O biosynthesis; heme O from protoheme: step 1/1. Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature. Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily. +Involved in the regulation of glutamine synthetase GlnA, a key enzyme in the process to assimilate ammonia. When cellular nitrogen levels are high, the C-terminal adenylyl transferase (AT) inactivates GlnA by covalent transfer of an adenylyl group from ATP to specific tyrosine residue of GlnA, thus reducing its activity. Conversely, when nitrogen levels are low, the N-terminal adenylyl removase (AR) activates GlnA by removing the adenylyl group by phosphorolysis, increasing its activity. The regulatory region of GlnE binds the signal transduction protein PII (GlnB) which indicates the nitrogen status of the cell. [glutamine synthetase]-O(4)-(5'-adenylyl)-L-tyrosine + phosphate = [glutamine synthetase]-L-tyrosine + ADP [glutamine synthetase]-L-tyrosine + ATP = [glutamine synthetase]-O(4)-(5'-adenylyl)-L-tyrosine + diphosphate Belongs to the GlnE family. +Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L-methionine = adenine + epoxyqueuosine(34) in tRNA + H(+) + L-methionine tRNA modification; tRNA-queuosine biosynthesis. Monomer. Belongs to the QueA family. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Blocks human voltage-gated potassium channel Kv1.2/KCNA2 (IC(50)=3.6 nM) and Kv1.3/KCNA3 (IC(50)=72 nM). Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). Does not block voltage-gated potassium channel Kv1.1/KCNA1, intermediate conductance calcium-activated potassium channel KCa3.1/KCNN4 or the Shaker IR (with inactivation domain removed). Belongs to the short scorpion toxin superfamily. Potassium channel inhibitor family. Alpha-KTx 10 subfamily. +DNA-binding protein that binds to both single- and double-stranded DNA. Binds preferentially to UV-damaged DNA. May be involved in DNA-metabolic processes. Belongs to the WD repeat DDB2/WDR76 family. +Part of the ABC transporter complex UgpABCE involved in sn-glycerol-3-phosphate import. Responsible for energy coupling to the transport system. ATP + H2O + sn-glycerol 3-phosphate(out) = ADP + H(+) + phosphate + sn-glycerol 3-phosphate(in) The complex is composed of two ATP-binding proteins (UgpC), two transmembrane proteins (UgpA and UgpE) and a solute-binding protein (UgpB). Belongs to the ABC transporter superfamily. sn-glycerol-3-phosphate importer (TC 3.A.1.1.3) family. +Cell signaling peptide that may regulate plant stress, growth, and development. Mediates a rapid alkalinization of extracellular space by mediating a transient increase in the cytoplasmic Ca(2+) concentration leading to a calcium-dependent signaling events through a cell surface receptor and a concomitant activation of some intracellular mitogen-activated protein kinases (By similarity). Belongs to the plant rapid alkalinization factor (RALF) family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS7 family. +Alpha-glucosidase with specificity for isomaltase, methyl-alpha-glucoside, and palatinose. Hydrolysis of (1->6)-alpha-D-glucosidic linkages in some oligosaccharides produced from starch and glycogen by alpha-amylase, and in isomaltose. By ethanol. Belongs to the glycosyl hydrolase 13 family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 2 subfamily. +DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate. Belongs to the endonuclease V family. +Essential subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral membrane proteins such as Notch. It probably represents a stabilizing cofactor for the presenilin homodimer that promotes the formation of a stable complex. Component of the gamma-secretase complex, a complex composed of a presenilin (Psn) homodimer, nicastrin (Nct), Aph-1 and Pen-2. Belongs to the APH-1 family. +(4aS,6R)-4a-hydroxy-L-erythro-5,6,7,8-tetrahydrobiopterin = (6R)-L-erythro-6,7-dihydrobiopterin + H2O Belongs to the pterin-4-alpha-carbinolamine dehydratase family. +Stimulates the release of gastrin and other gastrointestinal hormones. Brain and stomach. In the stomach GRP was localized, at the base of the gastric pits, to occasional cells whose distribution and appearance were consistent with that of gut neuroendocrine cells. Belongs to the bombesin/neuromedin-B/ranatensin family. +Muscle-specific type III intermediate filament essential for proper muscular structure and function. Plays a crucial role in maintaining the structure of sarcomeres, inter-connecting the Z-disks and forming the myofibrils, linking them not only to the sarcolemmal cytoskeleton, but also to the nucleus and mitochondria, thus providing strength for the muscle fiber during activity. In adult striated muscle they form a fibrous network connecting myofibrils to each other and to the plasma membrane from the periphery of the Z-line structures. May act as a sarcomeric microtubule-anchoring protein: specifically associates with detyrosinated tubulin-alpha chains, leading to buckled microtubules and mechanical resistance to contraction. Contributes to the transcriptional regulation of the NKX2-5 gene in cardiac progenitor cells during a short period of cardiomyogenesis and in cardiac side population stem cells in the adult. Plays a role in maintaining an optimal conformation of nebulette (NEB) on heart muscle sarcomeres to bind and recruit cardiac alpha-actin. Homomer. Interacts with DST. Interacts with MTM1. Interacts with EPPK1; interaction is dependent of higher-order structure of intermediate filament. Interacts with CRYAB. Interacts with NEB (via nebulin repeats 160-164). Interacts (via rod region) with NEBL (via nebulin repeats 1-5). Interacts with ASB2; the interaction targets DES for proteasomal degradation (By similarity). Localizes in the intercalated disks which occur at the Z line of cardiomyocytes. Localizes in the nucleus exclusively in differentiating cardiac progenitor cells and premature cardiomyocytes. ADP-ribosylation prevents ability to form intermediate filaments. Phosphorylation at Ser-7, Ser-28 and Ser-32 by CDK1 and phosphorylation at Ser-60 by AURKB contribute to efficient separation of desmin intermediate filaments during mitosis. Ubiquitination by a SCF-like complex containing ASB2 leads to proteasomal degradation. Belongs to the intermediate filament family. +Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. Binds two Mg(2+) per subunit. Monomer. Belongs to the type IA topoisomerase family. +In the C-terminal section; belongs to the GatC family. +Part of a tripartite efflux system composed of MdtA, MdtB and MdtC. MdtC forms a heteromultimer with MdtB (By similarity). Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family. MdtC subfamily. +Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Binds 2 magnesium ions per subunit. Monomer. Belongs to the DNA polymerase type-Y family. +May be a heme chaperone, appears to bind heme. Homologous bacterial proteins do not have oxygen-independent coproporphyrinogen-III oxidase activity (Probable). Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine (By similarity). Might carry two S-adenosyl-L-methionine binding sites with only one binding to the iron-sulfur cluster. Belongs to the anaerobic coproporphyrinogen-III oxidase family. HemW subfamily. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG. Belongs to the NqrB/RnfD family. +Belongs to the bacterial ribosomal protein bL28 family. +Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis. Homotrimer; each monomer consists of a S1 and a S2 subunit. The resulting peplomers protrude from the virus surface as spikes. Accumulates in the endoplasmic reticulum-Golgi intermediate compartment, where it participates in virus particle assembly. Some S oligomers are transported to the host plasma membrane, where they may mediate cell-cell fusion. Fusion peptide 1 (FP1) and fusion peptide 2 (FP2) function cooperatively and have a membrane-ordering effect on lipid headgroups and shallow hydrophobic regions of target bilayers. They are considered as two domains of an extended, bipartite FP. The membrane-ordering activity is calcium-dependent and also dependent on correct folding, which is maintained by an internal disulfide bond in FP2. Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host cell furin or another cellular protease to yield the mature S1 and S2 proteins. Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor. The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes. Belongs to the betacoronaviruses spike protein family. +Catalyzes the reversible oxidation of malate to oxaloacetate. (S)-malate + NAD(+) = H(+) + NADH + oxaloacetate Belongs to the LDH/MDH superfamily. MDH type 2 family. +Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+) + H2O + oxidized [flavodoxin] = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + reduced [flavodoxin] Binds 1 [4Fe-4S] cluster. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 5/6. Belongs to the IspG family. +Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP. an acyl phosphate + sn-glycerol 3-phosphate = a 1-acyl-sn-glycero-3-phosphate + phosphate Lipid metabolism; phospholipid metabolism. Probably interacts with PlsX. Belongs to the PlsY family. +Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA). ATP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate} = ADP + {2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-beta-D-glucosaminyl}-(1->6)-{2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl phosphate}. Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 6/6. Belongs to the LpxK family. +Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import. Cofactor biosynthesis; adenosylcobalamin biosynthesis. Forms an energy-coupling factor (ECF) transporter complex composed of an ATP-binding protein (A component, CbiO), a transmembrane protein (T component, CbiQ) and 2 possible substrate-capture proteins (S components, CbiM and CbiN) of unknown stoichimetry. Belongs to the CbiN family. +Belongs to the UPF0319 family. +ATP + L-histidine + tRNA(His) = AMP + diphosphate + H(+) + L-histidyl-tRNA(His) Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Electrons originating from reduced cytochrome c in the intermembrane space (IMS) are transferred via the dinuclear copper A center (CU(A)) of subunit 2 and heme A of subunit 1 to the active site in subunit 1, a binuclear center (BNC) formed by heme A3 and copper B (CU(B)). The BNC reduces molecular oxygen to 2 water molecules using 4 electrons from cytochrome c in the IMS and 4 protons from the mitochondrial matrix. 4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O Binds 2 heme A groups non-covalently per subunit. Binds a copper B center. Energy metabolism; oxidative phosphorylation. Component of the cytochrome c oxidase (complex IV, CIV), a multisubunit enzyme composed of 14 subunits. The complex is composed of a catalytic core of 3 subunits MT-CO1, MT-CO2 and MT-CO3, encoded in the mitochondrial DNA, and 11 supernumerary subunits COX4I, COX5A, COX5B, COX6A, COX6B, COX6C, COX7A, COX7B, COX7C, COX8 and NDUFA4, which are encoded in the nuclear genome. The complex exists as a monomer or a dimer and forms supercomplexes (SCs) in the inner mitochondrial membrane with NADH-ubiquinone oxidoreductase (complex I, CI) and ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII), resulting in different assemblies (supercomplex SCI(1)III(2)IV(1) and megacomplex MCI(2)III(2)IV(2)) (By similarity). As a newly synthesized protein, rapidly incorporates into a multi-subunit assembly intermediate in the inner membrane, called MITRAC (mitochondrial translation regulation assembly intermediate of cytochrome c oxidase) complex, whose core components are COA3/MITRAC12 and COX14. Within the MITRAC complex, interacts with COA3 and with SMIM20/MITRAC7; the interaction with SMIM20 stabilizes the newly synthesized MT-CO1 and prevents its premature turnover. Interacts with TMEM177 in a COX20-dependent manner (By similarity). Belongs to the heme-copper respiratory oxidase family. +The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[glycine-cleavage complex H protein] + CO2 The glycine cleavage system is composed of four proteins: P, T, L and H. In this organism, the P 'protein' is a heterodimer of two subunits. Belongs to the GcvP family. C-terminal subunit subfamily. +Involved in the recruitment of clathrin to the Golgi network and endosomes to form clathrin coated vesicles. Plays a role in the trafficking of clathrin between the Golgi network and endosomes. Binds to membranes enriched in phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P2) and, in association with VPS27, is involved in protein sorting at the multivesicular body (MVB). Interacts with the clathrin adapter GGA2 and the clathrin adapter complex AP-1. Found predominantly on endosomal structures. Present with 8100 molecules/cell in log phase SD medium. +Hybrid PKS-NRPS synthetase; part of the gene cluster that mediates the biosynthesis of aspyridones (PubMed:17369821, PubMed:20828130, Ref.5). The polyketide-amino acid backbone preaspyridone A is first assembled by the PKS-NRPS hybrid apdA (PubMed:17369821, PubMed:20828130). The assembly of preaspyridone A is initiated by loading of malonyl-CoA onto apdA, followed by decarboxylation to yield the acetyl starter unit (PubMed:20828130). The growing polyketide chain then elongates into a tetraketide (PubMed:20828130). The adpA PKS module catalyzes three Claisen condensations, as well as beta-keto processing and methylation (PubMed:17369821, PubMed:20828130). Alpha-methylation step during polyketide synthesis is a prerequisite and a key checkpoint for chain transfer between PKS and NRPS modules (PubMed:25494235). The downstream NRPS module contains the condensation (C), adenylation (A), and thiolation (T) domains and catalyzes the incorporation of tyrosine via the formation of the L-tyrosinyl-thioester and the amide linkage between L-tyrosinyl-thioester and the tetraketide (PubMed:20828130). The bimodular assembly line is terminated with a reductase (R) domain that facilitates formation and release of the tetramic acid product (PubMed:20828130). Because apdA lacks a designated enoylreductase (ER) domain, the required activity is provided the enoyl reductase apdC (PubMed:17369821, PubMed:20828130, Ref.5). ApdC appears to operate with different stereoselectivity in different PKS cycle (Ref.5). Combined with apdC, apdA is proposed to synthesize preaspyridone A via about 20 enzymatic steps (PubMed:20828130). A number of oxidative steps performed successively by the cytochrome P450 monooxygenases apdE and apdB are required for the conversion of preaspyridone A to aspyridone A (PubMed:17369821). The cytochrome P450 monooxygenase apdE is responsible for the oxidative dephenylation of preaspyridone A (Ref.5). Finally, the predicted FAD-dependent monooxygenase apdD and the acyl-CoA dehydrogenase apdG may be involved in the transformation of aspyridone A into aspyridone B (PubMed:17369821) (Probable). Secondary metabolite biosynthesis. Expression is positively regulated by the aspyridones cluster specific transcription regulator apdR (PubMed:17369821). ApdA has the following domain architecture: KS-MAT-DH-MT-KR-ACP-C-A-T-R (Probable). The apdA PKS module (domains KS to ACP) is responsible for the biosynthesis of the polyketide chain and catalyzes three Claisen condensations, as well as beta-keto processing and methylation (PubMed:20828130, PubMed:25494235). The downstream NRPS module contains the condensation (C), adenylation (A), and thiolation (T) domains and catalyzes the formation of the L-tyrosinyl-thioester and the amide linkage between L-tyrosinyl-thioester and the tetraketide (PubMed:20828130, PubMed:25494235). The bimodular assembly line is terminated with a putative reductase (R) domain that facilitates formation and release of the tetramic acid product (PubMed:20828130, PubMed:25494235). In the C-terminal section; belongs to the NRP synthetase family. +Belongs to the bacterial ribosomal protein bL36 family. +Catalyzes the biosynthesis of histamine from histidine. H(+) + L-histidine = CO2 + histamine Amine and polyamine biosynthesis; histamine biosynthesis; histamine from L-histidine: step 1/1. Homodimer. Belongs to the group II decarboxylase family. +Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF-1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. PrfC subfamily. +Major attachment protein that mediates binding of the virus to cell surface heparan sulfate or chondroitin sulfate (By similarity). Also plays a role in host immune evasion by inhibiting the host complement cascade activation. Interacts with host complement component C3b; this interaction inhibits host immune response by disregulating complement cascade. There are seven external glycoproteins in HSV-1 and 2: gH, gB, gC, gG, gD, gI, and gE. Belongs to the herpesviridae glycoprotein C family. +Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 3/4. Homodimer. Belongs to the IlvD/Edd family. +Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes. Localizes to the plus end of microtubules and to the centrosome. Dimerization mediated by the LisH domain may be required to activate dynein. Belongs to the WD repeat LIS1/nudF family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +Mediates visceral muscle contractile activity (myotropic activity). Belongs to the periviscerokinin family. +RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site. 2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-bisphosphate + H2O D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + 2-phosphoglycolate + 2 H(+) Binds 1 Mg(2+) ion per subunit. Heterohexadecamer of 8 large chains and 8 small chains. The basic functional RuBisCO is composed of a large chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric 'cap' on each end of the 'barrel'. Belongs to the RuBisCO large chain family. Type I subfamily. +In the phosphorylated form it could act as an anti-anti-sigma factor that counteracts an anti-sigma factor and thus releases a sigma factor from inhibition. Phosphorylated on a serine residue. Belongs to the anti-sigma-factor antagonist family. +Synthesizes alpha-1,4-glucan chains using ADP-glucose. [(1->4)-alpha-D-glucosyl](n) + ADP-alpha-D-glucose = [(1->4)-alpha-D-glucosyl](n+1) + ADP + H(+) Glycan biosynthesis; glycogen biosynthesis. Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily. +This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. Monomer. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily. +Part of the ABC transporter complex PstSACB involved in phosphate import. The complex is composed of two ATP-binding proteins (PstB), two transmembrane proteins (PstC and PstA) and a solute-binding protein (PstS). Belongs to the PstS family. +Belongs to the DNA glycosylase MPG family. +May function as a ferroxidase for ferrous (II) to ferric ion (III) conversion and may be involved in copper transport and homeostasis. Implicated in iron homeostasis and may mediate iron efflux associated to ferroportin 1 (By similarity). Binds 6 Cu cations per monomer. Highly expressed in small intestine and colon. Belongs to the multicopper oxidase family. +Belongs to the UPF0060 family. +Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14. Belongs to the universal ribosomal protein uS3 family. +May be involved in the regulation of photosystem II. Associated with the photosystem II complex. By light. Belongs to the psbP family. +May play a role in photosystem I and II biogenesis. Belongs to the PsbN family. Originally thought to be a component of PSII; based on experiments in Synechocystis, N.tabacum and barley, and its absence from PSII in T.elongatus and T.vulcanus, this is probably not true. +Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. Minor subunit located with subunit a in the membrane (By similarity). F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. Belongs to the ATPase protein 8 family. +Acts as a component of the essential kinetochore-associated NDC80 complex, which is required for chromosome segregation and spindle checkpoint activity. Required for kinetochore integrity and the organization of stable microtubule binding sites in the outer plate of the kinetochore. The NDC80 complex synergistically enhances the affinity of the SKA1 complex for microtubules and may allow the NDC80 complex to track depolymerizing microtubules. Component of the NDC80 complex, which consists of NDC80/HEC1, CDCA1, SPBC24 and SPBC25. The NDC80 complex is formed by two subcomplexes composed of NDC80/HEC1-CDCA1 and SPBC24-SPBC25. Each subcomplex is formed by parallel interactions through the coiled-coil domains of individual subunits. Formation of a tetrameric complex is mediated by interactions between the C-terminal regions of both subunits of the NDC80/HEC1-CDCA1 subcomplex and the N-terminal regions of both subunits of the SPBC24-SPBC25 complex. The tetrameric NDC80 complex has an elongated rod-like structure with globular domains at either end (By similarity). Localizes to kinetochores from late prophase to anaphase. Localizes specifically to the outer plate of the kinetochore. Belongs to the SPC25 family. +Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 Binds 1 pyruvoyl group covalently per subunit. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase. Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Prokaryotic type I sub-subfamily. +Binds directly to 16S ribosomal RNA. Belongs to the bacterial ribosomal protein bS20 family. +Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod. Belongs to the FlgH family. +Probable component of the WASH complex. Belongs to the FAM21 family. +IRBP shuttles 11-cis and all trans retinoids between the retinol isomerase in the pigment epithelium and the visual pigments in the photoreceptor cells of the retina. Interphotoreceptor matrix that permeates the space between the retina and the contiguous layer of pigment epithelium cells. The disease is caused by variants affecting the gene represented in this entry. Belongs to the peptidase S41A family. It is uncertain whether Met-1 or Met-2 is the initiator. +Component of the acid-insoluble and acid-soluble organic matrix of calcified layers of the shell (at protein level). +Involved in the biodegradation of chlorinated nitroaromatic compounds. Catalyzes the reduction of 4-chloronitrobenzene to yield 1-hydroxylamino-4-chlorobenzene. Probably also able to catalyze the two-electron reduction of nitrobenzene (NB) to produce a nitrosobenzene (NOB) intermediate, which is immediately reduced to hydroxylaminobenzene (HAB) by a second two-electron transfer. H2O + N-phenylhydroxylamine + 2 NADP(+) = 2 H(+) + 2 NADPH + nitrobenzene Binds 1 FMN per subunit. Xenobiotic degradation; nitrobenzene degradation. Xenobiotic degradation; 4-chloronitrobenzene degradation. Belongs to the nitroreductase family. +Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase. Exhibits a low intrinsic GTPase activity, which is essential for nickel insertion (By similarity). Is able to bind 4 nickel ions per subunit. Can also bind zinc (PubMed:7928968). Is synthesized in microaerobic vegetative cells and pea bacteroids but not in aerobic vegetative cells. A histidine-rich region at the N-terminus is proposed to play a role in nickel binding, both in solution and in chelated form. Insertion mutant lacks any hydrogenase activity in symbiosis with peas, but is still able to synthesize the polypeptide for the hydrogenase large subunit. Belongs to the SIMIBI class G3E GTPase family. HypB/HupM subfamily. +Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield nucleoside 5'-phosphates. Heterooligomer composed of large and small subunits. Belongs to the XseB family. +Escorts unspliced or incompletely spliced viral pre-mRNAs (late transcripts) out of the nucleus of infected cells. These pre-mRNAs carry a recognition sequence called Rev responsive element (RRE) located in the env gene, that is not present in fully spliced viral mRNAs (early transcripts). This function is essential since most viral proteins are translated from unspliced or partially spliced pre-mRNAs which cannot exit the nucleus by the pathway used by fully processed cellular mRNAs (By similarity). Homomultimer; when bound to the RRE. Multimeric assembly is essential for activity (By similarity). The presence of both nuclear import and nuclear export signals leads to continuous shuttling between the nucleus and cytoplasm. The RNA-binding motif binds to the RRE present in incompletely spliced viral pre-mRNAs. This region also contains the NLS which mediates nuclear localization. These overlapping functions prevent Rev bound to RRE from undesirable return to the nucleus. When Rev binds the RRE, the NLS becomes masked while the NES remains accessible (By similarity). Phosphorylated. The sequence shown is that of isolate R29-127. +A methylase that recognizes DNA with the sequence 5'-GCGTC-3', methylates C-2, and protects the DNA from cleavage by the HgaI endonuclease. a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + H(+) + S-adenosyl-L-homocysteine The HgaI modification system consists of two cytosine methylase genes responsible for modification of different strands in the target DNA. Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family. Extended N-terminus. Extended N-terminus. +Mediates both low-affinity uptake and efflux of sugar across the plasma membrane. Required, in pollen, for microspore cell integrity and primexine pattern formation (PubMed:18434608, PubMed:25988582). Forms homooligomers and heterooligomers with SWEET4, SWEET5, SWEET6, SWEET7, SWEET9, SWEET10, SWEET11, SWEET13, SWEET15, SWEET16 and SWEET17. Expressed in inflorescences, embryo sacs and pollen, and at a lower level in stems. Barely detected in roots, leaves and seedlings. Expressed during anther development in tapetal cells and microsporocytes during meiosis. When the tapetum degenerates, detected only in pollen grains. Induced by the pathogenic bacteria P.syringae pv. tomato. Dramatically reduced fertility due to a postmeiotic rupture of microspores. Not detected in inflorescence (PubMed:18434608). Belongs to the SWEET sugar transporter family. +Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another. Belongs to the RRF family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 1/6. Belongs to the DXR family. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +Involved in the production of the root hair deformation (HAD) factor specifically on medicago. D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate In response to a plant signal such as luteolin via the regulatory gene NodD. +Catalyzes the facilitated diffusion of 2-acyl-glycero-3-phosphoethanolamine (2-acyl-GPE) into the cell. Belongs to the major facilitator superfamily. LplT (TC 2.A.1.42) family. +Mnh complex is a Na(+)/H(+) antiporter involved in Na(+) excretion. May form a heterooligomeric complex that consists of seven subunits: mnhA1, mnhB1, mnhC1, mnhD1, mnhE1, mnhF1 and mnhG1. Belongs to the CPA3 antiporters (TC 2.A.63) subunit B family. +Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol. 2 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) = a cardiolipin + glycerol Belongs to the phospholipase D family. Cardiolipin synthase subfamily. ClsA sub-subfamily. +Transfers two electrons from NADH to two molecules of cytochrome b5 through an enzyme-bound FAD. Electrons from the reduced cytochrome b5 are then transferred to various electron acceptors, thereby participating in methemoglobin reduction in red blood cells and in the desaturation and elongation of fatty acids, cholesterol biosynthesis and cytochrome P-450-mediated drug metabolism other tissues. 2 Fe(III)-[cytochrome b5] + NADH = 2 Fe(II)-[cytochrome b5] + H(+) + NAD(+) Component of a complex composed of cytochrome b5, NADH-cytochrome b5 reductase (CYB5R3) and MTARC2 (By similarity). Interacts with MTLN; the interaction is required to maintain cellular lipid composition and leads to stimulation of mitochondrial respiratory complex I activity (PubMed:31296841). Produces the soluble form found in erythrocytes. Belongs to the flavoprotein pyridine nucleotide cytochrome reductase family. +Involved in protein translation. Together with DOM34, may function in recognizing stalled ribosomes and triggering endonucleolytic cleavage of the mRNA, a mechanism to release non-functional ribosomes and degrade damaged mRNAs. Interacts with DOM34. Present with 2750 molecules/cell in log phase SD medium. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. +Plays a role in the elongation phase of viral strand displacement replication by unwinding the template in an ATP-independent fashion, employing its capacity to form multimers. Also enhances the rate of initiation. Released from template upon second strand synthesis. Assembles in complex with viral pTP, viral pol, host NFIA and host POU2F1/OCT1 on viral origin of replication. Covers the whole ssDNA genome during synthesis. The complementary strand synthesis induces its relese from DNA template. May inhibit cellular transcription mediated by the interaction between host SRCAP and CBP. Homomultimerizes on viral ssDNA bound to pTP. Forms a initiation complex with viral polymerase, pTP and hosts NFIA and POU2F1/OCT1. Interacts with host SRCAP. Accumulates in infected cells. The C-terminal arm bridges DBP molecules together, thereby creating a chain. Belongs to the adenoviridae E2A DNA-binding protein family. +Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + H(+) + L-threonyl-tRNA(Thr) Binds 1 zinc ion per subunit. Homodimer. Belongs to the class-II aminoacyl-tRNA synthetase family. +ATP + H2O = ADP + H(+) + phosphate This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation. Belongs to the helicase family. DnaB subfamily. +Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism. adenine + H(+) + H2O = hypoxanthine + NH4(+) Binds 1 zinc ion per subunit. Belongs to the metallo-dependent hydrolases superfamily. Adenosine and AMP deaminases family. Adenine deaminase type 2 subfamily. +Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine. phosphoenolpyruvate + UDP-N-acetyl-alpha-D-glucosamine = phosphate + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the EPSP synthase family. MurA subfamily. +Belongs to the serpin family. +Cilium-specific protein required for cilia structures. Belongs to the DNAAF1 family. +Required for the biogenesis of c-type cytochromes. Possible subunit of a heme lyase. Belongs to the CcmH/CycL/Ccl2/NrfF family. +Promotes the emission of terpenes volatile organic compounds (VOC) in response to damage mediated by arthropod herbivores (e.g. Spodoptera exigua), probably to attract natural enemies of the herbivores. (2E)-geranyl diphosphate = diphosphate + tricyclene (2E)-geranyl diphosphate = (E)-beta-ocimene + diphosphate Binds 3 Mg(2+) or Mn(2+) ions per subunit. Secondary metabolite biosynthesis; terpenoid biosynthesis. Expressed in leaves. Accumulates in response to wounding, methyl jasmonate (meJA) and infection by Spodoptera exigua (beet armyworm), a lepidopteran herbivory. Also induced by lepidopteran oral secretions. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg(2+). Belongs to the terpene synthase family. Tpsb subfamily. +Catalyzes the conversion of urocanate to 4-imidazolone-5-propionate. 4-imidazolone-5-propanoate = H2O + trans-urocanate Binds 1 NAD(+) per subunit. Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 2/3. Belongs to the urocanase family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +H(+) + NADP(+) + 2 reduced [2Fe-2S]-[ferredoxin] = NADPH + 2 oxidized [2Fe-2S]-[ferredoxin] Binds 1 FAD per subunit. Homodimer. Belongs to the ferredoxin--NADP reductase type 2 family. +ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys) Binds 1 zinc ion per subunit. Monomer. Belongs to the class-I aminoacyl-tRNA synthetase family. +Belongs to the SlyX family. +Required for resistance to DNA-damaging agents. Belongs to the universal stress protein A family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. The beta-hairpin motif is involved in DNA binding. Belongs to the UvrB family. +Catalyzes the second step of the urea cycle, the condensation of carbamoyl phosphate with L-ornithine to form L-citrulline (PubMed:7332529). The urea cycle ensures the detoxification of ammonia by converting it to urea for excretion (Probable). carbamoyl phosphate + L-ornithine = H(+) + L-citrulline + phosphate Inhibition by ornithine increases at higher pH. With an increase in pH, a decrease in KM values for ornithine and an increase in the extent of inhibition by ornithine are observed. Optimum pH is 7.5 in the presence of 5 mM ornithine. The curve shifts toward a more alkaline region with a decrease in ornithine concentration. Nitrogen metabolism; urea cycle; L-citrulline from L-ornithine and carbamoyl phosphate: step 1/1. Homotrimer. Expressed in kidney, brain, heart, liver, pancreas, gizzard, small intestine and breast muscle. More abundant in mitochondrion-rich organs (heart, liver and brain) than in other organs. Activity is only detected in the kidney. Activity detectable in embryos by day 14. Increases until 7 days post-hatching, then decreases again. By diet of egg yolk in animals which have a high level of OTC activity due to presence of OCB gene. Cleavage of the precursor form to the active form occurs only in the kidney. Ornithine transcarbamylase activity varies within and between different breeds of chicken. Belongs to the aspartate/ornithine carbamoyltransferase superfamily. OTCase family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. a ubiquinone + 5 H(+)(in) + NADH = a ubiquinol + 4 H(+)(out) + NAD(+) Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits. Belongs to the complex I subunit 4L family. +Potentially involved in docking of synaptic vesicles at presynaptic active zones. Belongs to the syntaxin family. +May be involved in transcriptional regulation. Belongs to the krueppel C2H2-type zinc-finger protein family. +Transfers a succinyl group from succinyl-CoA to L-homoserine, forming succinyl-L-homoserine. L-homoserine + succinyl-CoA = CoA + O-succinyl-L-homoserine Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; O-succinyl-L-homoserine from L-homoserine: step 1/1. Belongs to the MetA family. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The archaeal alpha chain is a catalytic subunit (By similarity). ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate Belongs to the ATPase alpha/beta chains family. +Repressor involved in the biosynthesis of the osmoprotectant glycine betaine. It represses transcription of the choline transporter BetT and the genes of BetAB involved in the synthesis of glycine betaine (By similarity). Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway [regulation]. +Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA Homodimer. Belongs to the tRNA pseudouridine synthase TruA family. +Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ATP + H2O + L-glutamine + L-glutamyl-tRNA(Gln) = ADP + H(+) + L-glutamate + L-glutaminyl-tRNA(Gln) + phosphate ATP + H2O + L-aspartyl-tRNA(Asn) + L-glutamine = ADP + 2 H(+) + L-asparaginyl-tRNA(Asn) + L-glutamate + phosphate Heterotrimer of A, B and C subunits. Belongs to the GatB/GatE family. GatB subfamily. +Catalyzes the first oxidative step of the phenylpropanoid pathway in higher plants by transforming trans-cinnamate into p-coumarate (By similarity). The compounds formed by this pathway are essential components for lignification, pollination, and defense against ultraviolet light, predators and pathogens (By similarity). (E)-cinnamate + O2 + reduced [NADPH--hemoprotein reductase] = (E)-4-coumarate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase] Phenylpropanoid metabolism; trans-4-coumarate biosynthesis; trans-4-coumarate from trans-cinnamate: step 1/1. Belongs to the cytochrome P450 family. +Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway. D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = beta-D-fructose 6-phosphate + D-erythrose 4-phosphate Carbohydrate degradation; pentose phosphate pathway; D-glyceraldehyde 3-phosphate and beta-D-fructose 6-phosphate from D-ribose 5-phosphate and D-xylulose 5-phosphate (non-oxidative stage): step 2/3. Homodimer. Belongs to the transaldolase family. Type 1 subfamily. +DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate. Belongs to the endonuclease V family. +Galactose-binding lectin (PubMed:23886951, PubMed:27010847, PubMed:9568372, PubMed:28636877). Binds both alpha and beta anomer of galactose (Gal), but has a stronger interaction with the glycans having alpha Gal at the non-reducing end and binds beta Gal weakly only in highly branched glycans. Has high affinity to Galalpha1-4Galbeta1-4GlcNAc (PubMed:28636877). Binds N-acetyl-2-deoxy-2-amino-galactose (2-deoxy-GalNAc) (PubMed:23886951, PubMed:9568372). Binds N-acetylgalactosamine (GalNAc) (PubMed:26439416). Binds porcine stomach mucin (PSM) with high affinity (PubMed:26439416, PubMed:30486373). Binds galactosamine (PubMed:27010847). Binds laminin, bovine submaxillary mucin (BSM), fibronectin, type I collagen and gelatin with a decreasing affinity, respectively (Ref.3). Has hemagglutinating activity towards human type A erythrocytes (PubMed:9568372, PubMed:26439416, Ref.3). Hemagglutinates also human type 0, B and AB erythrocytes as well as rabbit and mouse erythrocytes (PubMed:9568372). Agglutinates both Gram-positive and Gram-negative bacteria including B.subtilis ATCC 6633, S.aureus ATCC 21027 and E.coli 3254, respectively. No agglutination activity towards Gram-positive S.amurskyense CMM 3673. Has bacteriostatic activity on S.amurskyense CMM 3673, B.subtilis ATCC 6633, S.aureus ATCC 21027 and E.coli 3254. However, has no agglutination nor bacteriostatic activity on Gram-negative C.scophthalmum CIP 104199 or A.troitsensis KMM 3674 (PubMed:23886951). Inhibits growth of fungi from the genera Aspergillus, Penicillium, Trichoderma and st. Mycelia. Inhibits germination of spores and hyphal growth of them (PubMed:25482060). Has dose-dependent cytotoxic effect on the human globotriaosylceramide (Gb3)-expressing Burkitt's lymphoma (Raji) cell line. Binds to Gb3 in these cells leading to activation of caspase-9/3 and PARP (PubMed:28636877). Has dose-dependent cytotoxic effect on the Gb3-expressing human MCF-7 breast cancer cell line (PubMed:27010847). No cytotoxic effect on myelogenous leukemia K562 cell line, which does not express Gb3 (PubMed:28636877). Activates immune responses in mice and increases cytokine production of TNF-alpha, IL-6 and MCP-1 in the serum and the peritoneal lavage of mice. Induces TNF-alpha and IL-6 secretion in mouse RAW264.7 macrophages, mouse bone marrow-derived macrophages, human THP-1 macrophages, human peripheral blood mononuclear cells (PBMCs) and human blood monocyte-derived macrophages. TNF-alpha production in macrophages could not be inhibited by GalNAc, GalN or Gal, indicating that induced cytokine production is separate from its sugar binding activity. Increases intracellular reactive oxygen species levels, expression and phosphorylation of protein kinases PKC alpha/delta, expression of COX-2 and NF-kappaB, and activates the MAPK pathway by increasing the phosphorylation of ERK1/2, JNK1/2 and p38 in mouse RAW264.7 macrophages. Induces endotoxin tolerance in lipopolysaccharide(LPS)-activated macrophages by down-regulating IRAK2 expression, reducing JNK1/2 phosphorylation and NF-kappaB activation. Can slightly increase the bactericidal activity of RAW264.7 macrophages (PubMed:28740170). Has DNA-binding activity (PubMed:27010847). Recognizes pathogen-associated molecular patterns (PAMPs) and binds to LPS from E.coli, but has only little binding to beta-1,3-glucan from E.gracilis and peptidoglycan from S.aureus. Activates secretion of TNF-alpha and IFN-gamma by the human peripheral blood cells (HPBCs) (PubMed:31905927). May be involved in innate immunity acting as an antibacterial and antifungal agent involved in the recognition and clearance of pathogens (PubMed:23886951, PubMed:25482060, PubMed:31905927). Bacterial binding activity is inhibited by D-galactose (PubMed:23886951). Hemagglutinating activity is independent of divalent cations Ca2(+) or Mg2(+). It is strongly inhibited by N-acetyl-D-galactosamine (GalNAc), D-galactose and D-talose, and to a lesser extent by melibiose and raffinose. Also inhibited by glycoprotein asialo-bovine submaxillary mucin (BSM). Not inhibited by D-glucose, D-fucose, D-galactitol, N-acetyl-D-glucosamine or lactose (PubMed:9568372, PubMed:26439416). Fungal binding activity is inhibited by D-galactose (PubMed:25482060). Cytotoxic activity against Raji cell line is completely inhibited by galactose, melibiose and raffinose, but not by glucose or lactose (PubMed:28636877). Galactose inhibits binding to laminin and BSM, but not to collagen, gelatin or fibronectin (Ref.3). Optimum pH is between 8-10 for the hemagglutinating activity of the human erythrocytes. Hemagglutinating activity of the human erythrocytes is fully maintained after heating at 50 degrees Celsius for 3 hours. The activity is partially lost after heating at 55 degrees Celsius and completely lost after heating at 65 degrees Celsius for 30 minutes. Monomer in solution (PubMed:26527272). Homodimer in solution (PubMed:27010847). Exists as a monomer in solution when a low concentration (0.001 mg/ml) of it is present. Homodimers start to appear at a concentration of 0.01 mg/ml and tetramers at a concentration of 0.1 mg/ml (Ref.3). Highly expressed in mantle and to a lesser extent in muscle, hepatopancreas, gill and hemocytes. Up-regulated in mantle by challenge of yeast P.pastoris reaching the maximum level at 12 hours post challenge and recovering to the original level at 24 hours post challenge. Contains a collagen like domain, which probably promotes oligomerization. This protein may have potential in cancer diagnosis and treatment (PubMed:28636877, PubMed:27010847, PubMed:30486373, PubMed:31905927). A synthetic analog of this protein with enhanced carbohydrate-binding properties may be designed for the purpose of constructing a biosensor for cancer diagnostics or anticancer therapy (PubMed:30486373). May potentially be used as an immune modulator in mammals, because of its effects on macrophages and its ability to promote secretion of cytokines (PubMed:28740170). Cleavage of the collagen like domain may decrease the agglutinating ability and alter carbohydrate-binding properties. The function of this protein could potentially be regulated by proteolysis in vivo. +Catalyzes the alpha,beta-elimination reaction of D-cysteine and of several D-cysteine derivatives. It could be a defense mechanism against D-cysteine. D-cysteine + H2O = H(+) + hydrogen sulfide + NH4(+) + pyruvate Homodimer. Belongs to the ACC deaminase/D-cysteine desulfhydrase family. +Catalyzes the 3-beta-hydroxylation of (2S)-flavanones to 2R,3R-dihydroflavonols, which are intermediates in the biosynthesis of flavonols, anthocyanidins, catechins and proanthocyanidins in plants (PubMed:31004005). Can act on naringenin to produce dihydrokaempferol, and on eriodictyol to produced dihydroquercetin (PubMed:31004005). 2-oxoglutarate + a (2S)-flavan-4-one + O2 = a (2R,3R)-dihydroflavonol + CO2 + succinate (2S)-naringenin + 2-oxoglutarate + O2 = (2R,3R)-dihydrokaempferol + CO2 + succinate (S)-eriodictyol + 2-oxoglutarate + O2 = (2R,3R)-dihydroquercetin + CO2 + succinate Binds 1 ascorbate molecule per subunit. Binds 1 Fe(2+) ion per subunit. Flavonoid metabolism. Expressed in young cromes. Belongs to the iron/ascorbate-dependent oxidoreductase family. +Participates in the translocation of lipoproteins from the inner membrane to the outer membrane. Only forms a complex with a lipoprotein if the residue after the N-terminal Cys is not an aspartate (The Asp acts as a targeting signal to indicate that the lipoprotein should stay in the inner membrane). Monomer. Belongs to the LolA family. +Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system. Forms a complex with TatC. Belongs to the TatA/E family. +May function as a potassium transporter. Up-regulated by phagocytic stimuli. Belongs to the TrkH potassium transport family. +Catalyzes, although with low efficiency, the sulfur transfer reaction from thiosulfate to cyanide. hydrogen cyanide + thiosulfate = 2 H(+) + sulfite + thiocyanate Belongs to the GlpE family. +Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS11 family. +Belongs to the major facilitator superfamily. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-amino acid + H(+) Monomer. Belongs to the PTH family. +Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6. Belongs to the bacterial ribosomal protein bS18 family. +H(+) + 2 pyruvate = (2S)-2-acetolactate + CO2 Binds 1 Mg(2+) ion per subunit. Binds 1 thiamine pyrophosphate per subunit. Amino-acid biosynthesis; L-isoleucine biosynthesis; L-isoleucine from 2-oxobutanoate: step 1/4. Amino-acid biosynthesis; L-valine biosynthesis; L-valine from pyruvate: step 1/4. Dimer of large and small chains. Belongs to the TPP enzyme family. +Belongs to the transposase 8 family. +Catalyzes the formation of Delta(11) fatty acyl precursors in the pheromone gland. an 11,12-saturated fatty acyl-CoA + 2 Fe(II)-[cytochrome b5] + 2 H(+) + O2 = an (11Z)-Delta(11)-fatty acyl-CoA + 2 Fe(III)-[cytochrome b5] + 2 H2O Adult female pheromone gland. Increases by two or three orders of magnitude during the first 2 days after adult eclosion. The histidine box domains may contain the active site and/or be involved in metal ion binding. Belongs to the fatty acid desaturase type 1 family. +Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate + tRNA(n) Homohexameric ring arranged as a trimer of dimers. Belongs to the RNase PH family. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. Part of the 30S ribosomal subunit. Belongs to the universal ribosomal protein uS8 family. +ATPase subunit of a proteasome-like degradation complex; this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis. A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP. By heat shock. Belongs to the ClpX chaperone family. HslU subfamily. +Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Constitutes, with BamD, the core component of the assembly machinery. Part of the Bam complex, which is composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. Belongs to the BamA family. +D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 6/9. Belongs to the imidazoleglycerol-phosphate dehydratase family. +Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. Catalyzes Na(+) transport, most probably coupled to electron transfer from reduced ferredoxin to methanophenazine and heterodisulfide reductase. Involved in heterodisulfide reduction during methanogenesis from acetate. Binds 2 [4Fe-4S] clusters per subunit. The Rnf complex is probably composed of eight subunits, including RnfA, RnfB, RnfC, RnfD, RnfE and RnfG. Deletion of the rnf operon abolishes growth on acetate and ferredoxin:heterodisulfide oxidoreductase-coupled Na(+) transport. Belongs to the 4Fe4S bacterial-type ferredoxin family. RnfC subfamily. +Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate. (2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate + CO2 + NADH Binds 1 Mg(2+) or Mn(2+) ion per subunit. Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4. Homodimer. Belongs to the isocitrate and isopropylmalate dehydrogenases family. LeuB type 1 subfamily. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Antiporter transporting nucleotide sugars such as UDP-N-acetylglucosamine (UDP-GlcNAc), UDP-glucose (UDP-Glc) and GDP-mannose (GDP-Man) pooled in the cytosol into the lumen of the Golgi in exchange for the corresponding nucleosides monophosphates (UMP for UDP-sugars and GMP for GDP-sugars). May take part in heparan sulfate synthesis by supplying UDP-Glc-NAc, the donor substrate, and thus be involved in growth factor signaling. Highly expressed in heart, kidney, small intestine, placenta, lung and peripheral blood leukocyte. Weakly expressed in skeletal muscle and spleen. Not expressed in brain, colon and thymus. Belongs to the TPT transporter family. SLC35D subfamily. +Acts as a phosphoinositide 5- and phosphoinositide 6-phosphatase and regulates cellular levels of inositol pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) (PubMed:9472008). Also acts as a 2,3-bisphosphoglycerate 3-phosphatase, by mediating the dephosphorylation of 2,3-bisphosphoglycerate (2,3-BPG) to produce phospho-D-glycerate without formation of 3-phosphoglycerate (By similarity). May play a role in bone development (endochondral ossification) (By similarity). May play a role in the transition of chondrocytes from proliferation to hypertrophy (PubMed:8660956, PubMed:9472008). myo-inositol hexakisphosphate + H2O = myo-inositol pentakisphosphate (mixed isomers) + phosphate. (2R)-2,3-bisphosphoglycerate + H2O = (2R)-2-phosphoglycerate + phosphate Optimum pH is 4.5-7.5. Present in growth plate chondrocytes but not detectable in articular chondrocytes (at protein level) (PubMed:9472008). Spatially restricted to chondrocytes in the lower portion of the proliferative zone and the upper portion of the hypertrophic zone in the growth plate of long bones (at protein level) (PubMed:9472008). Weakly expressed in kidney, liver, lung, skin and spleen, and not detected in brain, heart and muscle (PubMed:8660956). Repressed by parathyroid hormone-related protein PTHLH/PTHRP. N-glycosylated. Monogastric animals cannot hydrolyze dietary inositol hexakisphosphate (InsP6) which makes up the bulk of organic phosphates in soybean, grains and other plant seeds which are the primary source of animal feed. The high activity of the chicken protein toward InsP6 offers a genetic strategy for improving InsP6 digestion in poultry and reducing the pollution that results from high phosphate content in manure. Belongs to the histidine acid phosphatase family. MINPP1 subfamily. +One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. This subunit is found at the monomer-monomer interface and is required for correct PSII assembly and/or dimerization. PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes. Belongs to the PsbL family. +Plays a central role in integrating RNA silencing and chromatin signals in 21 nt siRNA-dependent DNA methylation on cytosine pathway leading to transcriptional gene silencing of specific sequences. Involved in a chromatin-based RNA silencing pathway that encompasses both post-transcriptional gene silencing (PTGS) (e.g. RDR1, RDR6 and AGO2) and transcriptional gene silencing (TGS) (e.g. siRNA-dependent DNA methylation and histone H3) components. Mediates siRNA accumulation at specific chromatin loci. Binds H3K4me0 through its PHD to enforce low levels of H3K4 methylation and gene silencing at a subset of genomic loci. Interacts with unmethylated histone H3 and AGO2. The interaction with AGO2 in required to direct DNA methylation and silencing. Expressed in seedlings, mostly in the vasculature and shoot apices of young seedlings. The PHD-type zinc finger (599-665) binds to unmethylated histone H3 'Lys-4' (H3K4me0). Silencing-deficiency characterized by a lower siRNA accumulation and a transcriptional up-regulation of specific loci that correlates with a local loss of cytosine methylation on DNA and an increased methylation of histone H3 'Lys-4' (e.g. H3K4me2, H3K4me3) and 'Lys-36' (e.g. H3K36me3). Was originally thought to correspond to three different genes At2g16470, At2g16480 and At2g16485. Was originally thought to correspond to three different genes At2g16470, At2g16480 and At2g16485. Was originally thought to correspond to three different genes At2g16470, At2g16480 and At2g16485. +Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein. apo-[ACP] + CoA = adenosine 3',5'-bisphosphate + H(+) + holo-[ACP] Belongs to the P-Pant transferase superfamily. AcpS family. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Depressant insect beta-toxins cause a transient contraction paralysis followed by a slow flaccid paralysis. They bind voltage-independently at site-4 of sodium channels and shift the voltage of activation toward more negative potentials thereby affecting sodium channel activation and promoting spontaneous and repetitive firing. Aside from typical beta-toxin effects, this toxin also affects the inactivation process and ion selectivity of the insect voltage-gated sodium channel. This toxin is active only on insects (PubMed:15733572). Is active on the insect voltage-gated sodium channel para (PubMed:15733572). In vivo, when injected intraperitoneally, it exhibits analgesic activity, increasing hot plate and tail flick withdrawal latencies in a dose-dependent fashion (PubMed:20619318). This phenomenon might be partly due to an inhibitory mechanism activated by noxious stimuli (PubMed:20619318). Expressed by the venom gland. Has the structural arrangement of an alpha-helix connected to antiparallel beta-sheets by disulfide bonds (CS-alpha/beta). Does not affect the rat brain Nav1.2/SCN2A sodium channel. Belongs to the long (4 C-C) scorpion toxin superfamily. Sodium channel inhibitor family. Beta subfamily. +One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL24 family. +Calcium/calmodulin-dependent protein kinase (PubMed:2835766). Required in nuclear division cycle for progression from G2 to mitosis. Required for hyphal growth (PubMed:8898358). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Activated by Ca(2+)/calmodulin (PubMed:8898358). Binding of calmodulin may relieve intrasteric autoinhibition (Probable). Monomer. The autoinhibitory domain overlaps with the calmodulin binding region and interacts in the inactive folded state with the catalytic domain as a pseudosubstrate. Autophosphorylated in a calcium/calmodulin-dependent manner. Spores arrest with a single nucleus and fail to extend a germ tube. Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. CaMK subfamily. +Condensation of UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. 2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosaminyl 1-phosphate + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine = H(+) + lipid A disaccharide (E. coli) + UDP a lipid X + a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine = a lipid A disaccharide + H(+) + UDP Glycolipid biosynthesis; lipid IV(A) biosynthesis; lipid IV(A) from (3R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] and UDP-N-acetyl-alpha-D-glucosamine: step 5/6. Belongs to the LpxB family. +Forms non-fusogenic complexes with SNAP25 and STX1A and may thereby modulate the formation of functional SNARE complexes and exocytosis. Part of a ternary complex containing SNAP25 and STX1A that can be dissociated by NAPA and NSF. Interacts with STX4A (By similarity). +Belongs to the bacterial ribosomal protein bS16 family. +5-phospho-beta-D-ribosylamine + ATP + glycine = ADP + H(+) + N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate Binds 1 Mg(2+) or Mn(2+) ion per subunit. Purine metabolism; IMP biosynthesis via de novo pathway; N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-diphosphate: step 2/2. Belongs to the GARS family. +Catalyzes the oxidation of cytokinins, a family of N(6)-substituted adenine derivatives that are plant hormones, where the substituent is an isopentenyl group. A + H2O + N(6)-dimethylallyladenine = 3-methyl-2-butenal + adenine + AH2 Very weak expression in the young shoot tissues around two weeks after germination (PubMed:14555694). Present in the center of the floral meristem and the boundary between long stamen primordia and gynoecial primordia (PubMed:26390296). Regulated by GATA18/HAN. Belongs to the oxygen-dependent FAD-linked oxidoreductase family. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) Belongs to the class-I aminoacyl-tRNA synthetase family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. Belongs to the lyase 1 family. Argininosuccinate lyase subfamily. +Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + dUMP = 7,8-dihydrofolate + dTMP Pyrimidine metabolism; dTTP biosynthesis. Homodimer. Belongs to the thymidylate synthase family. Bacterial-type ThyA subfamily. +RNA-dependent RNA polymerase which is responsible for replication and transcription of virus RNA segments. The transcription of viral mRNAs occurs by a unique mechanism called cap-snatching. 5' methylated caps of cellular mRNAs are cleaved after 10-13 nucleotides by PA. In turn, these short capped RNAs are used as primers by PB1 for transcription of viral mRNAs. During virus replication, PB1 initiates RNA synthesis and copy vRNA into complementary RNA (cRNA) which in turn serves as a template for the production of more vRNAs. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Influenza RNA polymerase is composed of three subunits: PB1, PB2 and PA. Interacts (via N-terminus) with PA (via C-terminus). Interacts (via C-terminus) with PB2 (via N-terminus); this interaction is essential for transcription initiation. Phosphorylated by host PRKCA. Belongs to the influenza viruses polymerase PB1 family. +Catalyzes the conversion of heme O to heme A by two successive hydroxylations of the methyl group at C8. The first hydroxylation forms heme I, the second hydroxylation results in an unstable dihydroxymethyl group, which spontaneously dehydrates, resulting in the formyl group of heme A. 2 A + Fe(II)-heme o + H2O = 2 AH2 + Fe(II)-heme a Porphyrin-containing compound metabolism; heme A biosynthesis; heme A from heme O: step 1/1. Interacts with CtaB. Belongs to the COX15/CtaA family. Type 2 subfamily. +Gating-modifier toxin that inhibits mammalian and insect voltage-gated sodium channels. It shifts the voltage dependence of channel activation to more positive voltages. It shows potent activity on Nav1.4/SCN4A (IC(50)=103 nM), Nav1.5/SCN5A (IC(50)=268 nM) and Para/DmNav1 (IC(50)=555 nM) and lower activities on Nav1.2/SCN2A (IC(50)=1447 nM) and Nav1.6/SCN8A (IC(50)=3504 nM) (PubMed:25352595). In addition, at a concentration of 1 uM, the toxin inhibits 90-100% of sodium current through Nav1.2/SCN2A, Nav1.4/SCN4A, Nav1.5/SCN5A, Nav1.6/SCN8A and Para/DmNav1 channels, when the voltage of maximal activation of the channel in control conditions is applied (Ref.1). It binds to the S3-S4 helix-loop-helix motif in the voltage-sensing domain of repeat 1 (shown on hNav1.4/SCN4A) (PubMed:29636418). The toxin is amphiphilic and binds to both neutral and negatively charged lipid vesicles with high affinity (PubMed:29636418, PubMed:25352595). The hydrophobic face lies on the opposite side to the hydrophobic faces of classical gating modifiers (PubMed:25352595). Expressed by the venom gland. The presence of a 'disulfide through disulfide knot' structurally defines this protein as a knottin. May be interesting for the development of therapies to treat the periodic paralysis hypokalemic 2 (HOKPP2), since it inhibits I(GP) leak currents of HOKPP2 p.R222G/W channels. Does not inhibit Nav1.1/SCN1A, Nav1.3/SCN3A and Nav1.8/SCN10A sodium channels, Kv1.1/KCNA1, Kv1.3/KCNA3, Kv2.1/KCNB1, Kv4.2/KCND2 and Kv10.1/KCNH1 potassium channels and Cav3.3/CACNA1I calcium channels when 1 uM is tested. Belongs to the neurotoxin 07 (Beta/delta-agtx) family. +Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). adenosine(37) in tRNA + dimethylallyl diphosphate = diphosphate + N(6)-dimethylallyladenosine(37) in tRNA Monomer. Belongs to the IPP transferase family. +The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. an N-acyl-L-alpha-aminoacyl-tRNA + H2O = a tRNA + an N-acyl-L-amino acid + H(+) Monomer. Belongs to the PTH family. +DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) Binds 1 Mg(2+) ion per subunit. Binds 2 Zn(2+) ions per subunit. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase beta' chain family. +Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Can be acetylated to form H2BK6ac and H2BK33ac. Monoubiquitinated to form H2BK143ub1; may give a specific tag for epigenetic transcriptional activation. Phosphorylation of H2B was not detected. Belongs to the histone H2B family. To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BK6ac = acetylated Lys-7; H2BK33ac = acetylated Lys-27; H2BK143ub1 = monoubiquitinated Lys-134. +Acyl-CoA ligase; part of the siderophore biosynthetic pathway (PubMed:22106303). Aspergillus fumigatus produces 4 types of siderophores, low-molecular-mass iron chelators, including excreted fusarinine C (FsC) and triacetylfusarinine C (TAFC) for iron uptake and intacellular ferricrocin (FC) for hyphal and hydroxyferricrocin (HFC) for conidial iron distribution and storage. TAFC consists of 3 N(2)-acetyl-N(5)-anhydromevalonyl-N(5)-hydroxyornithine residues cyclically linked by ester bonds; FC is a cyclic hexapeptide with the structure Gly-Ser-Gly-(N(5)-acetyl-N(5)-hydroxyornithine)x3. The biosynthesis of all four siderophores depends on the hydroxylation of ornithine, catalyzed by the monooxygenase sidA (PubMed:15504822, PubMed:16113265). Subsequently, the pathways for biosynthesis of extra- and intracellular siderophores split (PubMed:17845073). For biosynthesis of extracellular siderophores, the transacylase sidF transfers anhydromevalonyl to N(5)-hydroxyornithine (PubMed:17845073). The required anhydromevalonyl-CoA moiety is derived from mevalonate by CoA ligation and dehydration catalyzed by sidI and sidH respectively (PubMed:22106303). The acetylation of N(5)-hydroxyornithine for FC biosynthesis involves the constitutively expressed sidL (PubMed:21622789). FC is hydroxylated to HFC by an as yet uncharacterized enzyme during conidiation (PubMed:17845073). Assembly of fusarinine C (FsC) and FC is catalyzed by two different nonribosomal peptide synthetases (NRPS), sidD and sidC respectively (PubMed:17845073). Subsequently, sidG catalyzes N2-acetylation of FsC for forming TAFC (PubMed:17845073). Both extra- and intracellular siderophores are crucial for growth during iron limitation and virulence (PubMed:16113265). Siderophore biosynthesis. Targeted to peroxisomes via its PTS2-type peroxisomal targeting signal and the corresponding receptor pexG (PubMed:23617799). Blocks TAFC biosynthesis, decreases resistance to oxidative stress, and attenuates virulence in a murine model of invasive pulmonary aspergillosis (PubMed:22106303). Belongs to the ATP-dependent AMP-binding enzyme family. +Secreted cytokine-like protein. Inhibits cell growth in vitro. Homodimer; disulfide-linked. Highly expressed in lung and prostate (PubMed:11481438). Also found in mammary gland, spleen, pancreas, testis and liver (PubMed:11481438). Detected throughout the airway epithelium in lung, with highest expression in large airways (PubMed:12406855). Found in lung submucosal glands where it localizes to acinar and ductile cells (PubMed:12406855). Not detected in respiratory bronchioles, alveolar ducts or alveolar epithelium (PubMed:12406855). In mammary gland, specifically localizes to luminal epithelial cells (PubMed:11481438). Belongs to the secretoglobin family. UGRP subfamily. +Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC8 binds to ARE-containing RNAs. Component of the RNA exosome complex (PubMed:29906447). Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which is believed to associate with catalytic subunits EXOSC10, and DIS3 or DIS3L in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits specifically containing the heterodimers EXOSC4-EXOSC9, EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and peripheral S1 domain-containing components EXOSC1, EXOSC2 and EXOSC3 located on the top of the ring structure. Binds outer membrane protein opap from Neisseria gonorrhoeae. The disease is caused by variants affecting the gene represented in this entry. EXOSC8 dysfunction causes myelin disruption through an imbalanced supply of myelin proteins due to dysregulation of their ARE-containing mRNAs (PubMed:24989451). Belongs to the RNase PH family. The six exosome core subunits containing a RNase PH-domain are not phosphorolytically active. +Component of NMDA receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Channel activation requires binding of the neurotransmitter glutamate to the epsilon subunit, glycine binding to the zeta subunit, plus membrane depolarization to eliminate channel inhibition by Mg(2+) (PubMed:16214956, PubMed:19524674, PubMed:21677647, PubMed:25008524, PubMed:26912815, PubMed:27135925, Ref.11, PubMed:28232581). Sensitivity to glutamate and channel kinetics depend on the subunit composition (Probable). Channel activity is modulated by zinc ions. The activity of the heterotetramer with grin2b is stimulated by micromolar levels of Zn(2+) (PubMed:19524674). The activity of the heterotetramer with grin2a is inhibited by nanomolar levels of Zn(2+) (Ref.11). Heterotetramer (PubMed:27062927). Forms heterotetrameric channels composed of two zeta subunits (grin1), and two epsilon subunits (grin2a, grin2b, grin2c or grin2d) (in vitro) (PubMed:16214956, PubMed:19524674, PubMed:21677647, PubMed:25008524, PubMed:26912815, PubMed:27135925, Ref.11, PubMed:28232581). Does not form functional channels by itself (PubMed:16214956). In vivo, the subunit composition may depend on the expression levels of the different subunits (Probable). A hydrophobic region that gives rise to the prediction of a transmembrane span does not cross the membrane, but is part of a discontinuously helical region that dips into the membrane and is probably part of the pore and of the selectivity filter. Belongs to the glutamate-gated ion channel (TC 1.A.10.1) family. NR1/GRIN1 subfamily. +Has a major role in enamel formation (PubMed:15235027). Required during the maturation stage of tooth development for clearance of enamel proteins and normal structural patterning of the crystalline matrix (By similarity). Expressed in prostate. N-glycosylated. The N-glycan structures are of complex diantennary or triantennary type, which may be further modified with up to 2 sialic acid residues. The disease is caused by variants affecting the gene represented in this entry. Belongs to the peptidase S1 family. Kallikrein subfamily. +May have a role in chylomicrons and VLDL secretion and catabolism. Required for efficient activation of lipoprotein lipase by ApoC-II; potent activator of LCAT. Apoa-IV is a major component of HDL and chylomicrons (By similarity). Homodimer. Secreted in plasma. Nine of the thirteen 22-amino acid tandem repeats (each 22-mer is actually a tandem array of two, A and B, related 11-mers) occurring in this sequence are predicted to be highly alpha-helical, and many of these helices are amphipathic. They may therefore serve as lipid-binding domains with lecithin:cholesterol acyltransferase (LCAT) activating abilities (By similarity). Belongs to the apolipoprotein A1/A4/E family. +Cell wall formation. NADP(+) + UDP-N-acetyl-alpha-D-muramate = H(+) + NADPH + UDP-N-acetyl-3-O-(1-carboxyvinyl)-alpha-D-glucosamine Cell wall biogenesis; peptidoglycan biosynthesis. Monomer. Belongs to the MurB family. +Belongs to the RemA family. +Required for proper progression of late cytokinetic stages. Interacts with RASGEF1B. Colocalizes with gamma-tubulin at interphase, prophase, metaphase, and anaphase. Relocates from centrosome to midbody at telophase (By similarity). Belongs to the CCDC124 family. +One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly. Belongs to the IF-1 family. +Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr) Homodimer. Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. +Hydrolyzes the cell wall of L.lactis and M.lysodeikticus. Required for cell separation during growth. Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins. The LysM domains are thought to be involved in peptidoglycan binding. Belongs to the glycosyl hydrolase 73 family. +ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. +Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine tRNA modification; N(7)-methylguanine-tRNA biosynthesis. Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family. +Belongs to the bacterial ribosomal protein bL28 family. +May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. +Probably involved in ribonucleotide reductase function. Belongs to the NrdI family. +Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) In cyanobacteria the RNAP catalytic core is composed of 2 alpha, 1 beta, 1 beta', 1 gamma and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Belongs to the RNA polymerase subunit omega family. +Involved in the positive regulation of oligodendrocyte differentiation during postnatal growth (PubMed:24481677). Involved in the morphogenesis of basket cells in the somatosensory cortex during embryogenesis. Involved in dendritic arborization, morphogenesis of spine density dendrite, and establishment of postsynaptic dendrite density in cortical pyramidal neurons (By similarity). Involved in the regulation of neurogenesis. Negatively regulates neurite outgrowth. Involved in homologous recombination (HR) repair pathway. Required for proper resolution of DNA double-strand breaks (DSBs) by HR. Is required for recovery of stalled replication forks, and directly contributes to genomic stability. Interacts with PARP1 and mediates MRE11-dependent DNA end resection during replication fork recovery. Contributes to genomic stability by preventing telomere dysfunction (By similarity). Homodimers. Interacts with NDE1 and NDEL1 (By similarity). Interacts with DISC1 (PubMed:17389905). Interacts with PARP1 (By similarity). Expressed in cerebral cortex, hippocampus, olfactory tubercle and striatum. +Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex. Belongs to the universal ribosomal protein uL10 family. +May play an important role in regulating the switch between different pathways for energy production during spermiogenesis and in the spermatozoon. Required for sperm motility and male fertility (By similarity). D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5. Homotetramer. The testis-specific N-terminal extension mediates tight association with the cytoskeletal fibrous sheath of the spermatozoa flagellum, possibly via interchain disulfide-bonding of Cys-21 with sheath components. Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. +Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Belongs to the universal ribosomal protein uS19 family. +Secreted subtilisin-like serine protease with keratinolytic activity that contributes to pathogenicity. Belongs to the peptidase S8 family. +RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion (PubMed:11118435). Binds preferentially to the 5'-[AU]UAAA-3' motif in vitro. Binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. Binds poly(A). RNA-binding abilities are down-regulated by tyrosine kinase PTK6 (By similarity). Involved in splice site selection of vascular endothelial growth factor. In vitro regulates CD44 alternative splicing by direct binding to purine-rich exonic enhancer (PubMed:11118435). Can regulate alternative splicing of neurexins NRXN1-3 in the laminin G-like domain 6 containing the evolutionary conserved neurexin alternative spliced segment 4 (AS4) involved in neurexin selective targeting to postsynaptic partners such as neuroligins and LRRTM family members. Targeted, cell-type specific splicing regulation of NRXN1 at AS4 is involved in neuronal glutamatergic synapse function and plasticity. May regulate expression of KHDRBS2/SLIM-1 in defined brain neuron populations by modifying its alternative splicing. Can bind FABP9 mRNA (By similarity). May play a role as a negative regulator of cell growth. Inhibits cell proliferation (By similarity). Self-associates to form homooligomers; dimerization increases RNA affinity (By similarity). Interacts with KHDRBS1/SAM68 and KHDRBS2/SLM-1; heterooligomer formation of KHDRBS family proteins may modulate RNA substrate specificity (PubMed:15345239). Interacts with the splicing regulatory proteins SFRS9, SAFB and YTHDC1. Interacts with HNRPL (PubMed:11118435). Interacts with RBMX, RBMY1A1, p85 subunit of PI3-kinase, SERPINB5 (By similarity). Ubiquitous. Highly expressed in brain, heart, testis and in Sertoli cells at all stages of spermatogenesis. Expressed in neurons. Detected in cortical layers of the forebrain and in the CA1 to CA4 regions of the hippocampus. The proline-rich site binds the SH3 domain of the p85 subunit of PI3-kinase. Phosphorylated on tyrosine residues. Belongs to the KHDRBS family. +(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5. Monomer. Belongs to the phosphoglycerate kinase family. +Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin. (2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2 H2O + phosphate Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Belongs to the DMRL synthase family. +Involved in the TCA cycle. FumC seems to be a backup enzyme for FumA under conditions of iron limitation and oxidative stress (PubMed:7592392). Catalyzes the stereospecific interconversion of fumarate to L-malate (PubMed:1917897, PubMed:3282546). (S)-malate = fumarate + H2O Inhibited by ATP, citrate and S-2,3-dicarboxyaziridine. kcat is 1149 sec(-1) for fumarate (at pH 7.9). kcat is 595.2 sec(-1) for S-malate (at pH 7.9). Optimum pH is 8. Thermostable. Carbohydrate metabolism; tricarboxylic acid cycle; (S)-malate from fumarate: step 1/1. Homotetramer. Under conditions of iron limitation and oxidative stress. Cells lacking this gene show an increase of biofilm formation. There are 2 substrate-binding sites: the catalytic A site, and the non-catalytic B site that may play a role in the transfer of substrate or product between the active site and the solvent. Alternatively, the B site may bind allosteric effectors. Belongs to the class-II fumarase/aspartase family. Fumarase subfamily. +Involved in DNA repair and in homologous recombination. May regulate the cleavage reactions of the branch-structured DNA. Has a very weak ATPase activity that is not stimulated by DNA. Binds DNA but does not promote DNA strands exchange (By similarity). Belongs to the eukaryotic RecA-like protein family. RadB subfamily. +Cell wall formation. ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) + phosphate Binds 2 magnesium or manganese ions per subunit. Cell wall biogenesis; peptidoglycan biosynthesis. Belongs to the D-alanine--D-alanine ligase family. +Belongs to the major facilitator superfamily. TsgA family. +ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) + L-phenylalanyl-tRNA(Phe) Binds 2 magnesium ions per tetramer. Tetramer of two alpha and two beta subunits. Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. +Receptor for neuromedin-B (By similarity). Contributes to the maintenance of basal sigh rate through signaling in the pre-Botzinger complex, a cluster of several thousand neurons in the ventrolateral medulla responsible for inspiration during respiratory activity (By similarity). Contributes to the induction of sneezing following exposure to chemical irritants or allergens which causes release of NMB by nasal sensory neurons and activation of NMBR-expressing neurons in the sneeze-evoking region of the brainstem (By similarity). These in turn activate neurons of the caudal ventral respiratory group, giving rise to the sneezing response (By similarity). Contributes to induction of acute itch, possibly through its activation on dorsal root ganglion neurons by the NMB peptide (By similarity). Plays a role in the innate immune response to influenza A virus infection by enhancing interferon alpha expression and reducing expression of IL6 (By similarity). Plays a role in CSF1-induced proliferation of osteoclast precursors by contributing to the positive regulation of the expression of the CSF1 receptor CSF1R (By similarity). Highly expressed in peripheral tissues where it is detected in the respiratory system, circulatory system, digestive system, urogenital system, lymphatic organs and endocrine system (at protein level) (PubMed:27010315). In the testis, expressed mainly in Leydig cells (at protein level) (PubMed:29632025). During the sow estrus cycle, highest levels are found in the hypothalamus at proestrus and estrus with a significant drop at metestrus and an increase at diestrus. In the pituitary gland, expression increases from proestrus to estrus, drops at metestrus and increases at diestrus. In the ovary, expression increases from proestrus to estrus, drops at metestrus and remains at a similar level at diestrus. During boar postnatal development, expression peaks in the hypothalamus at day 30 and decreases thereafter. In the pituitary gland, expression peaks at day 60, drops slightly at day 90 and increases again at day 120. In the testis, expression drops from day 3 to day 30 with peak levels at day 90 and a decrease at day 120. Belongs to the G-protein coupled receptor 1 family. +Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity. a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) Belongs to the DNA polymerase type-C family. PolC subfamily. +Belongs to the bacterial ribosomal protein bS16 family. +S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Truncated N-terminus. Truncated N-terminus. Truncated N-terminus. +Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones. Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines. 2 a quinone + H(+) + NADH = 2 a 1,4-benzosemiquinone + NAD(+) anthranilate + N,N-dimethyl-1,4-phenylenediamine + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 H(+) + 2 NADH Binds 1 FMN per subunit. Homodimer. Belongs to the azoreductase type 1 family. +Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. ATP + cytidine(34) in tRNA(Ile2) + L-lysine = AMP + diphosphate + H(+) + lysidine(34) in tRNA(Ile2) The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a P-loop motif involved in ATP binding. Belongs to the tRNA(Ile)-lysidine synthase family. +Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis: the synthesis of acetylglutamate from glutamate and acetyl-CoA, and of ornithine by transacetylation between acetylornithine and glutamate. L-glutamate + N(2)-acetyl-L-ornithine = L-ornithine + N-acetyl-L-glutamate acetyl-CoA + L-glutamate = CoA + H(+) + N-acetyl-L-glutamate Amino-acid biosynthesis; L-arginine biosynthesis; L-ornithine and N-acetyl-L-glutamate from L-glutamate and N(2)-acetyl-L-ornithine (cyclic): step 1/1. Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 1/4. Heterodimer of an alpha and a beta chain. The alpha and beta chains are autoproteolytically processed from a single precursor protein within the mitochondrion. This protein may be expected to contain an N-terminal transit peptide but none has been predicted. Belongs to the ArgJ family. +May be a serine protease inhibitor (By similarity). Essential for sperm maturation and fertility. Inhibits sperm acrosome reaction, protecting sperm from premature reaction. Secreted into the lumen of the initial segment of the epididymis and binds to sperm. In the initial segment of epididymis, localizes on the dorsal surface of the acrosomal region of sperm, gradually becomes more restricted to the acrosomal region in spermatozoa during epididymal transit. Restricted to the epididymis, with highest levels in the initial segment, including epithelial cells, lumen, and sperm (at protein level). Localizes to the sperm heads, where it is restricted to the acrosomal region in epididymal spermatozoa, but not in testicular spermatozoa (at protein level). First expressed at low levels at P15 in the epididymis. Expression increases from P30 onward. Reaches its highest level at P120 and remains at a stable level in mature animals. Up-regulated by testosterone. +Converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate, the first intermediate in the biosynthesis of coenzyme methanopterin. GTP + H2O = 7,8-dihydroneopterin 2',3'-cyclic phosphate + diphosphate + formate + H(+) Binds 1 Fe(2+) ion per subunit. Cofactor biosynthesis; 5,6,7,8-tetrahydromethanopterin biosynthesis. Homodimer. Belongs to the GTP cyclohydrolase IV family. +The glycine cleavage system catalyzes the degradation of glycine. (6S)-5,6,7,8-tetrahydrofolate + (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[protein] = (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + NH4(+) The glycine cleavage system is composed of four proteins: P, T, L and H. Belongs to the GcvT family. +Belongs to the universal ribosomal protein uL29 family. +Toll-related receptor which binds to the neurotrophin spz5 (PubMed:10973475, PubMed:23892553). Functions in olfactory circuit assembly by promoting synaptic partner matching between olfactory receptor neurons (ORN) axons and projection neurons (PN) dendrites partners in the antennal lobe (PubMed:25741726). Involved in the targeting of specific classes of PN dendrites (Va1d, Va1v, DC3 and DA1) (PubMed:25741726). Functions with Toll-7 to regulate motor axon targeting and neuronal survival in the central nervous system (CNS) (PubMed:23892553). Possibly functions with 18w and Toll-8 during convergent extension, to help direct proper planar cell polarity, cell intercalation and axis elongation (PubMed:25363762). Promotes heterophilic cell adhesion with 18w in vitro (PubMed:25363762). May be an upstream component of the NF-kappa-B (rel) regulatory cascade (PubMed:23892553). Expressed 48 hours after puparium formation in lateral glomeruli in the anterior and central regions of the antennal lobe, including the DA1, VA1d, VA1v, DC3. DC1, DA4l and DA4m glomeruli (at protein level) (PubMed:25741726). Expressed zygotically (PubMed:12617819). High levels of expression in embryos and pupae, and relatively low levels of expression in larvae and adults (PubMed:10973475). At cellular blastoderm stage, expressed as several segmentally separated stripes, with the anterior stripes appearing first (PubMed:12617819). At germ band extension, strongly expressed in the delaminating neuroblasts (PubMed:12617819). Expression decreases at germ band extension, remaining in a specific subset of neurons in the central nervous system (PubMed:12617819). Expressed in 6 segmentally repeated stripes in the germband (PubMed:25363762). In larvae, detected in the fat body (PubMed:12617819). In larvae, expressed in the optic lobes and the ventral nerve cord of the CNS (PubMed:23892553). Expressed 48 hours after puparium formation in ORN axons and PN dendrites that target to largely overlaping glomeruli (PubMed:25741726). Viable (PubMed:25741726). Dorsomedial or dorsolateral mistargeting of VA1d ORN axons (PubMed:25741726). No effect on the immune response to septic injury using a mixture of Gram-positive and Gram-negative bacteria; adult flies are able induce expression of antibacterial peptide genes (Drs, AttA, DptA and Mtk) and mount a proper innate immune response (PubMed:21158756). Belongs to the Toll-like receptor family. In some plant proteins and in human SARM1, the TIR domain has NAD(+) hydrolase (NADase) activity (By similarity). However, despite the presence of the catalytic Asp residue, the isolated TIR domain of human TLR4 lacks NADase activity (By similarity). Based on this, it is unlikely that Toll-like receptors have NADase activity. +Precursor of a cytotoxin that targets and disrupts the colonic epithelium, inducing the host inflammatory and innate immune responses and resulting in diarrhea and pseudomembranous colitis. TcdB constitutes the main toxin that mediates the pathology of C.difficile infection, an opportunistic pathogen that colonizes the colon when the normal gut microbiome is disrupted. Compared to TcdA, TcdB is more virulent and more important for inducing the host inflammatory and innate immune responses. This form constitutes the precursor of the toxin: it enters into host cells and mediates autoprocessing to release the active toxin (Glucosyltransferase TcdB) into the host cytosol. Targets colonic epithelia by binding to the frizzled receptors FZD1, FZD2 and FZD7, and enters host cells via clathrin-mediated endocytosis. Frizzled receptors constitute the major host receptors in the colonic epithelium, but other receptors, such as CSPG4 or NECTIN3/PVRL3, have been identified (By similarity). Binding to carbohydrates and sulfated glycosaminoglycans on host cell surface also contribute to entry into cells (By similarity). Once entered into host cells, acidification in the endosome promotes the membrane insertion of the translocation region and formation of a pore, leading to translocation of the GT44 and peptidase C80 domains across the endosomal membrane. This activates the peptidase C80 domain and autocatalytic processing, releasing the N-terminal part (Glucosyltransferase TcdB), which constitutes the active part of the toxin, in the cytosol (By similarity). Active form of the toxin, which is released into the host cytosol following autoprocessing and inactivates small GTPases. Acts by mediating monoglucosylation of small GTPases of the Rho family (Rac1, RhoA, RhoB, RhoC, RhoG and Cdc42) in host cells at the conserved threonine residue located in the switch I region ('Thr-37/35'), using UDP-alpha-D-glucose as the sugar donor. Monoglucosylation of host small GTPases completely prevents the recognition of the downstream effector, blocking the GTPases in their inactive form, leading to actin cytoskeleton disruption and cell death, resulting in the loss of colonic epithelial barrier function. L-threonyl-[protein] + UDP-alpha-D-glucose = 3-O-(alpha-D-glucosyl)-L-threonyl-[protein] + H(+) + UDP Binds 1 Zn(2+) ion per subunit. Zn(2+) is required for autocatalytic cleavage. Has higher activity with Mn(2+), but most likely uses Mg(2+) in host cells. Mn(2+) or Mg(2+) are required for glucosyltransferase activity. Protease activity is activated upon binding to 1D-myo-inositol hexakisphosphate (InsP6), which induces conformational reorganization. Interacts with host FZD1. Interacts with host FZD2; interaction promotes toxin entry into host cell and occupies the binding site for Wnt-adducted palmitoleate in FZD2, leading to prevent Wnt-binding and downstream Wnt signaling. Interacts with host FZD7. Interacts with host CSPG4. Interacts with host NECTIN3/PVRL3. Secreted from C.difficile cell into the extracellular environment via help of holin-like protein TcdE/UtxA. Binds to the cell surface receptors via the receptor-binding region and enters the cells via clathrin-mediated endocytosis. Acidification in the endosome triggers conformational changes that promote the membrane insertion of the translocation region, allowing formation of a pore, leading to translocation of the GT44 and peptidase C80 domains across the endosomal membrane. 1D-myo-inositol hexakisphosphate-binding (InsP6) activates the peptidase C80 domain and autoprocessing, generating the Glucosyltransferase TcdB form, which is released in the host cytosol. Binding to phospholipids, such as phosphatidylserine and phosphatidic acid promotes localization to the inner face of the cell membrane close to its membrane anchored substrates (small GTPases). Consists of 4 functional domains: (1) the N-terminal GT44 domain (glucosyltransferase, also named GTD), which mediates glucosylation of host small GTPases, (2) an autoprocessing region that catalyzes autoprocessing to release the N-terminal GT44 domain in the host cytosol, (3) the translocation region that forms a pore to promote translocation of the GT44 and peptidase C80 domains across the endosomal membrane and (4) the receptor-binding (CROPS) region that mediates binding to host cells and contribute to entry into cells. The receptor-binding (CROPS) region is dynamic and can have open and closed conformations depending of the pH: has an open conformation at endosomal pH and a closed conformation at neutral pH. The cell wall-binding repeats bind carbohydrates, probably contributing to entry into cells. The four-helical bundle region mediates binding to phospholipids, such as phosphatidylserine and phosphatidic acid (By similarity). This promotes localization to the inner face of the cell membrane close to small GTPases (By similarity). Undergoes autocatalytic cleavage to release the N-terminal part (Glucosyltransferase TcdB), which constitutes the active part of the toxin, in the host cytosol (PubMed:15632438). 1D-myo-inositol hexakisphosphate-binding (InsP6) activates the peptidase C80 domain and promotes autoprocessing (By similarity). Belongs to the clostridial glucosylating toxin (LCGT) family. +Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates. ATP + H2O + L-glutamine + UTP = ADP + CTP + 2 H(+) + L-glutamate + phosphate H2O + L-glutamine = L-glutamate + NH4(+) ATP + NH4(+) + UTP = ADP + CTP + 2 H(+) + phosphate Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition. Pyrimidine metabolism; CTP biosynthesis via de novo pathway; CTP from UDP: step 2/2. Homotetramer. CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor. Belongs to the CTP synthase family. +F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has four main subunits: a(1), b(1), b'(1) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta, b and b' chains. In plastids the F-type ATPase is also known as CF(1)CF(0). Belongs to the ATPase B chain family. +Relaxes both positive and negative superturns and exhibits a strong decatenase activity. ATP-dependent breakage, passage and rejoining of double-stranded DNA. Homodimer. Heterotetramer of two Top6A and two Top6B chains. Belongs to the TOP6A family. +Involved in transcription regulation induced by nuclear receptors, including in T3 thyroid hormone and all-trans retinoic acid pathways. Might promote the nuclear localization of the receptors (By similarity). Likely involved in the processes that promote cell division prior to the formation of differentiated tissues. Interacts with CH-TOG and YEATS4. Interacts with the AURKA and AURKB and AURKC. Interacts with LSM7, TDRD7 and SNRPG. Interacts with GCN5L2 and PCAF (By similarity). Interacts with the thyroid hormone receptors THRB and THRA, predominantly with isoform alpha-2. The interaction with THRA isoform alpha-1 and THRB is decreased in the presence of thyroid hormone T3 (PubMed:20078863). Interacts with RARA in the nucleus (PubMed:20078863). Also interacts with other nuclear receptors, including ESR1, NR3C1, PPARG and RXRA, preferentially in the absence of their hormonal ligands (By similarity). Nucleus during interphase. Weakly concentrated at centrosomes during mitosis and colocalizes with AURKC at the midbody during cytokinesis. Belongs to the TACC family. +Possible formation of a ternary complex RavA-ViaA-CadA. Belongs to the ViaA family. +Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. +The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. ATP + H2O = ADP + H(+) + phosphate Forms a complex with RuvB. Belongs to the RuvA family. +alpha-D-xylose = alpha-D-xylulofuranose Binds 2 magnesium ions per subunit. Homotetramer. Belongs to the xylose isomerase family. +Catalyzes the phosphorylation of ribose 1,5-bisphosphate to 5-phospho-D-ribosyl alpha-1-diphosphate (PRPP). alpha-D-ribose 1,5-bisphosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + ADP Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate biosynthesis; 5-phospho-alpha-D-ribose 1-diphosphate from D-ribose 5-phosphate (route II): step 3/3. Belongs to the ribose 1,5-bisphosphokinase family. +(S)-4-amino-5-oxopentanoate = 5-aminolevulinate Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2. Homodimer. Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily. +This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a 'molecular matchmaker', a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex. Belongs to the DNA mismatch repair MutL/HexB family. +Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS. ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro) Homodimer. Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain. Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily. +Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. Belongs to the bacterial ribosomal protein bL20 family. +Highly specific phosphatase involved in the metabolism of ADP-ribose 1''-phosphate (Appr1p) which is produced as a consequence of tRNA splicing. ADP-beta-D-ribose 1''-phosphate + H2O = ADP-D-ribose + phosphate Belongs to the POA1 family. +Alpha-conotoxins act on postsynaptic membranes, they bind to the nicotinic acetylcholine receptors (nAChR) and thus inhibit them. Expressed by the venom duct. The cysteine framework is I (CC-C-C). Alpha4/7 pattern. Exists in 4 forms due to different PTMs (In1907, In1891, In1874, and In1857). Hydroxylation at 'Pro-8' and 'Pro-14' (In1907). Hydroxylation at 'Pro-8' (In1891). Pyrrolidone carboxylic acid at 'Glu-1' and hydroxylation at 'Pro-8' (In1874). Pyrrolidone carboxylic acid at 'Glu-1' (In1857). Belongs to the conotoxin A superfamily. +One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. Part of the 30S ribosomal subunit. Contacts proteins S9 and S11. Belongs to the universal ribosomal protein uS7 family. +May bind long-chain fatty acids, such as palmitate, and may play a role in lipid transport or fatty acid metabolism. +Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide. 6-carboxyhexanoyl-[ACP] + H(+) + L-alanine = (8S)-8-amino-7-oxononanoate + CO2 + holo-[ACP] Cofactor biosynthesis; biotin biosynthesis. Homodimer. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily. +The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + H2O + L-tryptophan Amino-acid biosynthesis; L-tryptophan biosynthesis; L-tryptophan from chorismate: step 5/5. Tetramer of two alpha and two beta chains. Belongs to the TrpA family. +Essential for rapid growth and for sporulation. Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate Binds 2 manganese ions per subunit. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 3/5. Monomer. Belongs to the BPG-independent phosphoglycerate mutase family. +Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate Reduced FMN (FMNH(2)). Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7. Homotetramer. Belongs to the chorismate synthase family. +Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) that is part of the mitochondrial respiratory chain. The b-c1 complex mediates electron transfer from ubiquinol to cytochrome c. Contributes to the generation of a proton gradient across the mitochondrial membrane that is then used for ATP synthesis. Binds 2 heme b groups non-covalently. The cytochrome bc1 complex contains 11 subunits: 3 respiratory subunits (MT-CYB, CYC1 and UQCRFS1), 2 core proteins (UQCRC1 and UQCRC2) and 6 low-molecular weight proteins (UQCRH/QCR6, UQCRB/QCR7, UQCRQ/QCR8, UQCR10/QCR9, UQCR11/QCR10 and a cleavage product of UQCRFS1). This cytochrome bc1 complex then forms a dimer. Heme 1 (or BL or b562) is low-potential and absorbs at about 562 nm, and heme 2 (or BH or b566) is high-potential and absorbs at about 566 nm. Belongs to the cytochrome b family. The full-length protein contains only eight transmembrane helices, not nine as predicted by bioinformatics tools. +Belongs to the UPF0756 family. +Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. Homodimer. Belongs to the YbaB/EbfC family. +Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is transferred onto alpha-ketoisovalerate to form ketopantoate. (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = (6S)-5,6,7,8-tetrahydrofolate + 2-dehydropantoate Binds 1 Mg(2+) ion per subunit. Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-pantoate from 3-methyl-2-oxobutanoate: step 1/2. Homodecamer; pentamer of dimers. Belongs to the PanB family. +NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. Couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient (By similarity). a plastoquinone + (n+1) H(+)(in) + NADH = a plastoquinol + n H(+)(out) + NAD(+) a plastoquinone + (n+1) H(+)(in) + NADPH = a plastoquinol + n H(+)(out) + NADP(+) NDH is composed of at least 16 different subunits, 5 of which are encoded in the nucleus. Belongs to the complex I subunit 6 family. +Involved in strigolactones biosynthesis by catalyzing the isomerization of the C9-C10 double bond in all-trans-beta-carotene leading to 9-cis-beta-carotene and providing the substrate for CCD7 (PubMed:26503135). Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signals that stimulate hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds (PubMed:26503135). all-trans-beta-carotene = 9-cis-beta-carotene Highly expressed in roots (PubMed:22039214). Expressed at low levels in leaves and stems (PubMed:22039214). Induced by phosphate deprivation (PubMed:22039214, PubMed:26503135). Induced by Rhizobium lipo-chitooligosaccharide elicitors (PubMed:26503135). Roots of plants silencing D27 exhibit a strong reduction in strigolactone synthesis. Extended N-terminus. +Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors. Belongs to the bacterial ribosomal protein bL12 family. +Involved in mitochondrial genome encoded proteins translation. Component of the mitochondrial large ribosomal subunit. Belongs to the bacterial ribosomal protein bL27 family. +D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate Carbohydrate biosynthesis; gluconeogenesis. Carbohydrate degradation; glycolysis; D-glyceraldehyde 3-phosphate from glycerone phosphate: step 1/1. Homodimer. Belongs to the triosephosphate isomerase family. +Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding. Monomer. Belongs to the RNase H family. +D-altronate + NAD(+) = H(+) + keto-D-tagaturonate + NADH Carbohydrate metabolism; pentose and glucuronate interconversion. Belongs to the mannitol dehydrogenase family. UxaB subfamily. +Has a role in mitochondrial fission. Has a role in outer membrane fission but not matrix separation (By similarity). The C-terminus is required for mitochondrial localization, while the N-terminus is necessary for mitochondrial fission. Belongs to the FIS1 family. +MROH5 may be both a gene and a pseudogene in the human population, the reference genome corresponding currently to the non-functional allele with a stop codon at position 925. The sequence shown here with a Gln at that position is the one of the functional protein. +It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center (By similarity). This protein binds to the 23S rRNA, and is important in its secondary structure. Part of the 50S ribosomal subunit. Belongs to the universal ribosomal protein uL6 family. +2-(N(omega)-L-arginino)succinate = fumarate + L-arginine acetyl-CoA + L-glutamate = CoA + H(+) + N-acetyl-L-glutamate Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl-L-ornithine from L-glutamate: step 1/4. Amino-acid biosynthesis; L-arginine biosynthesis; L-arginine from L-ornithine and carbamoyl phosphate: step 3/3. In bacteria which possess the bifunctional enzyme ornithine acetyltransferase/N-acetylglutamate synthase (ArgJ), ArgA fulfills an anaplerotic role. In the N-terminal section; belongs to the lyase 1 family. Argininosuccinate lyase subfamily. In the C-terminal section; belongs to the acetyltransferase family. ArgA subfamily. +L-aspartate = D-aspartate Optimum pH is 8. Optimum temperature is 37 degrees Celsius. Homodimer. Belongs to the aspartate/glutamate racemases family. +Methyltransferase required for the conversion of demethylmenaquinol (DMKH2) to menaquinol (MKH2). a 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + H(+) + S-adenosyl-L-homocysteine Quinol/quinone metabolism; menaquinone biosynthesis; menaquinol from 1,4-dihydroxy-2-naphthoate: step 2/2. Belongs to the class I-like SAM-binding methyltransferase superfamily. MenG/UbiE family. +Expressed only in the forespore compartment of sporulating cells. Belongs to the SspN family. +Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins. Belongs to the glycosyl hydrolase 18 family. Chitinase class II subfamily. +Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Binds 1 zinc ion. Belongs to the endoribonuclease YbeY family. +The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. Interacts with UvrB in an incision complex. Belongs to the UvrC family. +Endoplasmic reticulum translocase required to remove mitochondrial transmembrane proteins mistargeted to the endoplasmic reticulum (PubMed:32973005). Acts as a dislocase that mediates the ATP-dependent extraction of mislocalized mitochondrial transmembrane proteins from the endoplasmic reticulum membrane (PubMed:32973005). Specifically binds mitochondrial tail-anchored transmembrane proteins: has an atypically large substrate-binding pocket that recognizes and binds moderately hydrophobic transmembranes with short hydrophilic lumenal domains (PubMed:32973005). [protein]-with a C-terminal TM segment(out) + ATP + H2O = [protein]-with a C-terminal TM segment(in) + ADP + H(+) + phosphate Experimental confirmation may be lacking for some isoforms. Contains a large substrate-binding pocket that recognizes alpha-helical transmembranes, which alternately faces the endoplasmic reticulum lumen and cytosol, while remaining accessible to the lipid bilayer through a lateral opening. The translocase alternates between two conformations: inward-open (E1) and outward-open (E2) states. Undergoes a series of conformational changes with ATP-binding, phosphorylation of the Asp active site and subsequent dephosphorylation in a Post-Albers cycle (i.e., E1 -> E1-ATP -> E1P-ADP -> E1P -> E2P -> E2-Pi -> E1). A substrate transmembrane helix with a short, preferentially positively charged lumenal segment binds to the outward-open pocket and the E2P-to-E1 transition flips the transmembrane by a switch from the outward-open to inward-open conformation. Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type V subfamily. Was initially thought to mediate manganese transport (PubMed:24392018). However, it was later shown to specifically bind moderately hydrophobic transmembrane with short hydrophilic lumenal domains that misinsert into the endoplasmic reticulum (PubMed:32973005). Wrong place - Issue 234 of March 2021 +Essential component of a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited by Ttk88 and probably acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. May serve as a molecular beacon for the recruitment of molecular machinery that imposes silencing across a chromosomal interval. Component of a complex that contains at least HDAC1/Rpd3, CoRest and Su(var)3-3/Hdm. Interacts with neuronal repressor ttk/Ttk88. Present in all of the tissues examined including both glia and neurons of the CNS (at protein level). Expressed ubiquitously in the embryo. In contrast, expression of isoform 3 is highly enriched in the nervous system. Belongs to the CoREST family. Truncated N-terminus. Truncated N-terminus. +Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. ATP + 4 H(+)(in) + H2O = ADP + 5 H(+)(out) + phosphate F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains. Belongs to the ATPase alpha/beta chains family. +Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. (6S)-10-formyltetrahydrofolate + L-methionyl-tRNA(fMet) = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N-formyl-L-methionyl-tRNA(fMet) Belongs to the Fmt family. +Transcription factor that binds the cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3') and displays two biological functions, as regulator of metabolic and redox processes under normal cellular conditions, and as master transcription factor during integrated stress response (ISR) (PubMed:8506317, PubMed:11106749, PubMed:12667446, PubMed:23624402). Binds to asymmetric CRE's as a heterodimer and to palindromic CRE's as a homodimer (PubMed:8506317, PubMed:23624402). Core effector of the ISR, which is required for adaptation to various stress such as endoplasmic reticulum (ER) stress, amino acid starvation, mitochondrial stress or oxidative stress (PubMed:11106749, PubMed:12667446). During ISR, ATF4 translation is induced via an alternative ribosome translation re-initiation mechanism in response to EIF2S1/eIF-2-alpha phosphorylation, and stress-induced ATF4 acts as a master transcription factor of stress-responsive genes in order to promote cell recovery (PubMed:11106749, PubMed:12667446). Promotes the transcription of genes linked to amino acid sufficiency and resistance to oxidative stress to protect cells against metabolic consequences of ER oxidation (PubMed:12667446). Activates the transcription of NLRP1, possibly in concert with other factors in response to ER stress (By similarity). Activates the transcription of asparagine synthetase (ASNS) in response to amino acid deprivation or ER stress (PubMed:15775988, PubMed:21159964). However, when associated with DDIT3/CHOP, the transcriptional activation of the ASNS gene is inhibited in response to amino acid deprivation (By similarity). Together with DDIT3/CHOP, mediates programmed cell death by promoting the expression of genes involved in cellular amino acid metabolic processes, mRNA translation and the terminal unfolded protein response (terminal UPR), a cellular response that elicits programmed cell death when ER stress is prolonged and unresolved (PubMed:23624402). Together with DDIT3/CHOP, activates the transcription of the IRS-regulator TRIB3 and promotes ER stress-induced neuronal cell death by regulating the expression of BBC3/PUMA in response to ER stress (PubMed:15775988, PubMed:17369260, PubMed:21159964). May cooperate with the UPR transcriptional regulator QRICH1 to regulate ER protein homeostasis which is critical for cell viability in response to ER stress (By similarity). In the absence of stress, ATF4 translation is at low levels and it is required for normal metabolic processes such as embryonic lens formation, fetal liver hematopoiesis, bone development and synaptic plasticity (PubMed:10096021, PubMed:10885750, PubMed:11806972, PubMed:12925279, PubMed:15109498, PubMed:22298775). Acts as a regulator of osteoblast differentiation in response to phosphorylation by RPS6KA3/RSK2: phosphorylation in osteoblasts enhances transactivation activity and promotes expression of osteoblast-specific genes and post-transcriptionally regulates the synthesis of Type I collagen, the main constituent of the bone matrix (PubMed:15109498). Cooperates with FOXO1 in osteoblasts to regulate glucose homeostasis through suppression of beta-cell production and decrease in insulin production (PubMed:22298775). Activates transcription of SIRT4 (PubMed:23663782). Regulates the circadian expression of the core clock component PER2 and the serotonin transporter SLC6A4 (PubMed:21768648, PubMed:22572884). Binds in a circadian time-dependent manner to the cAMP response elements (CRE) in the SLC6A4 and PER2 promoters and periodically activates the transcription of these genes (PubMed:21768648, PubMed:22572884). Mainly acts as a transcriptional activator in cellular stress adaptation, but it can also act as a transcriptional repressor: acts as a regulator of synaptic plasticity by repressing transcription, thereby inhibiting induction and maintenance of long-term memory (PubMed:12925279). Regulates synaptic functions via interaction with DISC1 in neurons, which inhibits ATF4 transcription factor activity by disrupting ATF4 dimerization and DNA-binding (PubMed:31444471). Binds DNA as a homodimer and as a heterodimer (PubMed:23624402). Heterodimer; heterodimerizes with CEBPB (PubMed:11018027). Heterodimer; heterodimerizes with DDIT3/CHOP (PubMed:23624402). Interacts with CEP290 (via an N-terminal region) (By similarity). Interacts with NEK6, DAPK2 (isoform 2) and ZIPK/DAPK3 (By similarity). Interacts (via its leucine zipper domain) with GABBR1 and GABBR2 (via their C-termini) (By similarity). Forms a heterodimer with TXLNG in osteoblasts (PubMed:15911876). Interacts (via its DNA binding domain) with FOXO1 (C-terminal half); the interaction occurs in osteoblasts and regulates glucose homeostasis through suppression of beta-cell proliferation and a decrease in insulin production (PubMed:22298775). Interacts with SATB2; the interaction results in enhanced DNA binding and transactivation by these transcription factors (PubMed:16751105). Interacts with ABRAXAS2 (PubMed:22974638). Interacts with TRIB3, inhibiting the transactivation activity of ATF4 (PubMed:17369260). Interacts with DISC1; which inhibits ATF4 transcription factor activity by disrupting ATF4 dimerization and DNA-binding (PubMed:31444471). Interacts with EP300/p300; EP300/p300 stabilizes ATF4 and increases its transcriptional activity independently of its catalytic activity by preventing its ubiquitination (By similarity). Colocalizes with GABBR1 in hippocampal neuron dendritic membranes. Colocalizes with NEK6 in the centrosome (By similarity). Recruited to nuclear speckles following interaction with EP300/p300 (By similarity). Ubiquitously expressed in adults. During embryonic development, expressed at high levels in anterior epithelial lens cells at 14.5 dpc (PubMed:10885750). At 16.5 dpc, expressed in osteoblasts surrounding newly formed trabecular bone (PubMed:19232401). At postnatal day 2, detected in most osteoblasts and lining cells (PubMed:19232401). By postnatal week 4, is detected in fewer osteoblasts, but remains present in lining cells (at protein level) (PubMed:19232401). Regulated at the translational level in response to various stress such as endoplasmic reticulum stress, amino acid starvation or oxidative stress (PubMed:11106749, PubMed:12667446, PubMed:15277680, PubMed:21159964). In the absence of stress, ribosomes re-initiate translation at an inhibitory open reading frame (uORF) upstream of the ATF4 transcript, which precludes AFT4 translation (PubMed:11106749, PubMed:15277680). In response to stress and subsequent EIF2S1/eIF-2-alpha phosphorylation, ribosomes bypass the inhibitory uORF and re-initiate translation at the AFT4 coding sequence (PubMed:15277680). Expressed in a circadian manner in the midbrain with an increased expression seen during the dark phase (at protein level) (PubMed:21768648, PubMed:22572884). Expressed in a circadian manner also in the suprachiasmatic nucleus (SCN) of the brain, cerebral cortex, kidney and small intestine (PubMed:21768648, PubMed:22572884). The BetaTrCP degron motif promotes binding to BTRC when phosphorylated. Ubiquitinated by SCF(BTRC) in response to mTORC1 signal, followed by proteasomal degradation and leading to down-regulate expression of SIRT4 (PubMed:23663782). Interaction with EP300/p300 inhibits ubiquitination by SCF(BTRC) (By similarity). Phosphorylation at Ser-251 by RPS6KA3/RSK2 in osteoblasts enhances transactivation activity and promotes osteoblast differentiation (PubMed:15109498). Phosphorylated on the betaTrCP degron motif at Ser-218, followed by phosphorylation at Thr-212, Ser-223, Ser-230, Ser-234 and Ser-247, promoting interaction with BTRC and ubiquitination (PubMed:23663782). Phosphorylation is promoted by mTORC1 (PubMed:23663782). Phosphorylation at Ser-214 by CK2 decreases its stability (By similarity). Phosphorylated by NEK6 (By similarity). Hydroxylated by PHD3, leading to decreased protein stability. Mice were born at a much lower rate than predicted by the Mendelian ratio (PubMed:10096021, PubMed:10885750). Homozygous pups generally die during the first hour after birth, although excess mortality occurrs throughout the first 3 weeks of life (PubMed:10096021, PubMed:11806972). Embryos are severely anemic during fetal development, due to an impairment in definitive hematopoiesis (PubMed:11806972). Surviving mice display defects in embryonic lens formation leading to severe microphthalmia in adults (PubMed:10096021, PubMed:10885750). Embryos show delayed bone formation and surviving mice display low bone mass throughout postnatal life (PubMed:15109498). Surviving null mice exhibit an increase in serum insulin levels and low blood glucose levels (PubMed:22298775). There is a decrease in total fat content, gonadal fat, lean mass and body weight (PubMed:22298775). Serum levels of osteocalcin/BGLAP are decreased (PubMed:22298775). PBK/AKT1-mediated phosphorylation of FOXO1 at 'Ser-258' is increased with a subsequent decrease of FOXO1-mediated transcriptional activity (PubMed:22298775). Belongs to the bZIP family. Truncated N-terminus. diff --git a/examples/downstream_Text2Protein/step_02_inference_ChatGPT.py b/examples/downstream_Text2Protein/step_02_inference_ChatGPT.py new file mode 100644 index 0000000..b032abd --- /dev/null +++ b/examples/downstream_Text2Protein/step_02_inference_ChatGPT.py @@ -0,0 +1,243 @@ +import openai +import os +import random +import argparse +import sys +import time +import re +openai.api_key = "" + +import torch +import torch.nn as nn +from torch.utils.data import DataLoader +from transformers import AutoModel, BertModel, BertTokenizer, AutoTokenizer +from utils import TextProteinPairDataset, evaluate +from ProteinDT.models import ProteinTextModel + + +def complete_chatgpt(messages): + received = False + temperature = 0 + while not received: + try: + response = openai.ChatCompletion.create( + # model="gpt-3.5-turbo", + # model="gpt-3.5-turbo-16k", + model="gpt-3.5-turbo-0301", + messages=messages, + temperature=temperature, + frequency_penalty=0.2, + n=None) + raw_generated_text = response["choices"][0]["message"]['content'] + received = True + except: + error = sys.exc_info()[0] + if error == openai.error.InvalidRequestError: # something is wrong: e.g. prompt too long + print(f"InvalidRequestError\nPrompt error.\n\n") + print("prompt too long") + return "prompt too long" + if error == AssertionError: + print("Assert error:", sys.exc_info()[1]) + else: + print("API error:", error) + time.sleep(1) + return raw_generated_text + + +def load_model(): + assert args.pretrained_folder is not None + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../../data/temp_pretrained_PotBert") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert", cache_dir="../../data/temp_pretrained_PotBert") + elif args.protein_backbone_model == "ProtBERT_BFD": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False, chache_dir="../../data/temp_pretrained_PotBert_BFD") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd", cache_dir="../../data/temp_pretrained_PotBert_BFD") + protein_dim = 1024 + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein_model.load_state_dict(state_dict) + + ##### Load pretrained text model + text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_dim = 768 + input_model_path = os.path.join(args.pretrained_folder, "text_model.pth") + print("Loading text model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text_model.load_state_dict(state_dict) + + ##### Load pretrained protein2latent model + protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein2latent_model.load_state_dict(state_dict) + + ##### Load pretrained text2latent model + text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "text2latent_model.pth") + print("Loading text2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text2latent_model.load_state_dict(state_dict) + + protein_model = protein_model.to(device) + protein_model.eval() + text_model = text_model.to(device) + text_model.eval() + protein2latent_model = protein2latent_model.to(device) + protein2latent_model.eval() + text2latent_model = text2latent_model.to(device) + text2latent_model.eval() + return protein_model, protein_tokenizer, text_model, text_tokenizer, protein2latent_model, text2latent_model + + +@torch.no_grad() +def extract_ChatGPT(num_repeat, protein_model, protein_tokenizer, text_model, text_tokenizer, protein2latent_model, text2latent_model): + pattern = re.compile('[A-Z]{5,}') + + optimal_text_sequence_list, optimal_protein_sequence_list = [], [] + + for idx, text_sequence in enumerate(text_sequence_list): + print("idx: ", idx) + output_file = "output/ChatGPT/{}.txt".format(idx) + f = open(output_file, "r") + lines = f.readlines() + + text_sequence = [lines[0]] + text_sequence_encode = text_tokenizer(text_sequence, truncation=True, max_length=args.text_max_sequence_len, padding='max_length', return_tensors='pt') + text_sequence_input_ids = text_sequence_encode.input_ids.squeeze(dim=1).to(device) + text_sequence_attention_mask = text_sequence_encode.attention_mask.squeeze(dim=1).to(device) + description_output = text_model(text_sequence_input_ids, text_sequence_attention_mask) + text_repr = description_output["pooler_output"] + text_repr = text2latent_model(text_repr) # [1, hidden_dim] + + protein_sequence_list = [] + for line in lines[1:]: + line = line.strip() + parsed_results = pattern.findall(line) + if len(parsed_results) == 0: + continue + protein_sequence = parsed_results[0] + protein_sequence = re.sub(r"[UZOB]", "X", protein_sequence) + protein_sequence = " ".join(protein_sequence) + protein_sequence_list.append(protein_sequence) + protein_sequence_list = protein_sequence_list[:num_repeat] + + protein_sequence_encode = protein_tokenizer(protein_sequence_list, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.to(device) + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.to(device) + protein_output = protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + protein_repr = protein_output["pooler_output"] + protein_repr = protein2latent_model(protein_repr) + + print("text_repr", text_repr.shape) + print("protein_repr", protein_repr.shape) + + similarity = torch.matmul(text_repr, protein_repr.transpose(0, 1)) # (num_repeat) + optimal_id = torch.argmax(similarity) + optimal_text_sequence_list.append(text_sequence) + optimal_protein_sequence_list.append(protein_sequence_list[optimal_id]) + + return optimal_text_sequence_list, optimal_protein_sequence_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=8) + parser.add_argument("--dataset_size", type=int, default=200) + + parser.add_argument("--input_text_file_path", type=str, default="step_01_text_retrieval.txt") + parser.add_argument("--num_repeat", type=int, default=32) + + parser.add_argument("--pretrained_folder", type=str, default="../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10") + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--text_max_sequence_len", type=int, default=512) + + args = parser.parse_args() + print("arguments", args) + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### generate and save protein sequence ##### + f = open(args.input_text_file_path, 'r') + text_sequence_list = [] + for line in f.readlines(): + text_sequence = line.strip() + text_sequence_list.append(text_sequence) + text_sequence_list = text_sequence_list[:args.dataset_size] + + for idx, text_sequence in enumerate(text_sequence_list): + output_file = "output/ChatGPT/{}.txt".format(idx) + if os.path.isfile(output_file): + continue + + f = open(output_file, "w") + + text_sequence = "Can you generate one protein amino acid sequences satisfying the following property (just AA sequence, and no explanation)? {}".format(text_sequence) + messages = [ + {"role": "system", "content": "You are an expert in protein design."}, + {"role": "user", "content": text_sequence}, + ] + protein_sequence_answer = complete_chatgpt(messages) + messages.append({"role": "assistant", "content": protein_sequence_answer}) + print(text_sequence, file=f) + print("=== answer 0 ===", file=f) + print(protein_sequence_answer, file=f) + + for idx in range(1, args.num_repeat): + print("=== answer {} ===".format(idx), file=f) + messages.append({"role": "user", "content": "Can you give me one more protein sequence that is different from the previous (just AA sequence, and no explanation)?"}) + protein_sequence_answer = complete_chatgpt(messages) + messages.append({"role": "assistant", "content": protein_sequence_answer}) + print(protein_sequence_answer, file=f) + if protein_sequence_answer == "prompt too long": + break + + f.flush() + f.close() + + protein_model, protein_tokenizer, text_model, text_tokenizer, protein2latent_model, text2latent_model = load_model() + + ###### extract ##### + num_repeat = 16 + optimal_text_sequence_list, optimal_protein_sequence_list = extract_ChatGPT( + num_repeat=num_repeat, + protein_model=protein_model, protein_tokenizer=protein_tokenizer, + text_model=text_model, text_tokenizer=text_tokenizer, + protein2latent_model=protein2latent_model, text2latent_model=text2latent_model) + + output_text_file_path = "output/ChatGPT/step_02_inference.txt" + if output_text_file_path is not None: + f = open(output_text_file_path, 'w') + for text_sequence, protein_sequence in zip(optimal_text_sequence_list, optimal_protein_sequence_list): + print(text_sequence, file=f) + print(protein_sequence, file=f) + f.flush() + f.close() + + # ###### evaluate ##### + model = ProteinTextModel(protein_model, text_model, protein2latent_model, text2latent_model) + model.eval() + model.to(device) + + dataset = TextProteinPairDataset( + data_path=output_text_file_path, + protein_tokenizer=protein_tokenizer, + text_tokenizer=text_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len, + text_max_sequence_len=args.text_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + evaluation_T_list = [4, 10, 20] + accuracy_list = evaluate(dataloader, model, evaluation_T_list, device) + for evaluation_T, accuracy in zip(evaluation_T_list, accuracy_list): + print("evaluation_T: {}\taccuracy: {}".format(evaluation_T, accuracy)) + \ No newline at end of file diff --git a/examples/downstream_Text2Protein/step_02_inference_Galactica.py b/examples/downstream_Text2Protein/step_02_inference_Galactica.py new file mode 100644 index 0000000..00b4d56 --- /dev/null +++ b/examples/downstream_Text2Protein/step_02_inference_Galactica.py @@ -0,0 +1,227 @@ +import os +import random +import argparse +import sys +import time +import re + +from transformers import AutoTokenizer, OPTForCausalLM + +import torch +import torch.nn as nn +from torch.utils.data import DataLoader +from transformers import AutoModel, BertModel, BertTokenizer +from utils import TextProteinPairDataset, evaluate +from ProteinDT.models import ProteinTextModel + + +def parse_Galatica_result(text_sequence, result): + result = result.replace(text_sequence, "") + result = result.split("[END_AMINO]")[0] + return result + + +def load_model(): + assert args.pretrained_folder is not None + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../../data/temp_pretrained_ProtBert") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert", cache_dir="../../data/temp_pretrained_ProtBert") + elif args.protein_backbone_model == "ProtBERT_BFD": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False, chache_dir="../../data/temp_pretrained_ProtBert_BFD") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd", cache_dir="../../data/temp_pretrained_ProtBert_BFD") + protein_dim = 1024 + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein_model.load_state_dict(state_dict) + + ##### Load pretrained text model + text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_dim = 768 + input_model_path = os.path.join(args.pretrained_folder, "text_model.pth") + print("Loading text model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text_model.load_state_dict(state_dict) + + ##### Load pretrained protein2latent model + protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein2latent_model.load_state_dict(state_dict) + + ##### Load pretrained text2latent model + text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "text2latent_model.pth") + print("Loading text2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text2latent_model.load_state_dict(state_dict) + + protein_model = protein_model.to(device) + protein_model.eval() + text_model = text_model.to(device) + text_model.eval() + protein2latent_model = protein2latent_model.to(device) + protein2latent_model.eval() + text2latent_model = text2latent_model.to(device) + text2latent_model.eval() + return protein_model, protein_tokenizer, text_model, text_tokenizer, protein2latent_model, text2latent_model + + +@torch.no_grad() +def extract_Galactica(num_repeat, protein_model, protein_tokenizer, text_model, text_tokenizer, protein2latent_model, text2latent_model): + + optimal_text_sequence_list, optimal_protein_sequence_list = [], [] + + for idx, text_sequence in enumerate(text_sequence_list): + print("idx: ", idx) + output_file = "output/Galactica/{}.txt".format(idx) + f = open(output_file, "r") + lines = f.readlines() + + text_sequence = [lines[0]] + text_sequence_encode = text_tokenizer(text_sequence, truncation=True, max_length=args.text_max_sequence_len, padding='max_length', return_tensors='pt') + text_sequence_input_ids = text_sequence_encode.input_ids.squeeze(dim=1).to(device) + text_sequence_attention_mask = text_sequence_encode.attention_mask.squeeze(dim=1).to(device) + description_output = text_model(text_sequence_input_ids, text_sequence_attention_mask) + text_repr = description_output["pooler_output"] + text_repr = text2latent_model(text_repr) # [1, hidden_dim] + + protein_sequence_list = [] + for line in lines[1:]: + line = line.strip() + + protein_sequence = line.split(":")[1] + protein_sequence = re.sub(r"[UZOB]", "X", protein_sequence) + protein_sequence = " ".join(protein_sequence) + protein_sequence_list.append(protein_sequence) + protein_sequence_list = protein_sequence_list[:num_repeat] + + protein_sequence_encode = protein_tokenizer(protein_sequence_list, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.to(device) + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.to(device) + protein_output = protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + protein_repr = protein_output["pooler_output"] + protein_repr = protein2latent_model(protein_repr) + + print("text_repr", text_repr.shape) + print("protein_repr", protein_repr.shape) + + similarity = torch.matmul(text_repr, protein_repr.transpose(0, 1)) # (num_repeat) + optimal_id = torch.argmax(similarity) + optimal_text_sequence_list.append(text_sequence) + optimal_protein_sequence_list.append(protein_sequence_list[optimal_id]) + + return optimal_text_sequence_list, optimal_protein_sequence_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=8) + parser.add_argument("--dataset_size", type=int, default=200) + + parser.add_argument("--input_text_file_path", type=str, default="step_01_text_retrieval.txt") + parser.add_argument("--num_repeat", type=int, default=32) + + parser.add_argument("--pretrained_folder", type=str, default="../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10") + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--text_max_sequence_len", type=int, default=512) + + args = parser.parse_args() + print("arguments", args) + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + f = open(args.input_text_file_path, 'r') + text_sequence_list = [] + for line in f.readlines(): + text_sequence = line.strip() + text_sequence_list.append(text_sequence) + text_sequence_list = text_sequence_list[:args.dataset_size] + + ##### generate and save protein sequence ##### + galactica_tokenizer = AutoTokenizer.from_pretrained("facebook/galactica-1.3b") + galactica_model = OPTForCausalLM.from_pretrained("facebook/galactica-1.3b", device_map="auto") + galactica_num_return_sequences = 4 + + for idx, text_sequence in enumerate(text_sequence_list): + print("idx: ", idx) + output_file = "output/Galactica/{}.txt".format(idx) + if os.path.isfile(output_file): + continue + + f = open(output_file, "w") + + print(text_sequence, file=f) + + text_sequence = "{} Question: Can you generate one similar protein amino acid sequences satisfying (just amino acids and keywords or references)? [START_AMINO]".format(text_sequence) + text_ids = galactica_tokenizer(text_sequence, return_tensors="pt").input_ids.to("cuda") + + count = 0 + for _ in range(args.num_repeat // galactica_num_return_sequences): + outputs = galactica_model.generate( + text_ids, + max_new_tokens=args.protein_max_sequence_len, + do_sample=True, + top_p=0.95, + temperature=1.0, + use_cache=True, + top_k=5, + repetition_penalty=1.0, + length_penalty=1, + num_return_sequences=galactica_num_return_sequences, + ) + + for i in range(galactica_num_return_sequences): + protein_sequence_answer = galactica_tokenizer.decode(outputs[i]) + protein_sequence_answer = parse_Galatica_result(text_sequence, protein_sequence_answer) + print("{}: {}".format(count, protein_sequence_answer), file=f) + count += 1 + + f.flush() + f.close() + + protein_model, protein_tokenizer, text_model, text_tokenizer, protein2latent_model, text2latent_model = load_model() + + ###### extract ##### + num_repeat = 16 + optimal_text_sequence_list, optimal_protein_sequence_list = extract_Galactica( + num_repeat=num_repeat, + protein_model=protein_model, protein_tokenizer=protein_tokenizer, + text_model=text_model, text_tokenizer=text_tokenizer, + protein2latent_model=protein2latent_model, text2latent_model=text2latent_model) + + output_text_file_path = "output/Galactica/step_02_inference.txt" + if output_text_file_path is not None: + f = open(output_text_file_path, 'w') + for text_sequence, protein_sequence in zip(optimal_text_sequence_list, optimal_protein_sequence_list): + print(text_sequence, file=f) + print(protein_sequence, file=f) + f.flush() + f.close() + + # ###### evaluate ##### + model = ProteinTextModel(protein_model, text_model, protein2latent_model, text2latent_model) + model.eval() + model.to(device) + + dataset = TextProteinPairDataset( + data_path=output_text_file_path, + protein_tokenizer=protein_tokenizer, + text_tokenizer=text_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len, + text_max_sequence_len=args.text_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + evaluation_T_list = [4, 10, 20] + accuracy_list = evaluate(dataloader, model, evaluation_T_list, device) + for evaluation_T, accuracy in zip(evaluation_T_list, accuracy_list): + print("evaluation_T: {}\taccuracy: {}".format(evaluation_T, accuracy)) diff --git a/examples/downstream_Text2Protein/step_02_inference_ProteinDT.py b/examples/downstream_Text2Protein/step_02_inference_ProteinDT.py new file mode 100644 index 0000000..eb69ae1 --- /dev/null +++ b/examples/downstream_Text2Protein/step_02_inference_ProteinDT.py @@ -0,0 +1,304 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import time +import re + +import torch +import torch.nn as nn + +from transformers import AutoModel, AutoTokenizer, BertModel, BertTokenizer, T5Tokenizer +from torch.utils.data import DataLoader + +from utils import TextDataset, TextProteinPairDataset, evaluate +from ProteinDT.models import MultinomialDiffusion, T5Decoder, GaussianFacilitatorModel, ProteinTextModel + + +@torch.no_grad() +def inference(dataloader): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + optimal_text_sequence_list, optimal_protein_sequence_list = [], [] + for batch_idx, batch in enumerate(L): + text_sequence = batch["text_sequence"] + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device) + optimal_text_sequence_list.extend(text_sequence) + B = len(text_sequence) + + description_output = text_model(text_sequence_input_ids, text_sequence_attention_mask) + text_repr = description_output["pooler_output"] + text_repr = text2latent_model(text_repr) # [B, hidden_dim] + + if args.use_facilitator: + condition_repr = facilitator_distribution_model.inerence(text_repr=text_repr) # [B, hidden_dim] + else: + condition_repr = text_repr + + repeated_condition_repr = condition_repr.unsqueeze(1).expand(-1, args.num_repeat, -1) # [B, num_repeat, hidden_dim] + repeated_condition_repr = repeated_condition_repr.reshape(-1, args.condition_dim) # [B*num_repeat, hidden_dim] + + if args.decoder_distribution in ["T5Decoder"]: + if args.AR_generation_mode == "01": + temperature = 1.0 + k = 40 + p = 0.9 + repetition_penalty = 1.0 + num_return_sequences = 1 + do_sample = True + num_beams = 1 + elif args.AR_generation_mode == "02": + temperature = 1.0 + k = 40 + p = 0.9 + repetition_penalty = 1.0 + num_return_sequences = 1 + do_sample = False + num_beams = 1 + protein_sequence_pred_ids = decoder_distribution_model.inference( + condition=repeated_condition_repr, protein_seq_attention_mask=None, max_seq_len=args.protein_max_sequence_len, + temperature=temperature, k=k, p=p, repetition_penalty=repetition_penalty, num_return_sequences=num_return_sequences, do_sample=do_sample, num_beams=num_beams + ) + + else: + ##### add variable length + protein_seq_attention_mask = torch.zeros((B*args.num_repeat, args.protein_max_sequence_len), device=device) + for protein_seq_attention_mask_each in protein_seq_attention_mask: + valid_length = random.randint(300, args.protein_max_sequence_len) + protein_seq_attention_mask_each[:valid_length] = 1 + protein_seq_attention_mask = protein_seq_attention_mask.bool() + + protein_sequence_output = decoder_distribution_model.inference( + condition=repeated_condition_repr, protein_seq_attention_mask=protein_seq_attention_mask, max_seq_len=args.protein_max_sequence_len, mode=args.SDE_sampling_mode) + protein_sequence_pred_ids = torch.argmax(protein_sequence_output, dim=-1) # (B*num_repeat, max_seq_len) + + ##### truncate after index + for protein_sequence_pred_id in protein_sequence_pred_ids: + index = None + for pid, pred_id in enumerate(protein_sequence_pred_id): + if pred_id != protein_decoder_tokenizer.pad_token_id: + continue + index = pid + break + if index is not None: + protein_sequence_pred_id[index:] = protein_decoder_tokenizer.pad_token_id + + ##### clean-ups + protein_sequence_list = protein_decoder_tokenizer.batch_decode(sequences=protein_sequence_pred_ids, skip_special_tokens=True) + protein_sequence_list = [protein_sequence.replace(" ", "") for protein_sequence in protein_sequence_list] + + ##### get protein representation + cleaned_protein_sequence_list = [] + for protein_sequence in protein_sequence_list: + protein_sequence = re.sub(r"[UZOB]", "X", protein_sequence) + protein_sequence = " ".join(protein_sequence) + cleaned_protein_sequence_list.append(protein_sequence) + protein_sequence_encode = protein_tokenizer(cleaned_protein_sequence_list, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.to(device) + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.to(device) + protein_output = protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + protein_repr = protein_output["pooler_output"] + protein_repr = protein2latent_model(protein_repr) + + ##### select the most similar protein sequence using ProteinCLIP + for text_id in range(B): + start, end = text_id * args.num_repeat, (text_id + 1) * args.num_repeat + text_repr_segment = text_repr[text_id] + protein_repr_segment = protein_repr[start:end] + similarity = torch.matmul(text_repr_segment, protein_repr_segment.transpose(0, 1)) # (num_repeat) + optimal_id = torch.argmax(similarity) + optimal_id = start + optimal_id + optimal_protein_sequence_list.append(protein_sequence_list[optimal_id]) + + return optimal_text_sequence_list, optimal_protein_sequence_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=8) + parser.add_argument("--dataset_size", type=int, default=200) + + parser.add_argument("--input_text_file_path", type=str, default="step_01_text_retrieval.txt") + parser.add_argument("--pretrained_folder", type=str, default=None) + parser.add_argument("--step_04_folder", type=str, default=None) + parser.add_argument("--output_text_file_path", type=str, default=None) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + parser.add_argument("--num_repeat", type=int, default=2) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--condition_dim", type=int, default=256) + + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--text_max_sequence_len", type=int, default=512) + + parser.add_argument("--facilitator_distribution", type=str, default="Gaussian", choices=["Gaussian"]) + parser.add_argument("--use_facilitator", dest="use_facilitator", action="store_true") + parser.add_argument("--no_use_facilitator", dest="use_facilitator", action="store_false") + parser.set_defaults(use_facilitator=True) + + parser.add_argument("--decoder_distribution", type=str, default="T5Decoder", choices=["T5Decoder", "MultinomialDiffusion"]) + + ##### for AR ##### + parser.add_argument("--AR_generation_mode", type=str, default="01", choices=["01", "02"]) + + ##### for SDE ##### + parser.add_argument("--hidden_dim", type=int, default=16) + parser.add_argument("--beta_min", type=float, default=0.1) + parser.add_argument("--beta_max", type=float, default=30) + parser.add_argument("--num_diffusion_timesteps", type=int, default=1000) + parser.add_argument("--SDE_type", type=str, default="VP") + parser.add_argument("--score_network_type", type=str, default="BertProtBFD") + parser.add_argument("--SDE_sampling_mode", type=str, default="simplified", choices=["simplified", "weighted"]) + + args = parser.parse_args() + print("arguments", args) + assert args.pretrained_folder is not None + assert args.step_04_folder is not None + step_01_folder = args.pretrained_folder + step_02_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + step_03_folder = os.path.join(args.pretrained_folder, "step_03_Gaussian_10") + step_04_folder = args.step_04_folder + + assert args.SSL_emb_dim == args.condition_dim + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../../data/temp_pretrained_ProtBert") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert", cache_dir="../../data/temp_pretrained_ProtBert") + elif args.protein_backbone_model == "ProtBERT_BFD": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False, chache_dir="../../data/temp_pretrained_ProtBert_BFD") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd", cache_dir="../../data/temp_pretrained_ProtBert_BFD") + protein_dim = 1024 + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein_model.load_state_dict(state_dict) + + ##### Load pretrained text model + text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../../data/temp_pretrained_SciBert") + text_dim = 768 + input_model_path = os.path.join(args.pretrained_folder, "text_model.pth") + print("Loading text model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text_model.load_state_dict(state_dict) + + ##### Load pretrained protein2latent model + protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein2latent_model.load_state_dict(state_dict) + + ##### Load pretrained text2latent model + text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "text2latent_model.pth") + print("Loading text2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text2latent_model.load_state_dict(state_dict) + + ##### Load pretrained facilitator model + if args.facilitator_distribution == "Gaussian": + facilitator_distribution_model = GaussianFacilitatorModel(args.SSL_emb_dim) + # TODO: will check later. + input_model_path = os.path.join(step_03_folder, "facilitator_distribution_model.pth") + print("Loading facilitator_distribution model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + facilitator_distribution_model.load_state_dict(state_dict) + + if args.decoder_distribution in ["T5Decoder"]: + protein_decoder_tokenizer = T5Tokenizer.from_pretrained("Rostlab/prot_t5_xl_uniref50", do_lower_case=False, chache_dir="../../data/temp_pretrained_t5_base") + else: + protein_decoder_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../../data/temp_pretrained_ProtBert") + print("protein_decoder_tokenizer pad_token_id", protein_decoder_tokenizer.pad_token_id) + print("protein_decoder_tokenizer sep_token_id", protein_decoder_tokenizer.sep_token_id) + print("protein_decoder_tokenizer eos_token_id", protein_decoder_tokenizer.eos_token_id) + + ##### Load pretrained decoder model + if args.decoder_distribution == "MultinomialDiffusion": + mask_id = 4 + decoder_distribution_model = MultinomialDiffusion( + hidden_dim=args.hidden_dim, + condition_dim=args.condition_dim, mask_id=mask_id, + beta_min=args.beta_min, beta_max=args.beta_max, num_diffusion_timesteps=args.num_diffusion_timesteps, + num_classes=protein_decoder_tokenizer.vocab_size, score_network_type=args.score_network_type) + elif args.decoder_distribution == "T5Decoder": + decoder_distribution_model = T5Decoder( + hidden_dim=args.condition_dim, + tokenizer=protein_decoder_tokenizer, + T5_model=args.score_network_type) + + model_file_path = os.path.join(step_04_folder, "decoder_distribution_model.pth") + print("Loading decoder_distribution model from {}...".format(model_file_path)) + state_dict = torch.load(model_file_path, map_location='cpu') + decoder_distribution_model.load_state_dict(state_dict) + + protein_model = protein_model.to(device) + protein_model.eval() + text_model = text_model.to(device) + text_model.eval() + protein2latent_model = protein2latent_model.to(device) + protein2latent_model.eval() + text2latent_model = text2latent_model.to(device) + text2latent_model.eval() + facilitator_distribution_model = facilitator_distribution_model.to(device) + facilitator_distribution_model.eval() + decoder_distribution_model.to(device) + decoder_distribution_model.eval() + + dataset = TextDataset( + data_path=args.input_text_file_path, + dataset_size=args.dataset_size, + text_tokenizer=text_tokenizer, + text_max_sequence_len=args.text_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + optimal_text_sequence_list, optimal_protein_sequence_list = inference(dataloader) + + if args.output_text_file_path is not None: + f = open(args.output_text_file_path, 'w') + for text_sequence, protein_sequence in zip(optimal_text_sequence_list, optimal_protein_sequence_list): + print(text_sequence, file=f) + print(protein_sequence, file=f) + f.flush() + f.close() + + ########## evaluate + model = ProteinTextModel(protein_model, text_model, protein2latent_model, text2latent_model) + model.eval() + model.to(device) + + dataset = TextProteinPairDataset( + data_path=args.output_text_file_path, + protein_tokenizer=protein_tokenizer, + text_tokenizer=text_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len, + text_max_sequence_len=args.text_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + evaluation_T_list = [4, 10, 20] + accuracy_list = evaluate(dataloader, model, evaluation_T_list, device) + for evaluation_T, accuracy in zip(evaluation_T_list, accuracy_list): + print("evaluation_T: {}\taccuracy: {}".format(evaluation_T, accuracy)) diff --git a/examples/downstream_Text2Protein/step_03_analyze.py b/examples/downstream_Text2Protein/step_03_analyze.py new file mode 100644 index 0000000..16d8084 --- /dev/null +++ b/examples/downstream_Text2Protein/step_03_analyze.py @@ -0,0 +1,132 @@ +import os +import itertools + + +def extract(file_path): + evaluation_result_list = [] + f = open(file_path, 'r') + for line in f.readlines(): + # print(line) + if not line.startswith("evaluation_T:"): + continue + line = line.replace("accuracy:", ",").replace(":", ",").split(",") + evaluation_T = int(line[1]) + accuracy = float(line[2]) + evaluation_result_list.append([evaluation_T, accuracy]) + + row = "" + for evaluation_result in evaluation_result_list: + row = "{} & {:.2f}".format(row, evaluation_result[1]) + + if "MultinomialDiffusion_RNN" in file_path: + head = "\\ProteinSDE{}-RNN" + elif "MultinomialDiffusion_BertBase" in file_path: + head = "\\ProteinSDE{}-BERT" + else: + head = "AR" + + if "no_use_facilitator" in file_path: + facilitator = "no_facilitator" + else: + facilitator = "facilitator" + + row = head + " & {}".format(facilitator) + row + "\\\\" + print(row) + print() + return + + +def extract_results_Diffusion(pretrained_mode, decoder_distribution, score_network_type): + for lr, hidden_dim, epochs, prob_unconditional in itertools.product(*[lr_list, hidden_dim_list, epochs_list, prob_unconditional_list]): + + step_04_folder = "../../output/{}/step_04_{}_{}_lr_{lr}_hidden_{hidden_dim}_e_{epochs}_unconditional_{prob_unconditional}".format( + pretrained_mode, decoder_distribution, score_network_type, lr=lr, hidden_dim=hidden_dim, epochs=epochs, prob_unconditional=prob_unconditional) + # print("step_04_folder", step_04_folder) + print("% step_04_{}_{}_lr_{lr}_hidden_{hidden_dim}_e_{epochs}_unconditional_{prob_unconditional}".format(decoder_distribution, score_network_type, lr=lr, hidden_dim=hidden_dim, epochs=epochs, prob_unconditional=prob_unconditional)) + + for num_repeat, facilitator, SDE_sampling_mode in itertools.product(*[num_repeat_list, facilitator_list, SDE_sampling_mode_list]): + print("% num_repeat: {}".format(num_repeat)) + retrieval_folder = os.path.join(step_04_folder, "downstream_Retrieval/num_repeat_{}_{}_{}".format(num_repeat, facilitator, SDE_sampling_mode)) + retrieval_file_path = os.path.join(retrieval_folder, "step_02_inference.out") + + try: + print("% ", retrieval_file_path) + extract(retrieval_file_path) + except: + print("file {} missing or still running.".format(retrieval_file_path)) + continue + + print() + + return + + +def extract_results_AR(pretrained_mode, decoder_distribution, score_network_type): + for lr, hidden_dim, epochs, prob_unconditional in itertools.product(*[lr_list, hidden_dim_list, epochs_list, prob_unconditional_list]): + + step_04_folder = "../../output/{}/step_04_{}_{}_lr_{lr}_hidden_{hidden_dim}_e_{epochs}_unconditional_{prob_unconditional}".format( + pretrained_mode, decoder_distribution, score_network_type, lr=lr, hidden_dim=hidden_dim, epochs=epochs, prob_unconditional=prob_unconditional) + # print("step_04_folder", step_04_folder) + print("% step_04_{}_{}_lr_{lr}_hidden_{hidden_dim}_e_{epochs}_unconditional_{prob_unconditional}".format(decoder_distribution, score_network_type, lr=lr, hidden_dim=hidden_dim, epochs=epochs, prob_unconditional=prob_unconditional)) + + for num_repeat, facilitator, AR_generation_mode in itertools.product(*[num_repeat_list, facilitator_list, AR_generation_mode_list]): + print("% num_repeat: {}\t{}".format(num_repeat, AR_generation_mode)) + retrieval_folder = os.path.join(step_04_folder, "downstream_Retrieval/num_repeat_{}_{}_inference_{}".format(num_repeat, facilitator, AR_generation_mode)) + # retrieval_file_path = os.path.join(retrieval_folder, "downstream_Retrieval_step_02_inference.out") + retrieval_file_path = os.path.join(retrieval_folder, "step_02_inference.out") + + try: + print("% ", retrieval_file_path) + extract(retrieval_file_path) + except: + print("file {} missing or still running.".format(retrieval_file_path)) + continue + + print() + + return + + +if __name__ == "__main__": + # Hyperparameters for step-04 pretraining + pretrained_mode_list = [ + "ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10", + "ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5", + "ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-InfoNCE-0.1-batch-9-gpu-8-epoch-5", + ] + prob_unconditional_list = [0, 0.1] + epochs_list = [10] + hidden_dim_list = [16, 32] + facilitator_list = ["use_facilitator", "no_use_facilitator"] + SDE_sampling_mode_list =["simplified", "weighted"] + + decoder_distribution = "MultinomialDiffusion" + score_network_type = "RNN" + lr_list = ["1e-4", "1e-5"] + num_repeat_list = [16, 32] + for pretrained_mode in pretrained_mode_list: + extract_results_Diffusion(pretrained_mode, decoder_distribution, score_network_type) + print("\n\n\n") + print("\n\n\n") + + decoder_distribution = "MultinomialDiffusion" + score_network_type = "BertBase" + lr_list = ["1e-4", "1e-5"] + num_repeat_list = [16, 32] + for pretrained_mode in pretrained_mode_list: + extract_results_Diffusion(pretrained_mode, decoder_distribution, score_network_type) + print("\n\n\n") + print("\n\n\n") + + # epochs_list = [10, 50] + epochs_list = [10] + decoder_distribution = "T5Decoder" + score_network_type = "T5Base" + lr_list = ["1e-4", "1e-5"] + # num_repeat_list = [16, 8] + num_repeat_list = [16] + AR_generation_mode_list = ["01", "02"] + for pretrained_mode in pretrained_mode_list: + extract_results_AR(pretrained_mode, decoder_distribution, score_network_type) + print("\n\n\n") + print("\n\n\n") diff --git a/examples/downstream_Text2Protein/step_04_gather.py b/examples/downstream_Text2Protein/step_04_gather.py new file mode 100644 index 0000000..61e27b1 --- /dev/null +++ b/examples/downstream_Text2Protein/step_04_gather.py @@ -0,0 +1,100 @@ +# lines = """ + +# Galactica & -- & --\\ + +# ChatGPT & -- & --\\ + +# % step_04_T5Decoder_T5Base_lr_1e-4_hidden_16_e_10_unconditional_0.1 +# AR & BERT & 49.25 & 27.14 & 97.38 & 91.62\\ + +# % step_04_MultinomialDiffusion_RNN_lr_1e-4_hidden_32_e_10_unconditional_0 +# \ProteinSDE{} & RNN & 23.08 & 9.89 & 38.07 & 17.26\\ + +# % step_04_MultinomialDiffusion_BertBase_lr_1e-4_hidden_32_e_10_unconditional_0 +# \ProteinSDE{} & BERT & 45.26 & 24.21 & 46.94 & 29.59\\ +# """ + +lines = """ + +Galactica & 51.5 & 29.0 & 19.0\\ + +ChatGPT & 38.5 & 23.0 & 15.5\\ + +% step_04_T5Decoder_T5Base_lr_1e-4_hidden_16_e_10_unconditional_0.1 +% num_repeat: 16 01 +% ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10/step_04_T5Decoder_T5Base_lr_1e-4_hidden_16_e_10_unconditional_0.1/downstream_Retrieval/num_repeat_16_use_prior_inference_01/step_02_inference.out +AR & prior & 97.00 & 91.00 & 83.50\\ + +% num_repeat: 16 01 +% ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10/step_04_T5Decoder_T5Base_lr_1e-4_hidden_16_e_10_unconditional_0.1/downstream_Retrieval/num_repeat_16_no_use_prior_inference_01/step_02_inference.out +AR & no_prior & 49.00 & 27.00 & 20.00\\ + + + + +% step_04_MultinomialDiffusion_RNN_lr_1e-4_hidden_32_e_10_unconditional_0 +% num_repeat: 16 +% ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_04_MultinomialDiffusion_RNN_lr_1e-4_hidden_32_e_10_unconditional_0/downstream_Retrieval/num_repeat_16_use_prior_simplified/step_02_inference.out +\ProteinSDE{}-RNN & prior & 40.50 & 21.50 & 15.00\\ + +% num_repeat: 16 +% ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1e-1-text-512-1e-5-1e-1-EBM_NCE-0.1-batch-9-gpu-8-epoch-5/step_04_MultinomialDiffusion_RNN_lr_1e-4_hidden_32_e_10_unconditional_0/downstream_Retrieval/num_repeat_16_no_use_prior_simplified/step_02_inference.out +\ProteinSDE{}-RNN & no_prior & 24.00 & 10.50 & 5.50\\ + + + + + +% step_04_MultinomialDiffusion_BertBase_lr_1e-4_hidden_32_e_10_unconditional_0 +% num_repeat: 16 +% ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10/step_04_MultinomialDiffusion_BertBase_lr_1e-4_hidden_32_e_10_unconditional_0/downstream_Retrieval/num_repeat_16_use_prior_simplified/step_02_inference.out +\ProteinSDE{}-BERT & prior & 51.50 & 25.00 & 13.50\\ + +% num_repeat: 16 +% ../../output/ProteinDT/ProtBERT_BFD-512-1e-5-1-text-512-1e-5-1-EBM_NCE-1-batch-9-gpu-8-epoch-10/step_04_MultinomialDiffusion_BertBase_lr_1e-4_hidden_32_e_10_unconditional_0/downstream_Retrieval/num_repeat_16_no_use_prior_simplified/step_02_inference.out +\ProteinSDE{}-BERT & no_prior & 35.50 & 17.50 & 9.50\\ +""" + + +if __name__ == "__main__": + baseline_results_list = [] + proteinDT_results_list_without_facilitator = [] + proteinDT_results_list_with_facilitator = [] + + for line in lines.split("\n"): + line = line.strip() + if line == "": + continue + + line = line.replace("\\", "") + line = line.split("&") + + if line[0].startswith("Galactica"): + # print(line) + baseline_results_list.append([line[1], line[2], line[3]]) + + elif line[0].startswith("ChatGPT"): + # print(line) + baseline_results_list.append([line[1], line[2], line[3]]) + + elif "AR" in line[0] or "ProteinSDE" in line[0]: + if "no_prior" in line[1]: + proteinDT_results_list_without_facilitator.append([line[2], line[3], line[4]]) + else: + proteinDT_results_list_with_facilitator.append([line[2], line[3], line[4]]) + + T_list = [4, 10, 20] + for T_idx, T in enumerate(T_list): + row = "T = {}".format(T) + + for baseline_results in baseline_results_list: + row = "{} & {}".format(row, baseline_results[T_idx]) + + for proteinDT_results in proteinDT_results_list_without_facilitator: + row = "{} & {}".format(row, proteinDT_results[T_idx]) + + for proteinDT_results in proteinDT_results_list_with_facilitator: + row = "{} & {}".format(row, proteinDT_results[T_idx]) + + row = "{} \\\\".format(row) + print(row) \ No newline at end of file diff --git a/examples/downstream_Text2Protein/utils.py b/examples/downstream_Text2Protein/utils.py new file mode 100644 index 0000000..819a021 --- /dev/null +++ b/examples/downstream_Text2Protein/utils.py @@ -0,0 +1,128 @@ +import re +import numpy as np +import torch +from torch.utils.data import Dataset + + +class TextDataset(Dataset): + def __init__(self, data_path, dataset_size, text_tokenizer, text_max_sequence_len): + self.data_path = data_path + self.dataset_size = dataset_size + + f = open(self.data_path, 'r') + text_sequence_list = [] + for line in f.readlines(): + text_sequence = line.strip() + text_sequence_list.append(text_sequence) + self.text_sequence_list = text_sequence_list[:self.dataset_size] + self.text_tokenizer = text_tokenizer + self.text_max_sequence_len = text_max_sequence_len + + return + + def __getitem__(self, index): + text_sequence = self.text_sequence_list[index] + + text_sequence_encode = self.text_tokenizer(text_sequence, truncation=True, max_length=self.text_max_sequence_len, padding='max_length', return_tensors='pt') + text_sequence_input_ids = text_sequence_encode.input_ids.squeeze() + text_sequence_attention_mask = text_sequence_encode.attention_mask.squeeze() + + batch = { + "text_sequence": text_sequence, + "text_sequence_input_ids": text_sequence_input_ids, + "text_sequence_attention_mask": text_sequence_attention_mask, + } + + return batch + + def __len__(self): + return len(self.text_sequence_list) + + +class TextProteinPairDataset(Dataset): + def __init__(self, data_path, protein_tokenizer, text_tokenizer, protein_max_sequence_len, text_max_sequence_len): + self.data_path = data_path + self.protein_tokenizer = protein_tokenizer + self.text_tokenizer = text_tokenizer + self.protein_max_sequence_len = protein_max_sequence_len + self.text_max_sequence_len = text_max_sequence_len + + text_sequence_list, protein_sequence_list = [], [] + f = open(self.data_path, 'r') + for line_idx, line in enumerate(f.readlines()): + line = line.strip() + if line_idx % 2 == 0: + text_sequence_list.append(line) + else: + line = re.sub(r"[UZOB]", "X", line) + line = " ".join(line) + protein_sequence_list.append(line) + + self.protein_sequence_list = protein_sequence_list + self.text_sequence_list = text_sequence_list + print("num of (protein-sequence, text) pair: {}".format(len(self.protein_sequence_list))) + + return + + def __getitem__(self, index): + protein_sequence = self.protein_sequence_list[index] + text_sequence = self.text_sequence_list[index] + + protein_sequence_encode = self.protein_tokenizer(protein_sequence, truncation=True, max_length=self.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze() + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze() + + text_sequence_encode = self.text_tokenizer(text_sequence, truncation=True, max_length=self.text_max_sequence_len, padding='max_length', return_tensors='pt') + text_sequence_input_ids = text_sequence_encode.input_ids.squeeze() + text_sequence_attention_mask = text_sequence_encode.attention_mask.squeeze() + + batch = { + "protein_sequence": protein_sequence, + "protein_sequence_input_ids": protein_sequence_input_ids, + "protein_sequence_attention_mask": protein_sequence_attention_mask, + "text_sequence": text_sequence, + "text_sequence_input_ids": text_sequence_input_ids, + "text_sequence_attention_mask": text_sequence_attention_mask, + } + + return batch + + def __len__(self): + return len(self.protein_sequence_list) + + +@torch.no_grad() +def evaluate(dataloader, model, evaluation_T_list, device): + protein_repr_list, text_repr_list = [], [] + for batch in dataloader: + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device) + + protein_repr, text_repr = model(protein_sequence_input_ids, protein_sequence_attention_mask, text_sequence_input_ids, text_sequence_attention_mask) + protein_repr = protein_repr.detach().cpu().numpy() + text_repr = text_repr.detach().cpu().numpy() + + protein_repr_list.append(protein_repr) + text_repr_list.append(text_repr) + + protein_repr_list = np.concatenate(protein_repr_list) + text_repr_list = np.concatenate(text_repr_list) + + similarity_matrix = np.matmul(protein_repr_list, text_repr_list.T) + N = similarity_matrix.shape[0] + + accuracy_list = [] + for evaluation_T in evaluation_T_list: + accuracy = 0 + for i in range(N): + start, end = i, i + evaluation_T + similarity_matrix_segment = [] + for j in range(start, end): + similarity_matrix_segment.append(similarity_matrix[i][j % N]) + optimal_index = np.argmax(similarity_matrix_segment) + accuracy += (optimal_index == 0) + accuracy = accuracy * 100. / N + accuracy_list.append(accuracy) + return accuracy_list diff --git a/examples/pretrain_step_01_CLAP.py b/examples/pretrain_step_01_CLAP.py new file mode 100644 index 0000000..182fa7e --- /dev/null +++ b/examples/pretrain_step_01_CLAP.py @@ -0,0 +1,288 @@ +import os +import random +import numpy as np +import argparse +from tqdm import tqdm +import time + +import torch +import torch.nn as nn +import torch.optim as optim +import torch.nn.functional as F + +from transformers import AutoModel, AutoTokenizer +from transformers import BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from ProteinDT.models import ProteinTextModel +from ProteinDT.datasets import SwissProtCLAPDataset + + +def cycle_index(num, shift): + arr = torch.arange(num) + shift + arr[-shift:] = torch.arange(shift) + return arr + + +def do_CL(X, Y, args): + if args.normalize: + X = F.normalize(X, dim=-1) + Y = F.normalize(Y, dim=-1) + + if args.CL_loss == 'EBM_NCE': + criterion = nn.BCEWithLogitsLoss() + neg_Y = torch.cat([Y[cycle_index(len(Y), i + 1)] for i in range(args.CL_neg_samples)], dim=0) + neg_X = X.repeat((args.CL_neg_samples, 1)) + + pred_pos = torch.sum(X * Y, dim=1) / args.T + pred_neg = torch.sum(neg_X * neg_Y, dim=1) / args.T + + loss_pos = criterion(pred_pos, torch.ones(len(pred_pos)).to(pred_pos.device)) + loss_neg = criterion(pred_neg, torch.zeros(len(pred_neg)).to(pred_neg.device)) + CL_loss = (loss_pos + args.CL_neg_samples * loss_neg) / (1 + args.CL_neg_samples) + + CL_acc = (torch.sum(pred_pos > 0).float() + torch.sum(pred_neg < 0).float()) / \ + (len(pred_pos) + len(pred_neg)) + CL_acc = CL_acc.detach().cpu().item() + + elif args.CL_loss == 'InfoNCE': + criterion = nn.CrossEntropyLoss() + B = X.size()[0] + logits = torch.mm(X, Y.transpose(1, 0)) # B*B + logits = torch.div(logits, args.T) + labels = torch.arange(B).long().to(logits.device) # B*1 + + CL_loss = criterion(logits, labels) + pred = logits.argmax(dim=1, keepdim=False) + CL_acc = pred.eq(labels).sum().detach().cpu().item() * 1. / B + + else: + raise Exception + + return CL_loss, CL_acc + + +def save_model(save_best): + if args.output_model_dir is None: + return + + if save_best: + global optimal_loss + print("save model with loss: {:.5f}".format(optimal_loss)) + model_file = "model.pth" + + saved_file_path = os.path.join(args.output_model_dir, "text_{}".format(model_file)) + torch.save(text_model.state_dict(), saved_file_path) + + saved_file_path = os.path.join(args.output_model_dir, "protein_{}".format(model_file)) + torch.save(protein_model.state_dict(), saved_file_path) + + saved_file_path = os.path.join(args.output_model_dir, "text2latent_{}".format(model_file)) + torch.save(text2latent_model.state_dict(), saved_file_path) + + saved_file_path = os.path.join(args.output_model_dir, "protein2latent_{}".format(model_file)) + torch.save(protein2latent_model.state_dict(), saved_file_path) + + else: + model_file = "model_final.pth" + + saved_file_path = os.path.join(args.output_model_dir, "text_{}".format(model_file)) + torch.save(text_model.state_dict(), saved_file_path) + + saved_file_path = os.path.join(args.output_model_dir, "protein_{}".format(model_file)) + torch.save(protein_model.state_dict(), saved_file_path) + + saved_file_path = os.path.join(args.output_model_dir, "text2latent_{}".format(model_file)) + torch.save(text2latent_model.state_dict(), saved_file_path) + + saved_file_path = os.path.join(args.output_model_dir, "protein2latent_{}".format(model_file)) + torch.save(protein2latent_model.state_dict(), saved_file_path) + + return + + +def train(dataloader): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + start_time = time.time() + accum_loss, accum_acc = 0, 0 + for batch_idx, batch in enumerate(L): + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device) + + protein_repr, description_repr = model(protein_sequence_input_ids, protein_sequence_attention_mask, text_sequence_input_ids, text_sequence_attention_mask) + + loss_01, acc_01 = do_CL(description_repr, protein_repr, args) + loss_02, acc_02 = do_CL(protein_repr, description_repr, args) + loss = (loss_01 + loss_02) / 2 + acc = (acc_01 + acc_02) / 2 + optimizer.zero_grad() + loss.backward() + optimizer.step() + + accum_loss += loss.item() + accum_acc += acc + if args.verbose and batch_idx % 100 == 0: + print(loss.item(), acc) + + accum_loss /= len(L) + accum_acc /= len(L) + global optimal_loss + temp_loss = accum_loss + if temp_loss < optimal_loss: + optimal_loss = temp_loss + save_model(save_best=True) + print("CL Loss: {:.5f}\tCL Acc: {:.5f}Time: {:.5f}".format(accum_loss, accum_acc, time.time() - start_time)) + return + + +def train_AMP(dataloader): + scaler = torch.cuda.amp.GradScaler() + + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + start_time = time.time() + accum_loss, accum_acc = 0, 0 + for batch_idx, batch in enumerate(L): + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device) + + with torch.cuda.amp.autocast(): + protein_repr, description_repr = model(protein_sequence_input_ids, protein_sequence_attention_mask, text_sequence_input_ids, text_sequence_attention_mask) + + loss_01, acc_01 = do_CL(description_repr, protein_repr, args) + loss_02, acc_02 = do_CL(protein_repr, description_repr, args) + loss = (loss_01 + loss_02) / 2 + acc = (acc_01 + acc_02) / 2 + + optimizer.zero_grad() + scaler.scale(loss).backward() + scaler.step(optimizer) + scaler.update() + + accum_loss += loss.item() + accum_acc += acc + if args.verbose and batch_idx % 100 == 0: + print(loss.item(), acc) + + accum_loss /= len(L) + accum_acc /= len(L) + global optimal_loss + temp_loss = accum_loss + if temp_loss < optimal_loss: + optimal_loss = temp_loss + save_model(save_best=True) + print("CL Loss: {:.5f}\tCL Acc: {:.5f}Time: {:.5f}".format(accum_loss, accum_acc, time.time() - start_time)) + return + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--epochs", type=int, default=32) + parser.add_argument("--batch_size", type=int, default=5) + parser.add_argument("--num_workers", type=int, default=8) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--text_max_sequence_len", type=int, default=512) + parser.add_argument("--protein_lr", type=float, default=1e-5) + parser.add_argument("--protein_lr_scale", type=float, default=1e-1) + parser.add_argument("--text_lr", type=float, default=1e-5) + parser.add_argument("--text_lr_scale", type=float, default=1e-1) + parser.add_argument("--CL_neg_samples", type=int, default=1) + parser.add_argument("--CL_loss", type=str, default="EBM_NCE") + parser.add_argument("--T", type=float, default=0.1) + parser.add_argument("--decay", type=float, default=0) + + parser.add_argument("--normalize", dest="normalize", action="store_true") + parser.add_argument("--no_normalize", dest="normalize", action="store_false") + parser.set_defaults(normalize=False) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--use_AMP", dest="use_AMP", action="store_true") + parser.add_argument("--no_AMP", dest="use_AMP", action="store_false") + parser.set_defaults(use_AMP=True) + + parser.add_argument("--output_model_dir", type=str, default=None) + + args = parser.parse_args() + print("arguments", args) + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + if args.protein_backbone_model == "ProtBERT": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../data/temp_pretrained_ProtBert") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert", cache_dir="../data/temp_pretrained_ProtBert") + elif args.protein_backbone_model == "ProtBERT_BFD": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False, chache_dir="../data/temp_pretrained_ProtBert_BFD") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd", cache_dir="../data/temp_pretrained_ProtBert_BFD") + protein_dim = 1024 + + # TODO: check https://github.com/huggingface/transformers/blob/main/src/transformers/models/bert/modeling_bert.py#L1501 + text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../data/temp_pretrained_SciBert") + text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../data/temp_pretrained_SciBert") + text_dim = 768 + + protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + + model = ProteinTextModel(protein_model, text_model, protein2latent_model, text2latent_model) + + if torch.cuda.device_count() > 1: + # parallel models + print("Let's use", torch.cuda.device_count(), "GPUs!") + model = nn.DataParallel(model) + neo_batch_size = args.batch_size * torch.cuda.device_count() + print("batch size from {} to {}".format(args.batch_size, neo_batch_size)) + args.batch_size = neo_batch_size + model.to(device) + + model_param_group = [ + {"params": protein_model.parameters(), "lr": args.protein_lr * args.protein_lr_scale}, + {"params": text_model.parameters(), "lr": args.text_lr * args.text_lr_scale}, + {"params": protein2latent_model.parameters(), "lr": args.protein_lr * args.protein_lr_scale}, + {"params": text2latent_model.parameters(), "lr": args.text_lr * args.text_lr_scale}, + ] + optimizer = optim.Adam(model_param_group, weight_decay=args.decay) + optimal_loss = 1e10 + + dataset = SwissProtCLAPDataset( + root="../data/SwissProtCLAP", + protein_tokenizer=protein_tokenizer, + text_tokenizer=text_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len, + text_max_sequence_len=args.text_max_sequence_len + ) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=True, num_workers=args.num_workers) + + for e in range(1, args.epochs+1): + print("Epoch {}".format(e)) + if args.use_AMP: + train_AMP(dataloader) + else: + train(dataloader) + \ No newline at end of file diff --git a/examples/pretrain_step_02_empty_sequence.py b/examples/pretrain_step_02_empty_sequence.py new file mode 100644 index 0000000..a71b558 --- /dev/null +++ b/examples/pretrain_step_02_empty_sequence.py @@ -0,0 +1,177 @@ +import os +import random +import numpy as np +import argparse +from tqdm import tqdm +import time + +import torch +import torch.nn as nn +import torch.optim as optim +import torch.nn.functional as F + +from transformers import AutoModel, AutoTokenizer +from transformers import BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from ProteinDT.models import ProteinTextModel +from ProteinDT.datasets import SwissProtCLAPDataset + + +@torch.no_grad() +def extract(dataloader): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + protein_repr_list, description_repr_list, protein_seq_list, text_seq_list = [], [], [], [] + for batch_idx, batch in enumerate(L): + protein_seq = batch["protein_sequence"] + text_seq = batch["text_sequence"] + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device) + + protein_repr, description_repr = model(protein_sequence_input_ids, protein_sequence_attention_mask, text_sequence_input_ids, text_sequence_attention_mask) + protein_repr_list.append(protein_repr.detach().cpu().numpy()) + description_repr_list.append(description_repr.detach().cpu().numpy()) + protein_seq_list.extend(protein_seq) + text_seq_list.extend(text_seq) + + protein_repr_array = np.concatenate(protein_repr_list) + description_repr_array= np.concatenate(description_repr_list) + return protein_repr_array, description_repr_array, protein_seq_list, text_seq_list + + +@torch.no_grad() +def extract_AMP(dataloader): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + protein_repr_list, description_repr_list, protein_seq_list, text_seq_list = [], [], [], [] + for batch_idx, batch in enumerate(L): + protein_seq = batch["protein_sequence"] + text_seq = batch["text_sequence"] + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device) + + with torch.cuda.amp.autocast(): + protein_repr, description_repr = model(protein_sequence_input_ids, protein_sequence_attention_mask, text_sequence_input_ids, text_sequence_attention_mask) + protein_repr_list.append(protein_repr.detach().cpu().numpy()) + description_repr_list.append(description_repr.detach().cpu().numpy()) + protein_seq_list.extend(protein_seq) + text_seq_list.extend(text_seq) + + protein_repr_array = np.concatenate(protein_repr_list) + description_repr_array= np.concatenate(description_repr_list) + return protein_repr_array, description_repr_array, protein_seq_list, text_seq_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=8) + parser.add_argument("--num_workers", type=int, default=8) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--text_max_sequence_len", type=int, default=512) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--use_AMP", dest="use_AMP", action="store_true") + parser.add_argument("--no_AMP", dest="use_AMP", action="store_false") + parser.set_defaults(use_AMP=True) + + parser.add_argument("--pretrained_folder", type=str, default=None) + + args = parser.parse_args() + print("arguments", args) + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../data/temp_pretrained_ProtBert") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert", cache_dir="../data/temp_pretrained_ProtBert") + elif args.protein_backbone_model == "ProtBERT_BFD": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False, chache_dir="../data/temp_pretrained_ProtBert_BFD") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd", cache_dir="../data/temp_pretrained_ProtBert_BFD") + protein_dim = 1024 + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein_model.load_state_dict(state_dict) + + ##### Load pretrained text model + text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../data/temp_pretrained_SciBert") + text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../data/temp_pretrained_SciBert") + text_dim = 768 + input_model_path = os.path.join(args.pretrained_folder, "text_model.pth") + print("Loading text model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text_model.load_state_dict(state_dict) + + ##### Load pretrained protein2latent model + protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein2latent_model.load_state_dict(state_dict) + + ##### Load pretrained text2latent model + text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "text2latent_model.pth") + print("Loading text2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text2latent_model.load_state_dict(state_dict) + + model = ProteinTextModel(protein_model, text_model, protein2latent_model, text2latent_model) + model.eval() + model.to(device) + + text_sequence = "" + text_sequence_encode = text_tokenizer(text_sequence, truncation=True, max_length=args.text_max_sequence_len, padding='max_length', return_tensors='pt') + text_sequence_input_ids = text_sequence_encode.input_ids.to(device) + text_sequence_attention_mask = text_sequence_encode.attention_mask.to(device) + + description_output = text_model(text_sequence_input_ids, text_sequence_attention_mask) + description_repr = description_output["pooler_output"] + description_repr = text2latent_model(description_repr) + description_repr = description_repr.detach().cpu().numpy() + print("description_repr", description_repr.shape) + + protein_sequence = "" + protein_sequence_encode = protein_tokenizer(protein_sequence, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.to(device) + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.to(device) + protein_output = protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + protein_repr = protein_output["pooler_output"] + protein_repr = protein2latent_model(protein_repr) + protein_repr = protein_repr.detach().cpu().numpy() + print("protein_repr", protein_repr.shape) + + assert args.pretrained_folder is not None + output_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + os.makedirs(output_folder, exist_ok=True) + + saved_file_path = os.path.join(output_folder, "empty_sequence") + np.savez(saved_file_path, description_repr=description_repr, protein_repr=protein_repr) diff --git a/examples/pretrain_step_02_pairwise_representation.py b/examples/pretrain_step_02_pairwise_representation.py new file mode 100644 index 0000000..1c5fae4 --- /dev/null +++ b/examples/pretrain_step_02_pairwise_representation.py @@ -0,0 +1,180 @@ +import os +import random +import numpy as np +import argparse +from tqdm import tqdm +import time + +import torch +import torch.nn as nn +import torch.optim as optim +import torch.nn.functional as F + +from transformers import AutoModel, AutoTokenizer +from transformers import BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from ProteinDT.models import ProteinTextModel +from ProteinDT.datasets import SwissProtCLAPDataset + + +@torch.no_grad() +def extract(dataloader): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + protein_repr_list, description_repr_list, protein_seq_list, text_seq_list = [], [], [], [] + for batch_idx, batch in enumerate(L): + protein_seq = batch["protein_sequence"] + text_seq = batch["text_sequence"] + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device) + + protein_repr, description_repr = model(protein_sequence_input_ids, protein_sequence_attention_mask, text_sequence_input_ids, text_sequence_attention_mask) + protein_repr_list.append(protein_repr.detach().cpu().numpy()) + description_repr_list.append(description_repr.detach().cpu().numpy()) + protein_seq_list.extend(protein_seq) + text_seq_list.extend(text_seq) + + protein_repr_array = np.concatenate(protein_repr_list) + description_repr_array= np.concatenate(description_repr_list) + return protein_repr_array, description_repr_array, protein_seq_list, text_seq_list + + +@torch.no_grad() +def extract_AMP(dataloader): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + protein_repr_list, description_repr_list, protein_seq_list, text_seq_list = [], [], [], [] + for batch_idx, batch in enumerate(L): + protein_seq = batch["protein_sequence"] + text_seq = batch["text_sequence"] + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + text_sequence_input_ids = batch["text_sequence_input_ids"].to(device) + text_sequence_attention_mask = batch["text_sequence_attention_mask"].to(device) + + with torch.cuda.amp.autocast(): + protein_repr, description_repr = model(protein_sequence_input_ids, protein_sequence_attention_mask, text_sequence_input_ids, text_sequence_attention_mask) + protein_repr_list.append(protein_repr.detach().cpu().numpy()) + description_repr_list.append(description_repr.detach().cpu().numpy()) + protein_seq_list.extend(protein_seq) + text_seq_list.extend(text_seq) + + protein_repr_array = np.concatenate(protein_repr_list) + description_repr_array= np.concatenate(description_repr_list) + return protein_repr_array, description_repr_array, protein_seq_list, text_seq_list + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=8) + parser.add_argument("--num_workers", type=int, default=8) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--text_max_sequence_len", type=int, default=512) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--use_AMP", dest="use_AMP", action="store_true") + parser.add_argument("--no_AMP", dest="use_AMP", action="store_false") + parser.set_defaults(use_AMP=True) + + parser.add_argument("--pretrained_folder", type=str, default=None) + + args = parser.parse_args() + print("arguments", args) + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + ##### Load pretrained protein model + if args.protein_backbone_model == "ProtBERT": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../data/temp_pretrained_ProtBert") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert", cache_dir="../data/temp_pretrained_ProtBert") + elif args.protein_backbone_model == "ProtBERT_BFD": + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False, chache_dir="../data/temp_pretrained_ProtBert_BFD") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd", cache_dir="../data/temp_pretrained_ProtBert_BFD") + protein_dim = 1024 + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein_model.load_state_dict(state_dict) + + ##### Load pretrained text model + text_tokenizer = AutoTokenizer.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../data/temp_pretrained_SciBert") + text_model = AutoModel.from_pretrained('allenai/scibert_scivocab_uncased', cache_dir="../data/temp_pretrained_SciBert") + text_dim = 768 + input_model_path = os.path.join(args.pretrained_folder, "text_model.pth") + print("Loading text model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text_model.load_state_dict(state_dict) + + ##### Load pretrained protein2latent model + protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein2latent_model.load_state_dict(state_dict) + + ##### Load pretrained text2latent model + text2latent_model = nn.Linear(text_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "text2latent_model.pth") + print("Loading text2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + text2latent_model.load_state_dict(state_dict) + + model = ProteinTextModel(protein_model, text_model, protein2latent_model, text2latent_model) + model.eval() + model.to(device) + + dataset = SwissProtCLAPDataset( + root="../data/SwissProtCLAP", + protein_tokenizer=protein_tokenizer, + text_tokenizer=text_tokenizer, + protein_max_sequence_len=args.protein_max_sequence_len, + text_max_sequence_len=args.text_max_sequence_len + ) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + if args.use_AMP: + protein_repr_array, description_repr_array, protein_seq_list, text_seq_list = extract_AMP(dataloader) + else: + protein_repr_array, description_repr_array, protein_seq_list, text_seq_list = extract(dataloader) + + assert args.pretrained_folder is not None + output_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + os.makedirs(output_folder, exist_ok=True) + + saved_file_path = os.path.join(output_folder, "pairwise_representation") + np.savez(saved_file_path, protein_repr_array=protein_repr_array, description_repr_array=description_repr_array) + + protein_sequence_file = os.path.join(output_folder, "protein_sequence.txt") + f = open(protein_sequence_file, 'w') + for protein_seq in protein_seq_list: + print(protein_seq, file=f) + + text_sequence_file = os.path.join(output_folder, "text_sequence.txt") + f = open(text_sequence_file, 'w') + for text_seq in text_seq_list: + print(text_seq, file=f) diff --git a/examples/pretrain_step_03_facilitator.py b/examples/pretrain_step_03_facilitator.py new file mode 100644 index 0000000..9223566 --- /dev/null +++ b/examples/pretrain_step_03_facilitator.py @@ -0,0 +1,177 @@ +import os +import random +import numpy as np +import argparse +from tqdm import tqdm +import time + +import torch +import torch.optim as optim + +from transformers import AutoModel, AutoTokenizer +from transformers import BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from ProteinDT.datasets import RepresentationPairDataset +from ProteinDT.models import GaussianPriorModel + + +def save_model(save_best): + if save_best: + global optimal_loss + print("save model with loss: {:.5f}".format(optimal_loss)) + model_file = "model.pth" + + saved_file_path = os.path.join(step_03_folder, "facilitator_distribution_{}".format(model_file)) + torch.save(facilitator_distribution_model.state_dict(), saved_file_path) + + else: + model_file = "model_final.pth" + + saved_file_path = os.path.join(step_03_folder, "facilitator_distribution_{}".format(model_file)) + torch.save(facilitator_distribution_model.state_dict(), saved_file_path) + + return + + +def train(dataloader): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + start_time = time.time() + accum_loss = 0 + for batch_idx, batch in enumerate(L): + protein_repr = batch["protein_repr"].to(device) + text_repr = batch["text_repr"].to(device) + + loss = facilitator_distribution_model(protein_repr=protein_repr, text_repr=text_repr) + + optimizer.zero_grad() + loss.backward() + optimizer.step() + + accum_loss += loss.item() + + accum_loss /= len(L) + global optimal_loss + temp_loss = accum_loss + if temp_loss < optimal_loss: + optimal_loss = temp_loss + save_model(save_best=True) + print("Loss: {:.5f}\tTime: {:.5f}".format(accum_loss, time.time() - start_time)) + return + + +def train_AMP(dataloader): + scaler = torch.cuda.amp.GradScaler() + + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + start_time = time.time() + accum_loss = 0 + for batch_idx, batch in enumerate(L): + protein_repr = batch["protein_repr"].to(device) + text_repr = batch["text_repr"].to(device) + + with torch.cuda.amp.autocast(): + loss = facilitator_distribution_model(protein_repr=protein_repr, text_repr=text_repr) + + optimizer.zero_grad() + scaler.scale(loss).backward() + scaler.step(optimizer) + scaler.update() + + accum_loss += loss.item() + + accum_loss /= len(L) + global optimal_loss + temp_loss = accum_loss + if temp_loss < optimal_loss: + optimal_loss = temp_loss + save_model(save_best=True) + print("Loss: {:.5f}\tTime: {:.5f}".format(accum_loss, time.time() - start_time)) + return + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--epochs", type=int, default=32) + parser.add_argument("--batch_size", type=int, default=5) + parser.add_argument("--num_workers", type=int, default=8) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--protein_backbone_model", type=str, default="ProtBERT_BFD", choices=["ProtBERT", "ProtBERT_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--text_max_sequence_len", type=int, default=512) + parser.add_argument("--protein_lr", type=float, default=1e-5) + parser.add_argument("--protein_lr_scale", type=float, default=1e-1) + parser.add_argument("--text_lr", type=float, default=1e-5) + parser.add_argument("--text_lr_scale", type=float, default=1e-1) + parser.add_argument("--CL_neg_samples", type=int, default=1) + parser.add_argument("--CL_loss", type=str, default="EBM_NCE") + parser.add_argument("--T", type=float, default=0.1) + parser.add_argument("--decay", type=float, default=0) + + parser.add_argument("--normalize", dest="normalize", action="store_true") + parser.add_argument("--no_normalize", dest="normalize", action="store_false") + parser.set_defaults(normalize=False) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--use_AMP", dest="use_AMP", action="store_true") + parser.add_argument("--no_AMP", dest="use_AMP", action="store_false") + parser.set_defaults(use_AMP=True) + + parser.add_argument("--facilitator_distribution", type=str, default="Gaussian", choices=["Gaussian"]) + parser.add_argument("--pretrained_folder", type=str, default=None) + parser.add_argument("--output_model_folder", type=str, default=None) + + args = parser.parse_args() + print("arguments", args) + assert args.pretrained_folder is not None + assert args.output_model_folder is not None + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + if args.facilitator_distribution == "Gaussian": + facilitator_distribution_model = GaussianPriorModel(args.SSL_emb_dim) + facilitator_distribution_model.train() + facilitator_distribution_model.to(device) + + model_param_group = [ + {"params": facilitator_distribution_model.parameters(), "lr": args.protein_lr * args.protein_lr_scale}, + ] + optimizer = optim.Adam(model_param_group, weight_decay=args.decay) + optimal_loss = 1e10 + + step_02_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + dataset = RepresentationPairDataset(step_02_folder) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + step_03_folder = args.output_model_folder + os.makedirs(step_03_folder, exist_ok=True) + + for e in range(1, args.epochs+1): + print("Epoch {}".format(e)) + if args.use_AMP: + train_AMP(dataloader) + else: + train(dataloader) + \ No newline at end of file diff --git a/examples/pretrain_step_04_decoder.py b/examples/pretrain_step_04_decoder.py new file mode 100644 index 0000000..54110ab --- /dev/null +++ b/examples/pretrain_step_04_decoder.py @@ -0,0 +1,226 @@ +import os +import random +import numpy as np +import argparse +from tqdm import tqdm +import time + +import torch +from torch import nn +import torch.optim as optim + +from transformers import BertTokenizer, T5Tokenizer +from torch.utils.data import DataLoader + + +from ProteinDT.datasets import RepresentationPairWithRawDataDataset +# from ProteinDT.models import GaussianSDEDecoderModel, ColdDiffusionDecoder, LatentDiffusionDecoder, MultinomialDiffusion, LSTMDecoder, T5Decoder +from ProteinDT.models import MultinomialDiffusion, T5Decoder + + +def save_model(save_best): + if save_best: + global optimal_loss + print("save model with loss: {:.5f}".format(optimal_loss)) + model_file = "model.pth" + + saved_file_path = os.path.join(step_04_folder, "decoder_distribution_{}".format(model_file)) + torch.save(decoder_distribution_model.state_dict(), saved_file_path) + + else: + model_file = "model_final.pth" + + saved_file_path = os.path.join(step_04_folder, "decoder_distribution_{}".format(model_file)) + torch.save(decoder_distribution_model.state_dict(), saved_file_path) + return + + +def train(dataloader): + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + start_time = time.time() + accum_SDE_loss, accum_decoding_loss = 0, 0 + for batch_idx, batch in enumerate(L): + protein_sequence = batch["protein_sequence"] + + protein_sequence_encode = protein_decoder_tokenizer(protein_sequence, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze(1).to(device) + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze(1).to(device) + + protein_repr = batch["protein_repr"].to(device) + + SDE_loss, decoding_loss = decoder_distribution_model(condition=protein_repr, protein_seq_input_ids=protein_sequence_input_ids, protein_seq_attention_mask=protein_sequence_attention_mask) + loss = args.alpha_1 * SDE_loss + args.alpha_2 * decoding_loss + if args.verbose and batch_idx % 100 == 0: + print("SDE Loss: {:.5f}\tDecoding Loss: {:.5f}".format(SDE_loss.item(), decoding_loss.item())) + + optimizer.zero_grad() + loss.backward() + optimizer.step() + + accum_SDE_loss += SDE_loss.item() + accum_decoding_loss += decoding_loss.item() + + accum_SDE_loss /= len(L) + accum_decoding_loss /= len(L) + global optimal_loss + temp_loss = args.alpha_1 * accum_SDE_loss + args.alpha_2 * decoding_loss + if temp_loss < optimal_loss: + optimal_loss = temp_loss + save_model(save_best=True) + print("SDE Loss: {:.5f}\tDecoding Loss: {:.5f}\tTime: {:.5f}".format(accum_SDE_loss, accum_decoding_loss, time.time() - start_time)) + return + + +def train_AMP(dataloader): + scaler = torch.cuda.amp.GradScaler() + decoder_distribution_model.train() + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + start_time = time.time() + accum_SDE_loss, accum_decoding_loss = 0, 0 + for batch_idx, batch in enumerate(L): + protein_sequence = batch["protein_sequence"] + + protein_sequence_encode = protein_decoder_tokenizer(protein_sequence, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze(1).to(device) + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze(1).to(device) + + protein_repr = batch["protein_repr"].to(device) + + with torch.cuda.amp.autocast(): + SDE_loss, decoding_loss = decoder_distribution_model(protein_seq_input_ids=protein_sequence_input_ids, protein_seq_attention_mask=protein_sequence_attention_mask, condition=protein_repr) + loss = args.alpha_1 * SDE_loss + args.alpha_2 * decoding_loss + + if args.verbose and batch_idx % 100 == 0: + if torch.is_tensor(decoding_loss): + print("SDE Loss: {:.5f}\tDecoding Loss: {:.5f}".format(SDE_loss.item(), decoding_loss.item())) + else: + print("SDE Loss: {:.5f}\tDecoding Loss: {:.5f}".format(SDE_loss.item(), decoding_loss)) + + optimizer.zero_grad() + scaler.scale(loss).backward() + scaler.step(optimizer) + scaler.update() + + accum_SDE_loss += SDE_loss.item() + if torch.is_tensor(decoding_loss): + accum_decoding_loss += decoding_loss.item() + + accum_SDE_loss /= len(L) + accum_decoding_loss /= len(L) + global optimal_loss + temp_loss = args.alpha_1 * accum_SDE_loss + args.alpha_2 * decoding_loss + if temp_loss < optimal_loss: + optimal_loss = temp_loss + save_model(save_best=True) + print("SDE Loss: {:.5f}\tDecoding Loss: {:.5f}\tTime: {:.5f}".format(accum_SDE_loss, accum_decoding_loss, time.time() - start_time)) + return + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--epochs", type=int, default=32) + parser.add_argument("--batch_size", type=int, default=8) + parser.add_argument("--num_workers", type=int, default=8) + + parser.add_argument("--hidden_dim", type=int, default=16) + parser.add_argument("--condition_dim", type=int, default=256) + parser.add_argument("--protein_backbone_model", type=str, default="ProtBert", choices=["ProtBert", "ProtBert_BFD"]) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--lr", type=float, default=1e-4) + parser.add_argument("--decay", type=float, default=0) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--use_AMP", dest="use_AMP", action="store_true") + parser.add_argument("--no_AMP", dest="use_AMP", action="store_false") + parser.set_defaults(use_AMP=True) + + parser.add_argument("--decoder_distribution", type=str, default="T5Decoder", choices=["T5Decoder", "MultinomialDiffusion"]) + parser.add_argument("--pretrained_folder", type=str, default=None) + parser.add_argument("--output_folder", type=str, default=None) + + # for GaussianSDE & diffusion + parser.add_argument("--beta_min", type=float, default=0.1) + parser.add_argument("--beta_max", type=float, default=30) + parser.add_argument("--num_diffusion_timesteps", type=int, default=1000) + parser.add_argument("--SDE_type", type=str, default="VP") + parser.add_argument("--score_network_type", type=str, default="Toy") + parser.add_argument("--alpha_1", type=float, default=1) + parser.add_argument("--alpha_2", type=float, default=0) + parser.add_argument("--prob_unconditional", type=float, default=0) + + args = parser.parse_args() + print("arguments", args) + assert args.pretrained_folder is not None + assert args.output_folder is not None + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + if args.decoder_distribution in ["T5Decoder"]: + protein_decoder_tokenizer = T5Tokenizer.from_pretrained("Rostlab/prot_t5_xl_uniref50", do_lower_case=False, chache_dir="../data/temp_pretrained_t5_base") + print(protein_decoder_tokenizer.get_vocab()) + else: + protein_decoder_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../data/temp_pretrained_ProtBert") + + if args.decoder_distribution == "MultinomialDiffusion": + mask_id = 4 + decoder_distribution_model = MultinomialDiffusion( + hidden_dim=args.hidden_dim, + condition_dim=args.condition_dim, mask_id=mask_id, + beta_min=args.beta_min, beta_max=args.beta_max, num_diffusion_timesteps=args.num_diffusion_timesteps, + num_classes=protein_decoder_tokenizer.vocab_size, score_network_type=args.score_network_type) + + elif args.decoder_distribution == "T5Decoder": + decoder_distribution_model = T5Decoder( + hidden_dim=args.condition_dim, + tokenizer=protein_decoder_tokenizer, + T5_model=args.score_network_type) + + if torch.cuda.device_count() > 1: + # parallel models + print("Let's use", torch.cuda.device_count(), "GPUs!") + model = nn.DataParallel(decoder_distribution_model) + neo_batch_size = args.batch_size * torch.cuda.device_count() + print("batch size from {} to {}".format(args.batch_size, neo_batch_size)) + args.batch_size = neo_batch_size + decoder_distribution_model.to(device) + + model_param_group = [ + {"params": decoder_distribution_model.parameters(), "lr": args.lr}, + ] + optimizer = optim.Adam(model_param_group, weight_decay=args.decay) + optimal_loss = 1e10 + + step_02_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + dataset = RepresentationPairWithRawDataDataset(step_02_folder, prob_unconditional=args.prob_unconditional) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=True, num_workers=args.num_workers) + + step_04_folder = args.output_folder + os.makedirs(step_04_folder, exist_ok=True) + + for e in range(1, 1+args.epochs): + print("Epoch {}".format(e)) + if args.use_AMP: + train_AMP(dataloader) + else: + train(dataloader) diff --git a/examples/pretrain_step_05_AE.py b/examples/pretrain_step_05_AE.py new file mode 100644 index 0000000..4c065bc --- /dev/null +++ b/examples/pretrain_step_05_AE.py @@ -0,0 +1,174 @@ +import os +import random +import numpy as np +import argparse +from tqdm import tqdm +import time + +import torch +from torch import nn +import torch.optim as optim + +from transformers import BertModel, BertTokenizer +from torch.utils.data import DataLoader + +from ProteinDT.datasets import ProteinSequenceDataset +from ProteinDT.models import RNNPrediction + + +def save_model(save_best): + if save_best: + global optimal_loss + print("save model with loss: {:.5f}".format(optimal_loss)) + model_file = "model.pth" + + saved_file_path = os.path.join(step_05_folder, "AE_{}".format(model_file)) + torch.save(auto_encoding_model.state_dict(), saved_file_path) + + else: + model_file = "model_final.pth" + + saved_file_path = os.path.join(step_05_folder, "AE_{}".format(model_file)) + torch.save(auto_encoding_model.state_dict(), saved_file_path) + return + + +def train_AMP(dataloader): + scaler = torch.cuda.amp.GradScaler() + auto_encoding_model.train() + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + start_time = time.time() + accum_AE_loss, accum_decoding_loss = 0, 0 + for batch_idx, batch in enumerate(L): + protein_sequence_input_ids = batch["protein_sequence_input_ids"].to(device) + protein_sequence_attention_mask = batch["protein_sequence_attention_mask"].to(device) + + with torch.no_grad(): + protein_output = protein_model(protein_sequence_input_ids, protein_sequence_attention_mask) + token_repr = protein_output["last_hidden_state"] # [B, max_seq_len, 1024] + token_repr = CLIP_protein2latent_model(token_repr) # [B, max_seq_len, SSL_emb_dim] + + with torch.cuda.amp.autocast(): + logit = auto_encoding_model(token_repr) # [B, max_seq_len, vocab_size] + + target_protein_seq_input_ids = protein_sequence_input_ids # [B, max_sequence_len] + target_protein_seq_attention_mask = protein_sequence_attention_mask # [B, max_sequence_len] + flattened_logits = torch.flatten(logit, start_dim=0, end_dim=1) # [B * max_sequence_len, vocab_size] + flattened_ids = torch.flatten(target_protein_seq_input_ids, start_dim=0, end_dim=1) # [B * max_sequence_len] + flattened_mask = torch.flatten(target_protein_seq_attention_mask, start_dim=0, end_dim=1) # [B * max_sequence_len] + total_loss = CE_criterion(flattened_logits, flattened_ids) # [B * max_sequence_len] + masked_loss = total_loss * flattened_mask # [B * max_sequence_len] + total_loss = torch.mean(total_loss) + masked_loss = masked_loss.sum() / flattened_mask.sum() + + loss = (total_loss + masked_loss) / 2 + + if args.verbose and batch_idx % 100 == 0: + print("CE Loss: {:.5f}".format(loss.item())) + temp = logit.argmax(-1) + print('temp', temp[:, :10]) # [B, max_seq_len] + print("protein_sequence_input_ids", protein_sequence_input_ids[:, :10]) + + optimizer.zero_grad() + scaler.scale(loss).backward() + scaler.step(optimizer) + scaler.update() + + accum_AE_loss += loss.item() + + accum_AE_loss /= len(L) + accum_decoding_loss /= len(L) + global optimal_loss + temp_loss = accum_AE_loss + if temp_loss < optimal_loss: + optimal_loss = temp_loss + save_model(save_best=True) + print("SDE Loss: {:.5f}\tDecoding Loss: {:.5f}\tTime: {:.5f}".format(accum_AE_loss, accum_decoding_loss, time.time() - start_time)) + return + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--epochs", type=int, default=32) + parser.add_argument("--batch_size", type=int, default=32) + parser.add_argument("--num_workers", type=int, default=0) + + parser.add_argument("--SSL_emb_dim", type=int, default=256) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + parser.add_argument("--lr", type=float, default=1e-4) + parser.add_argument("--decay", type=float, default=0) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--pretrained_folder", type=str, default=None) + parser.add_argument("--output_folder", type=str, default=None) + + args = parser.parse_args() + print("arguments", args) + assert args.pretrained_folder is not None + assert args.output_folder is not None + step_01_folder = args.pretrained_folder + step_02_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + step_05_folder = args.output_folder + os.makedirs(step_05_folder, exist_ok=True) + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + CE_criterion = nn.CrossEntropyLoss() + + ##### Load pretrained protein model + protein_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert_bfd", do_lower_case=False, chache_dir="../data/temp_pretrained_ProtBert_BFD") + protein_model = BertModel.from_pretrained("Rostlab/prot_bert_bfd", cache_dir="../data/temp_pretrained_ProtBert_BFD") + input_model_path = os.path.join(args.pretrained_folder, "protein_model.pth") + print("Loading protein model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + protein_model.load_state_dict(state_dict) + protein_model.to(device) + protein_model.eval() + protein_dim = 1024 + + ##### Load pretrained protein2latent model + CLIP_protein2latent_model = nn.Linear(protein_dim, args.SSL_emb_dim) + input_model_path = os.path.join(args.pretrained_folder, "protein2latent_model.pth") + print("Loading protein2latent model from {}...".format(input_model_path)) + state_dict = torch.load(input_model_path, map_location='cpu') + CLIP_protein2latent_model.load_state_dict(state_dict) + CLIP_protein2latent_model.to(device) + CLIP_protein2latent_model.eval() + + for param in protein_model.parameters(): + param.requires_grad = False + for param in CLIP_protein2latent_model.parameters(): + param.requires_grad = False + + # ### Add prediction head + auto_encoding_model = RNNPrediction(args.SSL_emb_dim, protein_tokenizer.vocab_size) + auto_encoding_model.to(device) + + model_param_group = [ + {"params": auto_encoding_model.parameters(), "lr": args.lr}, + ] + optimizer = optim.Adam(model_param_group, weight_decay=args.decay) + optimal_loss = 1e10 + + dataset = ProteinSequenceDataset(step_02_folder, protein_tokenizer=protein_tokenizer, protein_max_sequence_len=args.protein_max_sequence_len) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=True, num_workers=args.num_workers) + + for e in range(1, 1+args.epochs): + print("Epoch {}".format(e)) + train_AMP(dataloader) diff --git a/examples/pretrain_step_05_inference.py b/examples/pretrain_step_05_inference.py new file mode 100644 index 0000000..2286934 --- /dev/null +++ b/examples/pretrain_step_05_inference.py @@ -0,0 +1,194 @@ +import os +import random +import argparse +import numpy as np +from tqdm import tqdm +import time + +import torch +from transformers import BertTokenizer, T5Tokenizer +from torch.utils.data import DataLoader + +from ProteinDT.datasets import RepresentationPairWithRawDataDataset +# from ProteinDT.models import GaussianSDEDecoderModel, ColdDiffusionDecoder, LatentDiffusionDecoder, MultinomialDiffusion, LSTMDecoder, T5Decoder +from ProteinDT.models import MultinomialDiffusion, T5Decoder + + +def eval(dataloader): + decoder_distribution_model.eval() + if args.verbose: + L = tqdm(dataloader) + else: + L = dataloader + + fuzzy_match_acc_accum, exact_match_acc_accum = 0, 0 + for batch_idx, batch in enumerate(L): + protein_sequence = batch["protein_sequence"] + + protein_sequence_encode = protein_decoder_tokenizer(protein_sequence, truncation=True, max_length=args.protein_max_sequence_len, padding='max_length', return_tensors='pt') + + protein_sequence_input_ids = protein_sequence_encode.input_ids.squeeze().to(device) # (B, max_seq_len) + protein_sequence_attention_mask = protein_sequence_encode.attention_mask.squeeze().to(device) # (B, max_seq_len) + + raw_input_sequence_list = protein_decoder_tokenizer.batch_decode(sequences=protein_sequence_input_ids, skip_special_tokens=True) + for i in range(5): + raw_input_ids = protein_sequence_input_ids[i].cpu().numpy() + raw_input_sequence = raw_input_sequence_list[i].replace(" ", "") + print("id:", i, len(raw_input_ids), len(raw_input_sequence)) + print(raw_input_ids[:20], raw_input_ids[-20:]) + print(raw_input_sequence[:20], raw_input_sequence[-20:]) + print() + print() + + protein_repr = batch["protein_repr"].to(device) + if args.decoder_distribution in ["T5Decoder"]: + protein_sequence_pred_ids = decoder_distribution_model.inference(condition=protein_repr, protein_seq_attention_mask=protein_sequence_attention_mask, max_seq_len=args.protein_max_sequence_len) + elif args.decoder_distribution in ["LSTMDecoder"]: + protein_sequence_pred_ids = decoder_distribution_model.inference(condition=protein_repr, protein_seq_attention_mask=protein_sequence_attention_mask, max_seq_len=args.protein_max_sequence_len) + else: + protein_sequence_output = decoder_distribution_model.inference(condition=protein_repr, protein_seq_attention_mask=protein_sequence_attention_mask, max_seq_len=args.protein_max_sequence_len) + protein_sequence_pred_ids = torch.argmax(protein_sequence_output, dim=-1) # (B, max_seq_len) + + pred_sequence_list = protein_decoder_tokenizer.batch_decode(sequences=protein_sequence_pred_ids, skip_special_tokens=True) + for i in range(5): + print("ground-truth", protein_sequence_input_ids[i]) + print("prediction", protein_sequence_pred_ids[i]) + pred_sequence = pred_sequence_list[i].replace(" ", "") + print("pred", i, len(pred_sequence)) + print("prediction", pred_sequence[:20], pred_sequence[-20:]) + print() + print() + + if args.decoder_distribution in ["T5Decoder"]: + fuzzy_match_count = (protein_sequence_input_ids[:, :-1] == protein_sequence_pred_ids[:, 1:]) # (B, max_seq_len) + exact_match_count = fuzzy_match_count * protein_sequence_attention_mask[:, :-1] # (B, max_seq_len) + else: + fuzzy_match_count = (protein_sequence_input_ids == protein_sequence_pred_ids) # (B, max_seq_len) + exact_match_count = fuzzy_match_count * protein_sequence_attention_mask # (B, max_seq_len) + + B, max_len = fuzzy_match_count.size() + fuzzy_match_acc = 100. * fuzzy_match_count.sum().item() / (B * max_len) + exact_match_acc = 100. * exact_match_count.sum().item() / protein_sequence_attention_mask.sum().item() + fuzzy_match_acc_accum += fuzzy_match_acc + exact_match_acc_accum += exact_match_acc + + print("fuzzy: {:.2f}\texact: {:.2f}".format(fuzzy_match_acc, exact_match_acc)) + exit() + + # fuzzy_match_acc_accum /= len(L) + # exact_match_acc_accum /= len(L) + # print("fuzzy match acc: {:.5f}".format(fuzzy_match_acc_accum)) + # print("exact match acc: {:.5f}".format(exact_match_acc_accum)) + return + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--device", type=int, default=0) + parser.add_argument("--seed", type=int, default=42) + parser.add_argument("--batch_size", type=int, default=16) + parser.add_argument("--num_workers", type=int, default=8) + + parser.add_argument("--hidden_dim", type=int, default=16) + parser.add_argument("--condition_dim", type=int, default=256) + parser.add_argument("--protein_max_sequence_len", type=int, default=512) + + parser.add_argument("--verbose", dest="verbose", action="store_true") + parser.set_defaults(verbose=False) + + parser.add_argument("--decoder_distribution", type=str, default="GaussianSDE", choices=["GaussianSDE", "LSTMDecoder", "T5Decoder", "ColdDiffusion", "LatentDiffusion", "MultinomialDiffusion"]) + parser.add_argument("--pretrained_folder", type=str, default=None) + parser.add_argument("--step_04_folder", type=str, default=None) + + # for LSTM + parser.add_argument("--LSTM_layer", type=int, default=5) + parser.add_argument("--LSTM_epsilon", type=float, default=0.05) + + parser.add_argument("--beta_min", type=float, default=0.1) + parser.add_argument("--beta_max", type=float, default=30) + parser.add_argument("--num_diffusion_timesteps", type=int, default=1000) + parser.add_argument("--SDE_type", type=str, default="VP") + parser.add_argument("--score_network_type", type=str, default="BertProtBFD") + + args = parser.parse_args() + print("arguments", args) + assert args.pretrained_folder is not None + assert args.step_04_folder is not None + + random.seed(args.seed) + os.environ['PYTHONHASHSEED'] = str(args.seed) + np.random.seed(args.seed) + torch.manual_seed(args.seed) + torch.cuda.manual_seed(args.seed) + torch.cuda.manual_seed_all(args.seed) + torch.backends.cudnn.deterministic = True + torch.backends.cudnn.benchmark = True + + device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu") + + if args.decoder_distribution in ["T5Decoder"]: + protein_decoder_tokenizer = T5Tokenizer.from_pretrained("Rostlab/prot_t5_xl_uniref50", do_lower_case=False, chache_dir="../data/temp_pretrained_t5_base") + else: + protein_decoder_tokenizer = BertTokenizer.from_pretrained("Rostlab/prot_bert", do_lower_case=False, chache_dir="../data/temp_pretrained_ProtBert") + + if args.decoder_distribution == "MultinomialDiffusion": + mask_id = 4 + decoder_distribution_model = MultinomialDiffusion( + hidden_dim=args.hidden_dim, + condition_dim=args.condition_dim, mask_id=mask_id, + beta_min=args.beta_min, beta_max=args.beta_max, num_diffusion_timesteps=args.num_diffusion_timesteps, + num_classes=protein_decoder_tokenizer.vocab_size, score_network_type=args.score_network_type) + + elif args.decoder_distribution == "T5Decoder": + decoder_distribution_model = T5Decoder( + hidden_dim=args.condition_dim, + tokenizer=protein_decoder_tokenizer, + T5_model=args.score_network_type + ) + decoder_distribution_model.to(device) + + ########## Load model weight ########## + step_04_folder = args.step_04_folder + model_file_path = os.path.join(step_04_folder, "decoder_distribution_model.pth") + print("Loading decoder model from {}...".format(model_file_path)) + state_dict = torch.load(model_file_path, map_location='cpu') + decoder_distribution_model.load_state_dict(state_dict) + decoder_distribution_model.eval() + + step_02_folder = os.path.join(args.pretrained_folder, "step_02_pairwise_representation") + dataset = RepresentationPairWithRawDataDataset(step_02_folder, prob_unconditional=0) + dataloader = DataLoader(dataset, batch_size=args.batch_size, shuffle=False, num_workers=args.num_workers) + + eval(dataloader) + """ + 0 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